Oncology Master Guide 2007/2008

Contents

Contents

1 Introduction 9 1.1 What to find in this study guide 9 1.2 Oncology at VUmc 9 1.3 Aim of the study programme 10 1.4 Structure of organization 10

2 Structure and contents of the Master Course in Oncology 11 2.1 General 11 2.2 Items to be examinated 11 2.2.1 Topmaster's programme 11 2.2.2 Compulsory courses 12 2.2.3 Optional courses 12 2.2.4 Placements 13 2.2.5 Thesis 13 2.2.6 Study of literature 14 2.2.7 Learning outcomes and objectives 14

3 Norms concerning the education 17 3.1 Admission requirements and previous education 17 3.1.1 Admission to the Master's Programme 17 3.1.2 Admission to the Topmaster's Programme 17 3.2 Progress of education 18 3.2.1 Access to educational results 18 3.2.2 Control to progress of education 18 3.2.3 Study advise 18 3.3 Education and examination regulation 18 3.4 Short summary of norms and guidelines for participation in items to be

examinated 19

4 Oncology 21 4.1 Compulsory courses 21 4.1.1 Course descriptions 21 4.2 Optional courses 26 4.2.1 Course descriptions 26 4.3 Practical training 42 4.3.1 Short description 42 4.4 Study of literature 42 4.4.1 Short description 42

5 Options to placements and studies of literature 43 5.1 Regulation for placements and literature surveys 2007-2008 43 5.2 Options for a placement at departments of the VUmc 48 5.2.1 Department of Radiation Oncology 48 5.2.2 Department of Molecular Cell Biology and Immunology 50 5.2.3 Department of Pediatric Oncology/Hematology 51 5.2.4 Department of Medical Oncology 54

Contents 5

5.2.5 Department of Otolaryngology/ Head and Neck Surgery 56 5.2.6 Department of Opthalmology 57 5.2.7 Department of Clinical Genetics 58 5.2.8 Department of Nuclear Medicine & PET Research 60 5.2.9 Department of Heamatology 61 5.2.10 Department Obstetrics and Gynaecology 62 5.2.11 Department of Pathology 63

6 List of addresses and telephone numbers 65

Appendices 67 Appendix 1 - Important websites 67 Appendix 2 - Programme & Procedures; Master Courses 68 Appendix 3 - Programme & Procedures; Research Training (Placement) 69 Appendix 4 - Programme & Procedures; Study of Literature 70 Form 1 71 Form 2 72 Form 3 73 Form 4 74 Form 5 75 Form 6 76 Form 7 77 Form 8 78 Form 9 80

Contents

Contents 7

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1 Introduction

1.1 What to find in this study guide This study guide contains information on the Master’s Programme in Oncology programmes provided by VU University Medical Center (VUmc). In this first chapter one can find general information on cancer research at the VUmc and the aim of the study programme. Chapters 2 and 3 provide information regarding admission, planning, time tables, course registration, interim examinations, student facilities…etc. Course information and timetables for compulsory and optional courses can be found Chapter 4. The 5th chapter provides information on all research departments at VUmc linked to the master’s programme and the students’ manual for placement and study of literature. Please note, that all information in this study guide and recent announcements are also available on the Blackboard-site “Communication site master oncology”; www.bb.vu.nl

1.2 Oncology at VUmc The VU University Medical Center (VUmc) has been known by this name since January 1st 2001. That date marks the integration of the VU hospital and the Faculty of Medicine of the Vrije Universiteit. Next to its leading role in the Dutch health service, principal tasks of the VUmc are scientific research, academic programmes and training. The VUmc has identified cancer research as one of the core research areas. Subsequently, the VUmc has taken initiative to develop the Master's Programme in Oncology under the umbrella of the VUmc Cancer Centre Amsterdam (CCA) , and the VUmc research institute for Immunology and cancer research (V-ICI); an ideal environment to study oncology at the highest level. The Master’s Programme started in 2002 and received in 2003 the label Topmaster’s Programme from the Dutch Ministry of Education, Culture and Science (OC&W). VUmc is responsible for the organization and coordination of the Master's Programme in Oncology. This includes quality assurance, programme development and student guidance. The prospectus of the Master's Programme in Oncology provides information on organization of the educational programme and descriptions of courses and other components that can be examined. Members of the programme committee (‘opleidingsccommissie’) are highly dedicated to the Master’s Programme. Students, VU/VUmc-staff members and other interested persons are welcome to contact us for any questions and suggestions in regard to the Master’s Programm. Names and addresses of the programme coordinator, programme committee, professors and student-representatives can be found at the end of this catalogue. For general questions please visit the website of the Master’s Programme (www.masteroncology.nl) or the Blackboard site “Communication site Master Oncology".

Introduction 9

1.3 Aim of the study programme Cancer is one of the main causes of death in the Western world. In our ageing society the number of cancer patients continues to rise, since the incidence of the disease is highest among the elderly. Research in order to prevent, diagnose and treat this disease is therefore of vital importance. The same applies to research into the causes of cancer and the long-term effects of treatment. Cancer research is multidisciplinary and takes place within a global network. A researcher in such a demanding environment needs to be well equipped. The Master's Programme in Oncology aims to transfer the unique combination of translational oncology research at the VUmc to the next generation of students. The programme is research-oriented and has a multidisciplinary character. Students are trained in state-of-the-art techniques in cancer research and therapy. This also includes skills in order to develop, organize and realize of oncological research.

1.4 Structure of organization The Master's Programme in Oncology is covered by the responsibility of the executive board of the VUmc (‘Raad van Bestuur’). Education is a part of the institute for medical education, which gives the educational director responsibility. Within the institute for medical education a coordinator takes care of the organization and gearing of the curriculum. The Master's Programme in Oncology has an examination board and a programme committee. The coordinator of the Master's Programme in Oncology is official secretary of both boards. The programme committee advises the executive board of the VUmc and the educational director about the contents of the Master’s Programme and the quality of execution. The examination board decrees norms concerning admission of students, it makes sure that bachelors comply with the commencing norms, it decrees norms concerning examination of different disciplines and it looks over the results of examinations, placements and the Master Thesis. Furthermore, the examination board evaluates the combinations of optional courses and placements of each individual student. All compulsory and optional courses are coordinated by different course instructors. The composition of both the examination board and the programme committee is pointed out in Chapter 6 of this catalogue. General information about organisation, education, research and patient's care within VUmc can be found on the website of the VUmc, http://www.vumc.nl/. Dr. Ramon Puras Coordinator Master's Programme in Oncology Telephone: 020-4446345 Email: masteroncology@vumc.nl

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2 Structure and contents of the Master Course in Oncology

2.1 General The Master's Programme in Oncology aims to train (bio) medically focused bachelors and related bachelors in life sciences to become masters with in depth knowledge, attitudes and skills in the field of cancer research. This includes development, execution, organization and evaluation of oncological scientific research. Duration of the programme is two years (120 ECTS). One ECTS is equivalent to 28 hours of study load. Each item of examination that is finished successfully is equal to a given number of ECTS credit points. All ECTS credit points per study-component are listed in this prospectus and in the Education and Examination Norms. In order to receive the degree of Master of Science in Oncology a student has to collect 120 ECTS credit-points. Tuition is in English. For more information: see www.masteroncology.nl -> Programme

2.2 Items to be examinated The items that have to be assessed are compulsory courses, optional courses, a study of literature and two practical training periods (placements). These items all have their own code of administration. Each item will be assessed separately and students will receive final marks after completion. This final mark can be the result of an examination, report, or an oral presentation at the end of a course or it can be the result of partial marks, derived from more than one examination and/or practical assessments. It can also occur that attendance during lessons is one of the obligated conditions to successfully finish the item to be assessed. Only if the student meets all conditions, he/she will receive a final mark for an item to be assessed. The final Master Examination consists of all items to be assessed, which means in practice that all examinations will be added up. The board of examiners will eventually decide whether the Master Examination is finished successfully. The Master's Programme in Oncology consists of the following items: Compulsory courses 27 ECTS Optional courses 15 ECTS Practical training I 29-40 ECTS Practical training II 29-40 ECTS Study of literature 9 ECTS

2.2.1 Topmaster's programme The Topmaster's Programme includes all components of the Master's Programme plus • the compulsion to do additional courses of 12 ECTS to be completed within the

course period of 2 years • the compulsion to do one placement in a renowned research institute abroad • during the Topmaster’s Programme the level of the marks has to be continued at

7,5 at least.

Structure and contents of the Master Course in Oncology 11

Students are required to write a study of literature which is suitable for publication in a peer reviewed journal. For more information: see www.masteroncology.nl -> Topmaster Programme Admission requirements are described in chapter 3.1.2.

2.2.2 Compulsory courses Compulsory courses for the academic year 2007-2008 are listed below. Course Data ECTS Oncogenesis 3 September – 28 September 2007 6 Immunity 1 October – 26 October 2007 6 Tumour Biology and Clinical Behaviour

29 October – 23 November 2007 6

Innovative Tumourtherapies 26 November – 21 December 2007 6 Scientific Writing in English 7 January – 18 January 2008 3

The description of the individual courses can be found under Compulsory Courses (chapter 4.1).

2.2.3 Optional courses The Master's Programme in Oncology has reserved 15 ECTS credit points for optional courses. The optional courses are listed in the table (chapter 4.2) at the time that this catalogue was published. All courses listed in chapter 4.2 are approved by the examination board of the Master's Programme in Oncology and do not need individual student approvals. It is likely, that the list optional courses for 2007/08 will be expanded with more approved courses. These courses will be announced on the blackboard site "Communication site Master Oncology". If a student wants to follow a course which is not indicated, an individual approval by the examination board is required. Some optional courses are organized together with or by other faculties, like FALW (Faculty of Earth and Life Sciences), the Medical faculty and OOA-Graduate School Amsterdam. Please note: • Deadline for inscription for all optional courses is 4 weeks, especially for courses

organized by other faculties (see detailed information ‘registration optional courses’ on Blackboard).

• For all OOA-PhD-courses: please apply per e-mail to: v-ici@vumc.nl. The examination board can, to a limited extent of 6 ECTS credits, grant the student permission to extend a period of work placement. The student must request this before the end of the research project. Approval for the extension of a placement is given once-only. The extension is at the expense of optional courses. The mark for the extension is equal to the mark for the placement and is registered as a separate component. A special form for extension of the placement can be downloaded from Blackboard. Appendix 2- flow chart Programme and procedures; Compulsory and optional courses.

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2.2.4 Placements In total, a student has to spend 69 ECTS credit points for two placements: It is possible to spend: • two periods with the same length or • a longer (corresponding to maximal 40 ECTS credit points ~ ca. 27 weeks) and a

shorter one (corresponding to minimal 29 ECTS credit points ~ ca.19 weeks). One week full-time (40h/week) is an equivalent of 1.5 ECTS.

Both placements have to be performed at a research laboratory, acknowledged by the examination board of the Master's Programme in Oncology: One placement has to be performed at one of the departments/laboratories of the VU/VUmc and the other one preferentially "outside" the VU. It is not allowed to do both placements outside the VU/VUmc. Short procedure approval of placement(s). For more information see chapter 5 and appendix 3: • Before starting a placement, a student always has to ask for approval of the

examination board of the Master's Programme in Oncology. • Within 6 weeks after initiating a placement, a student has to write and hand in a

research proposal to the examination board. Furthermore, a list of appointments made between the student and the department on which the student is working has to be filled in and handed in.

• Within 6 weeks after initiation of a placement, an interim assessment has to be made to let the student know how he/she is doing.

• At the end of the placement an assessment for a placement of the Master's in Oncology has to be filled in as well as a "Credits Registration Form" on which the total mark is written.

• Placements performed "outside" the VU or VUmc have to have an internal student supervisor. This internal student supervisor determines the total mark, based on advice of an external student supervisor of the institution in which a placement was performed.

• All forms necessary for internal and external placements can be downloaded via the website of the Master's Programme in Oncology’s (ww.masteroncology.nl)

A necessary condition is that one placement must have an oncological character. The other training may be focused on a related topic, which has to be relevant for biomedical research. The package of placements has to be approved by the examination board. All placements have to include the following elements: • Theoretical deepening in the relevant field of oncological research • Elaboration, execution and analysis of the research question • Formulation of conclusions and recommendations • Written report in English in the format of a scientific paper. • Oral presentation in English The total mark is based on the quality of the practical work (50%), the written report (25%) and the oral presentation (25%).

2.2.5 Thesis The Master's thesis includes the results of an oncological research project of the work placement, integrated with and from the perspective of the knowledge acquired in the cursory education. The Master’s thesis includes the results of an oncological

Structure and contents of the Master Course in Oncology 13

placement and thus the report of the longest placement or the last placement, when both placements are of equal length and have an oncological character. The Master's thesis will get an uniform cover provided and designed by the Master. The Master’s thesis will be defended in public.

2.2.6 Study of literature The study of literature will be carried out under supervision, yet highly independent. It’s also possible that the student proposes his or her own subject and presents an own question. The study may be focused on a scientific biomedical question, but a more applied or social question is also allowed. The aim of the literature study is that the student will be able to select, evaluate and discuss critically relevant literature. Based on the study, the student has to explain clearly not only the state of the art, but also the limitations and problems. Depending on the context of the study the student has to formulate recommendations and strategies for further research to solve the problem. The literature study is written in the format of a review paper. For more information about supervision and approval see chapter 5 and appendix 4.

2.2.7 Learning outcomes and objectives The graduated Master of Science in Oncology will have an academic attitude, academic skills and specific knowledge with respect to oncology and oncological research. We assume that an academic attitude and academic skills are inextricably bound up with each other, so the Master of Science in Oncology will be able to: • acquire independently information in biomedical, particularly oncological

sciences and to analyse and critically evaluate this information • select, organize and summarize information, to distinguish major from minor

things and to connect relevant points. • think in a multidisciplinary way and to have insight in (sub) disciplines, which are

important in oncological research. Within this framework, the master will be able to create translational connections between fundamental and clinical questions.

• collaborate and communicate with scientists from other disciplines. • analyse critically and independently the own research, in relation to study design

and performance as well as to the results. • prepare a plan of investigation in which are described the background, the

planning, the methods and the analysis. • set up and carry out biomedical, particularly oncological experiments, based on

this plan of investigation. • prepare written reports and oral presentations of research in English. • translate scientific oncological know-how into social questions. • contribute to scientific discussions by planning relevant research and discussing

results. • evaluate own functioning / self reflection • continue to improve knowledge and skills and to update knowledge and skills

regularly • think about ethical aspects of research and its application and to take these

considerations in account in decision-making • work according to Good Laboratory Practice standards

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With respect to specific knowledge, the Master of Science in Oncology will have: • knowledge of oncological concepts, the most important research questions and of

the state of the art of development of theories • understanding of the position of oncology within the field of medicine,

biomedical and natural life sciences • experience with general scientific, general medical and specific oncological

journals • understanding of the scientific and social relevance of oncology and current

research in this field • knowledge of statistical methods and its implementation in oncological research • working knowledge of relevant computer programs

Structure and contents of the Master Course in Oncology 15

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3 Norms concerning the education

3.1 Admission requirements and previous education

3.1.1 Admission to the Master's Programme Students with a bachelor’s degree in Biomedical Sciences, Medicine, Medical Natural Sciences, Biology, Biochemistry or other related Life Sciences are eligible to the Master's Programme in Oncology, providing that they possess elementary knowledge about immunology and oncology. This basic knowledge comprises the following two books: Lauren Pecorino, Molecular Biology of Cancer (ISBN 0-19-926472-4) and the first nine chapters of the book of Charles A. Janeway, Immunobiology, 5th edition (ISBN 0-4430-7098). (see www.masteroncology.nl -> admission requirements -> basic knowledge) All students (dutch and international) have to meet the educational entry requirements. They should possess knowledge of the English language at the level of VWO. International students: TOEFL (>570 or >213) or IELTS (6.5), in case they have not followed an English bachelor’s programme. The rules mentioned above are coupled to admission requirements: 1. Students with a Bachelor of Science degree in Biomedical Sciences, Medical Natural Sciences or Medicine are directly admitted to the Master's Programme in Oncology 2. Students with a Bachelor of Science degree in Biology, Life Sciences, (bio) Chemistry or (bio) Physics are not admitted directly to the Master's Programme in Oncology. The board of examiners evaluate the previous study results, combination of courses and motivation of each individual student. 3. Students with a Bachelor of Science degree at the level of “Hoger Beroeps Onderwijs” (e.g. HLO) can be admitted to the Master's Programme in Oncology after evaluation of their combination of courses by the board of examiners. An oncology-assessment is compulsory. 4. International students can be admitted to the Master's Programme in Oncology after evaluation of their previous education and certificate by the board of examiners. 5. In all other situations not mentioned above the board of examiners has to give it’s approval on admittance. The board of examiners can define additional entry-requirements including the oncology-assessment. The board of examiners can admit students to attending courses and/or taking examinations of the Master's Programme in Oncology before they have the degree of Bachelor of Science in Biomedical Sciences, providing that they have at least accumulated 168 ECTS during the bachelor education in Biomedical Sciences. The period in which a student can participate in the Master's Programme in Oncology without having the degree of Bachelor of Science endures maximal 9 months, counted from the initiation of the academic year.

3.1.2 Admission to the Topmaster's Programme Access to the Topmaster Programme is open for at most 20% of the best students of the Master’s Programme in Oncology, who have to comply with the following requirements. 1. The marks of the compulsory master courses are on average >7,5,

Norms concerning the education 17

with a minimum score of 7. 2. All courses have to be completed successfully in the first instance. 3. The mark of the bachelor or HLO work placement is >7,5. (see www.masteroncology.nl -> Topmaster Programme)

3.2 Progress of education

3.2.1 Access to educational results Each student has access to his/her educational results by using TISVU (Examination Information System VU). All final marks are announced in TISVU. To get access to TISVU, each student needs to have an account (student responsibility). Both access to educational results as well as apply for an account can be found on www.tisvu.vu.nl In case of incorrect registration of educational results the student can make an appeal to the board of examiners. Correspondence will be led by the coordinator of the Master's Programme in Oncology.

3.2.2 Control to progress of education Names of students that do not meet the norms of progress of education stated in the law for Student Grants will be send to IBG (Informatie Beheer Groep) before the 1st of November. Concerning students will be informed before the November 1st by the department of student administration, on behalf of the Board of Governors. Consequences for the received student grants of that year will be pointed out, as well as their right of appeal.

3.2.3 Study advise If the educational results give cause for problems students of the first year of the Master's Programme in Oncology receive an invitation to discuss their results with the coordinator of the Master's Programme in Oncology. During this meeting an advise will be given about the continuation of the Master's Programme in Oncology, based on the results of the compulsory courses. Furthermore, the educational results of all students will be followed accurately during the whole 2-year period of the Master's Programme in Oncology. If necessary, the coordinator of the Master's Programme in Oncology will contact the students for a discussion about their study-progress.

3.3 Education and examination regulation The Master's Programme in Oncology has its own regulation for both education and examination, which is called OER (“onderwijs- en examenregeling”). Besides the aim of the education, OER also contains all norms concerning the demanded preparatory training, contents of the education, taking examinations, acquire dispensations, progress of education and coaching of students. OER is determined on a yearly basis by the Board of Governors of the VUmc. The actual version of OER and the extensive norms and guidelines for the academic year 2007-2008 will be placed on the website www.masteroncology.nl and on Blackboard.

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3.4 Short summary of norms and guidelines for participation in items to be examinated Compulsory courses All students of the Master's Programme in Oncology have to attend the compulsory Courses of the programme. If more study places are available, students of other Master’s programmes can attend the course, providing that they meet the entry requirements. Optional courses Via this catalogue and the blackboard site “Communication site Master Oncology” optional courses will be announced. For registration students can use TISVU. If registration isn’t possible by using TISVU (e.g. external courses), the mode of inscription and corresponding e-mail addresses are indicated on each course description. Students have to have a written consent of the board of examiners, if they want to attend an optional course other than those announced by the Master's Programme in Oncology. A form can be downloaded for this written consent from the blackboard site “Communication site Master Oncology” (see flow chart, appendix 2). Attending courses without the written consent of the board of examiners will not be registered. Possible financial consequences will be recovered from the student. Practical training periods and study of literature The board of examiners has to give its approval of all practical training periods. Forms and guidelines for practical training periods can be downloaded from the blackboard site “Communication site Master Oncology” (see flow chart, appendix 3 and 4). Unapproved practical training periods will not be registered by the educational secretarial office. Possible financial consequences will be recovered from the student. The same regulation consists for the approval of studies of literature. The extensive norms for practical training periods and studies of literature board is pointed out in chapter 5 of this catalogue. Availability of course programmes Programmes of compulsory courses will be announced via the blackboard site “Communication site Master Oncology”.

Norms concerning the education 19

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4 Oncology

4.1 Compulsory courses

4.1.1 Course descriptions Please find below an overview and descriptions of all compulsory courses Master's Programme in Oncology. For all five courses holds: • attendance of lectures, workshops, demonstrations and literature-sessions is

obligatory. • students Master's Programme in Oncology are registered automatically; all other

students have to contact the coordinator of the Master's Programme, prior to enrolment

Course code

Course name Cr. Period

311101 Mastercourse Oncogenesis 6 3 September - 28 September 2007

311102 Mastercourse Tumor Biology and Clinical Behaviour

6 29 October - 23 November 2007

311103 Mastercourse Immunity 6 1 October - 26 October 2007 (week 40 to 43)

311104 Mastercourse Innovative Tumortherapies 6 26 November - 21 December 2007

311105 Scientific Writing in English 3 7- 18 January 2008

subject Mastercourse Oncogenesis code 311101

credits 6 co-ordinators prof.dr. R.H.A. Brakenhoff; prof.dr. P.J.F. Snijders; dr. J. de Winter

period 3 September - 28 September 2007 aim The aim of this course is to acquire knowledge of and insight in the general

concepts of oncogenesis, which includes the different genetic alterations and classes of genes involved, the (molecular) tools to study carcinogenesis, and model systems used in the field of oncogenesis. In addition, cancer predisposition syndromes, exogenous factors involved in oncogenesis with emphasis on viruses, and markers of progression, genetic counselling, screening, as well as intervention options will be studied. The student will be given an up-to-date overview of the current knowledge and opinions in this exciting field. Furthermore, the student will acquire insight into how to interpret literature on specific topics in oncogenesis and present its their findings in a clear and concise manner.

content The contents of this course are largely determined by the latest developments in the field of cancer research. Depending on these developments, the course program is yearly updated. Topics include: • cancer genes and oncogenic microRNAs • cell cycle • cancer genetics • signalling pathways • progression models

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• inherited cancer predisposition • DNA repair mechanisms • immortalisation • factors: viral oncogenesis • model systems • early detection and screening

form of tuition 50 hours (20 literature survey, 30 active participation). Interactive sessions with lectures on various topics in oncogenesis. Lecture repetition by the students, and literature (self-) study on a familial cancer syndrome followed by a group presentation in the last week of the course. Students are required to have a large self-motivation. The course will be highly interactive and will consist of contact hours with a teacher and project groups in which lectures are repeated and recent publications are being discussed.

literature The course material will consist of a reader with (review) articles on the various topics as well as handouts of the presentations of the lectures.

mode of assessment The course will be concluded with a 3 hours examination (open questions) on the contents of the lectures. Also the lecture repetitions and presentations on the literature studies will be judged and the final mark of this course will be determined by the average of the scores for the examination (counting for 70%), the lecture repetition (counting for 10%), and the literature presentation (counting for 20%). Students need to be present and actively participate during the course. More than 20% absence will have consequences for crediting the course.

target audience This course is compulsory for students of the Master in Oncology. When positions are available, students of the general master in Biomedical Sciences can also attend the course, provided that they have completed the optional course "Oncologie" during the bachelor phase.

remarks The student will have acquired insight in the latest developments in the field of oncogenesis and cancer genetics. Furthermore, the student will be able to integrate knowledge and insight in the formation of opinions concerning research questions about the development of cancer. Application: Students of the Master's Programme in Oncology class 2007/08 are automatically enrolled. Other students interested in the course can apply by sending an e-mail to the coordinator of the Master's Programme in Oncology.

subject Mastercourse Tumor Biology and Clinical Behaviour code 311102

credits 6 co-ordinators dr. J.J. Oudejans; dr. R. Fijneman

period 29 October - 23 November 2007 aim The aim of the course is provide in depth knowledge of and insight in the

relationship of gene expression, biology and clinical behaviour of tumours. The student will have a broad overview of development of theories in this field of oncological research.

content To a great extent, recent developments in the research on gene expression, biology and clinical behaviour of tumours will determine the programme of the course. Depending on these developments, the programme of the course can be adjusted at any time.

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Topics: • epidemiology of tumours • natural course and clinical behaviour of tumours • haematological malignancies • solid tumours • tumour profiling and clinical outcome • homing and metastases • sentinel node concepts • social and psychosocial aspects

form of tuition 46 hours (20 seminar, 6 discussion groups, 20 lectures). This course is characterized by a high level of interactive education. This program includes lectures, seminars, literature discussions and training in writing a research proposal. Students are expected to participate actively in discussions.

literature The course material consists of recent reviews in the field of gene expression, biology and clinical behaviour of tumours.

mode of assessment A major aspect of the course is preparing of a research proposal by power point presentation in groups of 2 students. Tutors will help in preparing these proposals by detailed discussion sessions each Friday of the course. The complete proposal will be presented at the end of the course. Marks will be given by both tutors and will determine 50% of the final mark. The other 50% of the assessment will be done by a multiple-choice exam covering the major topics of the lectures. In principle, students have to be present all over the course and have to participate in the course actively.

target audience The course is compulsory for students of the Master in Oncology. When positions are available, students of the General Master in Biomedical Sciences are allowed to participate, providing that they have completed the optional course "Oncologie" during the bachelor phase.

remarks The student will have insight in the most recent developments in the field of gene expression, biology and clinical behaviour of tumours and in relevant theories. The student will be capable to integrate this knowledge and insight into the formation of his own opinion on relevant research questions. Application: Students of the Master's Programme in Oncology class 2006/07 are automatically enrolled. Other students interested in the course can apply by sending an e-mail to the coordinator of the Master's Programme in Oncology.

subject Mastercourse Immunity code 311103

credits 6 co-ordinators prof.dr. R.J. Scheper; prof.dr. R.H.J. Beelen (Questions regarding the course:

lm.vddobbelsteen@vumc.nl; regarding internships in Tumor Immunology and Experimental Pathology: rj.scheper@vumc.nl, phone 020-444 4002, or Tumor Immunology and Molecular Cell Biology: rhj.beelen@vumc.nl, phone 020-4448055/8065)

period 1 October - 26 October 2007 (week 40 to 43) aim • Expanding knowledge obtained during the introductory course on

Immunology, focusing on cancer and implications for several other immunological disease processes.

• Trainings in ways to study primary and secundary immunological literature on selected immune disorders.

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• Introduction to critical research questions regarding immunological aspects of various diseases.

Final level, the student should be able to: • Explain how and to which extent immune defense mechanisms are

disturbed in cancer and a broad variety of clinically relevant disease processes.

• Point out which diagnostic methodologies provide the information which is most relevant to the selection of therapeutic interventions.

• Summarize pros and cons of preventive and therapeutic measures. content Chapters 10 - 14 and Appendix I of Janeway's `Immunobiology`, also used

for the introductory course. After having dealt with the fundamentals in the first parts of the book, these chapters focus on infectious diseases, immune deficiencies, allergies and hypersensitivity disorders, autoimmune diseases, graft rejection, tumorimmunology, and therapeutic and technical issues, respectively.

form of tuition Independent study (approx. 120 hrs), complemented with training sessions first, during the initial lecture and discussion sessions (up to 6 x 2 hours) knowledge on the first 9 Chapters will be refreshed and rehearsed. Subsequently, the above mentioned chapters, including Appendix I, will be studied and discussed. Moreover, small-scale working group sessions are scheduled to provide highly interactive discussions on recent literature selected in order to highlight cutting edge research questions (2 x 4 hours).

literature Janeway, Travers, Walport and Shlomchik: Immunobiology, 6th edition, Garland Science Eds (approx 73 EUR). Complementary literature on selected topics will be provided during the course.

mode of assessment The course will be closed off with a written assignment based on answering essay questions. The course takes place yearly (next opportunity October 2007), with written finals at the end of each course, and in December

target audience This course is compulsory for the Differentiation Immunology in the Master Biomedical Sciences. Given the broad relevance of immunology in life sciences this course also provides excellent opportunities for other differentations within this Master program. Within the VUmc, the master course Immunity also serves as an indispensable and compulsory course for the Master Oncology program.

subject Mastercourse Innovative Tumortherapies code 311104

credits 6 co-ordinators prof.dr. G.J. Peters; dr. E. Hooijberg

period 26 November - 21 December 2007 aim After completion of the course the student will have acquired knowledge of

and insight in the background and development concerning the treatment of cancer. The student has been given a broad overview of the development of theories in this field.

content The contents of this course are largely determined by the latest developments in the field of research concerning cancer therapies. Depending on these developments, the course program can be adjusted at any time. Topics: • Chemotherapy and targeted therapy • Pharmacodynamics/pharmacogenomics

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• proteomics • gene therapy and RNAi • immunotherapy • radiotherapy • antibody therapy • angiogenesis • clinical trials • social and psychosocial aspects

form of tuition 38 hours (12 working group, 20 active participation, 6 demonstration). In principal, the course will be given in English. Students are required to have a large self-motivation. The course will be highly interactive and will consist of contact hours with a teacher and project groups in which recent publications are being discussed. Excursions will be incorporated, in which one type of therapy is topic of study. • Workgroup and lectures: recent publications are being discussed. • Active participation: protocol writing and presentation. Students are

required to have a large self-motivation. The course will be highly interactive.

• Patient demonstrations: excursions will be incorporated, in which one type of anti cancer therapy is topic of study.

literature The course material will consist of recent reviews in the field of innovative therapies, which will be handed out just before the course. All course material can be found on the blackboard site "Communication site Master Oncology".

mode of assessment The course will be terminated by a written assessment. Insight in the knowledge acquired will be tested. Students are obligated to be present during contact hours and excursions (one time being absent is allowed) and need to participate actively during the course. Absence can have consequences for attending the written assessment.

target audience This course is compulsory for students of the Master in Oncology. When positions are available, students of the General Master in Biomedical Sciences can also attend the course, providing that they have completed the optional course "Oncologie" during the bachelor phase.

remarks The student will have acquired knowledge of the latest developments in the field of cancer treatment and will have acquired insight in the development of theories. The student will be able to integrate his/hers acquired knowledge of and insight in the formation of opinions concerning research questions in this field. Application: Students of the Master's Programme in Oncology class 2007 - 2008 are automatically enrolled. Other students interested in the course can apply by sending an e-mail to the coordinator of the Master's Programme in Oncology.

subject Scientific Writing in English code 311105

credits 3 co-ordinator dr. R. Puras

period 7- 18 January 2008 aim The aim of this course is to provide the writing student with the essential

linguistic means for producing English academic texts, which are effective,

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idiomatically and stylistically appropriate and grammatically correct. content Focus will be on the following subjects:

• writing texts • writing sentences • writing a curriculum vitae • writing a letter of application • writing emails

form of tuition 25 hours (25 active participation). The course is focussed on self-tuition in 10 sessions of 2,5 hours each. The plenary sessions concentrate on the process of writing and the product is part of writing. Homework is part of the course.

literature The course material consists of a syllabus containing all relevant information. Students also work with their own material: they write reports, letters, papers, emails, which are reviewed by, and together with, the teacher. Course Reader: Eur 15,-

mode of assessment No examination will be held. However, students of the Master Course in Oncology will receive their credits only when they have participated in at least 80% of the lessons and, also, when they have done all their homework. Students will receive a v (not a mark) when they have finished the course.

target audience This course is compulsory for students of the Master Course in Oncology. remarks After completing the course, the student will

• be able to employ a series of expressions and techniques for writing clear and effective English.

• be able to employ a wide range of linguistic expressions covering the most frequent textual functions in written English.

• have a better command of the grammatical structures which are frequent in English academic writing and which traditionally cause problems for the Dutch writer.

Application: Students of the Master's Programme in Oncology class 2007/08 are automatically enrolled.

4.2 Optional courses

4.2.1 Course descriptions Here you can find descriptions of the optional courses of the Master Course in Oncology. The optional courses listed below have been approved of by the board of examiners of the Master's Programme in Oncology. Some optional courses are organized together with or by other faculties, like the faculty for Earth and Life Sciences (FALW), the Medical faculty or the "Onderzoeksschool Oncologie Amsterdam" (OOA). All courses organized by FALW, students have to register via TISVU. Deadline of inscription is at least four weeks in advance. For all other courses the mode of inscription and corresponding e-mail addresses are indicated on each course description (see below). The number of courses can be supplemented with new courses. Those new courses can be seen on the blackboard site "Communication site Master Oncology".

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Courses organized by OOA: Course Period Organizer Predicting Outcome of Cancer Treatment

October 22-26 2007 NKI

Melanoma November 2007 VUmc Drug discovery and development

to be announced NKI

Genetherapy to be announced VUmc

For more details and course description see: www.ooa.vu.nl/course/program/index.html Apply by e-mail to the course-co-ordinator

Course code

Course name Cr. Period

311160 Clinical Oncology 6 to be announced 311162 Radiation Oncology 3 Spring 2008 311163 Macroscopic, microscopic & pathological

anatomy of the mouse 3 March/April 2008

311164 Radiation Protection Course, level 5B 3 Various periods 311167 Glycoimmunology 3 10 December - 21

December 2007 311168 Viral Oncogenesis 3 26 November -7

December 2007 311169 In the footsteps of Antoni van

Leeuwenhoek 3 to be announced

311170 The Symbolic and Cultural Meanings of Cancer

3 21 January - 1 February 2008

311172 Animal experimentation (Proefdierkunde voor onderzoekers)

3 22 October thru 2 November 2007. Further course data will be announced on Blackboard.

311173 Systems Biology of Cancer 3 May 2008 430045 Sequence Analysis 6 December-January 430046 DNA Protein Structure-Function Analysis

and Prediction 6 4

430047 Genome Analysis 6 1 430048 Bioinformatic Data Analysis and Tools 6 5 470076 Genomics 6 03.09.2007-28.09.2007 470121 Philosophy of Systems Biology and its

Relation to Society 3 26.05.2008-06.06.2008

470606 Caput Epigenetics 6 In consultation, contact the co-ordinator

470609 Biological fluorescence 6 04.02.2008-29.02.2008 471014 Wetenschapsjournalistiek (science

journalism) 6 03.09.2007-28.09.2007

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subject Clinical Oncology code 311160

credits 6 co-ordinator dr. P. Keblusek

period to be announced remarks Course information on Blackboard: see also `keuzevak oncology'.

Apply by e-mail to the course co-ordinator: p.keblusek@vumc.nl

subject Radiation Oncology code 311162

credits 3 co-ordinators dr. M.V.M. Lafleur; dr. P. Sminia

period Spring 2008 content In the course the rationale for the use of radiotherapy in oncological patients

will be elucidated. Topics of the course include: effects of irradiation on DNA, the cellular basis of radiotherapy, radiation injury to tumours and normal tissues, the physical principles of radiotherapy and the use of radiotherapy in the treatment of common malignant diseases. Practical work in treatment planning of a virtual patient is part of the course. New and exciting developments in radiotherapy will be addressed as well.

form of tuition 17 hours (6 discussion group, 5 demonstration, 6 lecture). The course consists of lectures, literature discussions and practicals. The course will be attended together with PhD-students from the AMC, NKI and VU.

literature The course material consists of recent reviews in the field of radiobiology. mode of assessment The course will be terminated by an oral presentation about a study of

literature. target audience This is a PhD-students' course organized by the "Onderzoeksschool

Oncologie Amsterdam" (OOA). OOA courses are open for Master Oncology students as optional courses under certain conditions..

remarks Apply per email to v-ici@vumc.nl For further information: http://www.ooa-graduateschool.org

subject Macroscopic, microscopic & pathological anatomy of the mouse code 311163

credits 3 co-ordinators prof.dr. W. Lamers; prof.dr. C.J.F. van Noorden

period March/April 2008 aim Most biomedical PhD students perform animal experiments at some stage of

their research career, but most students have never had practical instructions with respect to anatomy, histology and pathological anatomy of experimental animals. For this reason, experimental animals are usually not subjected to a thorough and systematic inspection to assess whether, besides the local (expected) effects in the organ(s) under study, other organs are affected as well. The present course aims to provide practical insight(s) in the anatomy and histology of the mouse, presently the most frequently used experimental animal. In addition, the course focuses on recognition of pathological changes in the mouse

content During the course each student will dissect a mouse to learn the topographic

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anatomy of this species. The microscopic part of the course focuses on the study and understanding of the architecture of normal and pathologically changed mouse tissues. During the practical part, recognition of cell and tissue types, and changes in architecture of tissues as a result of pathological processes, are studied microscopically. In addition to standard staining techniques, functional staining techniques are demonstrated. The course lasts four days and takes place once a year: in March or April 2007. In the table you will find an overview of the subjects. • Anatomy of the adult male and female mouse • Dissection of male and female mouse • Microscopic and pathological anatomy • Microscopic anatomy of normal and pathologically changed tissues and

organs • Neural-anatomy and pathological anatomy • Neural-anatomy and mouse pathology • Dealing with pathologically changed animals

target audience This is a PhD-students' course organized by the "Onderzoeksschool Oncologie Amsterdam" (OOA). OOA courses are open for Master Oncology students as optional courses under certain conditions.

remarks Apply per email to v-ici@vumc.nl For further information: http://www.ooa-graduateschool.org

subject Radiation Protection Course, level 5B code 311164

co-ordinator dr. G.W.M. Visser credits 3 period Various periods

aim Aim of the course "Working with Radioactivity" is preparing researchers, assistants and students for safely working with radioactive substances and/or apparatus emitting ionising radiation.

form of tuition The course encloses one week, divided in theory (~ 40%) and practical work (~60%). For both parts there will be a guide book in Dutch or English available. The experiments will lead to a practical work report to be used as the guidance for futural radiological activities. Participants shall receive a certificate as proof of their participation at the course, if they are judged to work safely with radioactivity. The with this certificate related allowance to work with radioactivity is limited to the laboratories of the Vrije Universiteit / VUmc.

mode of assessment Written exam, twice a year. Only students who pass the Dutch exam and thus obtain the governmental diploma "Stralingshygiëne, deskundigheidsniveau 5B" get 3 ECTS. The diploma gives allowance to work with radioactivity in the Netherlands, and most often even in Europe and America.

target audience The course given in the Radionuclide Centre is for students who need the course for working with radioactivity during their study at the Vrije Universiteit / VUmc, and for students who are strongly interested to work with radioactivity in future.

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remarks For each course the maximal number of participants is 12. During the year 4 courses (twice in Dutch, twice in English) are given. During the year the possibility of 3 extra courses exists provided the number of participants is at least 8. See for more information: http://www.rnc.vu.nl M.C. Stolker-Bouknecht is the administrator of the RNC-course, Tel: 020-4449101, mstolker@rnc.vu.nl . N.B. People who do want to do the course but do not understand Dutch, are before application requested to contact: G.W.M. Visser, co-ordinator of the course, Tel: 020-4449710, gvisser@rnc.vu.nl

subject Glycoimmunology code 311167

credits 3 co-ordinator dr. I.M. van Die

period 10 December - 21 December 2007 aim After the completion of the course, students will have aqcuired knowledge of

and insight in: • the molecular interactions of glycans with the innate immune system in

infectious disease. • the biosynthetic defects that cause aberrant glycosylation in cancer and

the correlational patterns between altered glycosylation and clinical prognosis.

• the role of endogenous lectins in the functional consequences of interactions between aberrant glycans (on tumour cells) or foreign glycans (on pathogens) with the innate immune system.

content The following topics will be discussed: • biological roles of glycans in the immune system • conservation and diversity of glycosylation patterns in different

organisms • classification and functions of carbohydrate binding proteins (lectins) • molecular interactions between glycans and lectins • role of glycans in infectious diseases, focussed on bacterial and parasite

infections • glycosylation changes in cancer and their biosynthetic basis • techniques and approaches in the study of glycan functions • application of glycans and glycoproteins as therapeutics in medicine

form of tuition 24 hours (12 self-study, 6 discussion group, 6 lecture). The course is accessible for small groups of students. The course consists of: • self-study, in combination with contact-hours with the teacher • discussion sessions about recent publications

literature The course material consists of recent research publications and reviews and chapters from "Essentials of Glycobiology", eds A. Varki et al., Cold Spring Harbor laboratory Press.

mode of assessment Oral assessment, presentation of a recent publication. target audience This course is optional for students of the Master Course in Oncology.

remarks Protein- and lipid-linked carbohydrates play critical roles in many cellular functions and in disease. Prominent examples of their importance are found in their role in regulation of immune functions, in infectious disease and in tumour metastases. • Glycans occurring on the surface of pathogens differ in structure from

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normal human glycans and may cause cellular and/or humoral immune responses. Pathogen-derived glycans may be regarded as PAMPs (pathogen associated molecular patterns), that are recognized by specific receptors (lectins) on cells of the innate immune system. Upon interaction, these lectins transmit information about the pathogen, setting thereby the scene for the development of a pro- or an anti-inflammatory immune response.

• Altered glycosylation is a universal feature of cancer cells, and certain types of glycan structures are well known markers for tumour progression. Although not much is known at present, it is becoming evident that the abberant glycosylation is not simply the consequence of disordered biology in tumour cells, since there is only a limited subset of biosynthesis pathways correlated with tumour progression. Some of these glycan alterations have a genetic basis.

Apply per email to the course coordinator: im.vandie@vumc.nl.

subject Viral Oncogenesis code 311168

credits 3 co-ordinators prof.dr. J.J.M. Middeldorp; prof.dr. P.J.F. Snijders

period 26 November -7 December 2007 aim The aim of the course is to give students an up-to-date insight into the

mechanism of viral oncogenesis in humans. content The subjects of the course may include several of the following issues:

• General aspects of DNA and RNA tumour viruses • Human papillomavirus (HPV) and cervical cancer • Hepatitis B/C viruses (HBV/HCV) and hepatocellular carcinoma • Human papillomavirus (HPV) and non-melanoma skin cancer • Epstein Barr virus (EBV) in lymphoma and carcinoma • Human Herpes Virus 8 (HHV8) and Kaposi's sarcoma

form of tuition 6-12 contact hours. In addition the course consists of independent learning on the basis of a literature study on selected topics. Introduction session with basic lectures will be provided by the teachers. Question time with the teachers to decide in consultation.

literature Literature consists of recent (review) papers in the field of viral oncogenesis.mode of assessment The course will be concluded by group presentations on literature studies (3

hours). Moreover, findings on literature studies should be summarized in a short written summary to be delivered at the end of the course.

target audience This course is optional for students of the Master Course in Oncology who have completed three compulsory courses of the Master Course in Oncology.

remarks After the course the students will have thorough knowledge and in depth insight into: • the fundamental processes which play a role in viral oncogenesis • the mechanisms of the various oncogenic viruses • the translation of fundamental research into clinical applications Apply per email to the coordinator of the Master's Programme in Oncology.

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subject In the footsteps of Antoni van Leeuwenhoek code 311169

credits 3 co-ordinators prof.dr. P. Peters; prof.dr. C.J.F. van Noorden; dr. J.A.M. Beliën

period to be announced aim A graduate course on microscopy "In the footsteps of Antoni van

Leeuwenhoek". This six-days course will cover a wide range of aspects of microscopy, starting with basal knowledge of the microscope, preparation and staining of microscopic specimens, quantitative analysis of microscopic images, electron microscopy and confocal laser scanning microscopy.

content The program includes lectures from international renowned experts in the different fields of microscopy, and there will be plenty of opportunity for interaction between the experts and the participants. Moreover, there will be hands on sessions related to all aspects dealt with the course.

form of tuition 26 hours (10 practical, 6 discussion group, 10 lecture). This course consists of lectures, literature discussions and practicals. This course will be attended together with PhD-students from the AMC, NKI and VU.

literature Course literature consists of recent review papers. mode of assessment The course will be terminated by a presentation of a recent paper and/or a

written assessment. target audience This is a PhD-students' course organized by the "Onderzoeksschool

Oncologie Amsterdam" (OOA). OOA courses are open for Master Oncology students as optional courses under certain conditions.

remarks The course will highlight the application of several techniques that the participants have learned during the course, for resolving biological problems. Apply per email to the course coordinator (secretary): v-ici@vumc.nl For more information: www.ooa-graduateschool.org

subject The Symbolic and Cultural Meanings of Cancer code 311170

co-ordinator dr. A.K. Oderwald credits 3 period 21 January - 1 February 2008

aim The aim of this course is to acquire insight in the symbolic and cultural meanings of cancer.

content Reading and analyzing stories of cancer patients, reading of secondary articles.

form of tuition The course will be given in English. The course consists of discussion groups and a symposium. Students are required to have a large self-motivation. The course will be highly interactive. An active participation is required.

literature The course material consists of a reader, autobiographies of cancer patients and novels about cancer.

mode of assessment The course will be terminated with a paper and a presentation. More than 20% absence without agreement will have consequences for crediting the course.

target audience This course is optional for students of the Masters in Oncology. When positions are available, students of other masters can attend the course after an intake with the teacher.

remarks Apply per email before December 15th, 2006 to the course coordinator:

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ak.oderwald@vumc.nl. A minimum of five participants is needed.

subject Animal experimentation (Proefdierkunde voor onderzoekers) code 311172

credits 3 co-ordinator I. Boumans

lecturers H. Griffioen; J. Wolters; T. de Cock Buning; A. van Halteren; C. Hendriksen; P. Kroon; R. Ottenhof; P. Reuzel; M. Ritskes-Hoitinga; F. van den Broek; W. Wadman; M. Tanck; F. de Jong; M. van der Valk; P. Rooymans; C. Pool; A. Maas; H. van Herck; J. van der Harst; P. Dortant; W. Florijn; M. Berendsen

period 22 October thru 2 November 2007. Further course data will be announced on Blackboard.

aim The course is focused on the respectful and responsible use of laboratory animals in biomedical research.

content It consists of: legal, ethical and social aspects of animal tests; comparative biology and zoological techniques of most used laboratory animals; lodging and care taking; pathology, genetics, anaesthesiology; experimental techniques, experimental set-up and statistics; aspects of stress and immunology research; alternatives for animal testing and exam.

form of tuition The course will be given in Dutch. Papers are in Dutch too. During the course, lectures and hands-on workshops alternate with demonstrations, videos and discussions.

literature The theoretical part of the course is covered by a multi-author textbook (which has been translated into several other languages): L.F.M. van Zutphen, V. Baumans and A.C. Beynen (eds.), Principles of Laboratory Animal Science: A contribution to the humane use and care of animals and the quality of experimental results, Elsevier Science Publishers, Amsterdam, 1993 (1st ed), 2001 (2nd ed). Also a CD-ROM Humane Endpoints in Laboratory Animal Experimentation is used and additional information is given with hand-outs from presentations, etc.

mode of assessment In order to obtain the certificate, course members must attend all lectures of the course and pass the exam.

entry requirements The participant must have graduated in one of the biomedical studies mentioned in the Law on Animal Testing, or must comply with entrance requirements: for specifications please contact the DEC-secretariat. Admission for this course requires at least training which meets the legal requirements of 500 SBU biological basic subjects (of which 200 SBU comparing anatomy/ zoology and 200 SBU comparing physiology). 1 week fulltime study = 40 SBU¿s. (SBU = Studie Belasting Uur = one hour study load) Also master students can participate on the course, but they must have a strong motivation for laboratory animal experimentation. It should be proven that they do, did, or have done a scientific training, in which animal experimentation plays a role.

target audience The course is required by law for every researcher conducting animal tests (art.9 Law on Animal Testing). Also master students Oncology and other biomedical masters with strong motivation to work in laboratory animal experimentation can participate in the course.

remarks Application by contacting the DEC secretariat AMC/UvA, tel. 020-5667113 or the Course coordinator I. Boumans: I.J.Boumans@amc.uva.nl/ tel. 020-

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5666479. Students must apply by the coordinator of their own master.

subject Systems Biology of Cancer code 311173

co-ordinator prof.dr. J. Lankelma credits 3 period May 2008

aim In this graduate course the topology of cellular regulatory networks will be identified ("who talks to who?"), especially those interactions which are corrupted in cancer. The student will get acquainted with kinetics of biochemical reactions and how those influence the properties of cellular regulatory networks. Insight into quantitative analysis of networks will be obtained, both from combined modeling and experimental perspective. The students will increase their insight into mechanisms of cellular and supracellular decision making leading to cancer.

content Starting from a bachelor level knowledge on cellular biology this course will focus on the analysis and the consequences of molecular interactions in networks. Such networks have systemic properties, which do not result of single biochemical reactions but rather emerge from their joint activities. Interesting and profound systemic properties are for instance "toggle switches" or binary cellular decisions, e.g. for apoptosis, angiogenesis or cell division. Computer models will be designed during the course, that allow for "in silico" experiments in which we can vary biochemical parameters of biochemical reactions and study their effects on system properties. With such experiments we can perform network-based drug design and propose real world experiments to validate and refine our models and to learn more about the biology of cancer. For this process we will need quantitative data as readouts of the system. Insight in the required accuracy of data will be trained.

form of tuition During the morning sessions, lectures will be given by experts in their field. In the afternoon there will be practical computer modeling sessions using existing models and on modeling design.

literature Course literature consists of documents provided by the teachers. mode of assessment The students will be offered a test with open theoretical questions as well as

computer modelling tasks. target audience This an optional course for masters (not advised for students that have

followed the FALW bachelor¿s course "Integrative Tumour Cell Biology"). remarks The student should be interested in basic mechanisms of cancer (treatment)

as well as working with computers. Some basic computer experience is essential (e.g. familiarity with Excel). Apply per email to the course coordinator: j.lankelma@vumc.nl

subject Sequence Analysis code 430045

coördinator prof.dr. J. Heringa lecturer prof.dr. J. Heringa (and other lecturers) credits 6 period December-January

aim A theoretical and practical bioinformatics course about biological sequence analysis. The course provides an introduction to the algorithmic and

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biological principles of sequence analysis, as well as practical implications. Goals: • At the end of the course, the student will be aware of the major issues,

methodology and available algorithms in sequence analysis. • At the end of the course, the student will have hands-on experience in

tackling biological problems in sequence analysis. content Theory:

• Dynamic programming, Sequence homology searching, pairwise and multiple alignment, probabilistic methods, pattern matching, evolutionary models, and phylogeny.

Practical: • Assignment programming own alignment software based on dynamic

programming • Assignment homology searching and pattern recognition using biological

and disease examples • Assignment multiple alignment of biological sequences

form of tuition 13 Lectures (2 two-hour lectures per week), Assignment introductions, Computer practicals, Hands-on support

literature • E-course material: http://ibivu.cs.vu.nl • Richard Durbin, Sean R Eddy, Anders Krogh, Graeme Mitchison,

Biological Sequence Analysis, Cambridge University Press, 350 pp., ISBN 0521629713, 1998.

mode of assessment Assignment results and oral or written exam (depending on number of course students)

entry requirements Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, Medical Natural Sciences. Some experience in programming is required.

target audience Students with Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, or Medical Natural Sciences, with a strong interest in Bioinformatics

remarks Active participation is required. The course is taught in English.

subject DNA Protein Structure-Function Analysis and Prediction code 430046

coördinator prof.dr. J. Heringa lecturer dr.ir. K.A. Feenstra credits 6 period 4

aim A theoretical and practical bioinformatics course on the analysis and prediction of structure-function relationships of DNA and protein molecules. The course provides an introduction to the molecular principles of structure and function, available bioinformatics analysis and prediction techniques, and biological databases. Goals: • At the end of the course, students will be aware of the major

issues and methodology. • At the end of the course, the student will have hands-on experience in

molecular modeling and studying structure-function relationships. content Theory:

Protein folding and energetics, experimental structure determination, protein

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fold families, protein structure databases, protein secondary structure prediction, fold prediction, molecular modeling, protein-protein interactions, DNA/RNA structure/function, DNA/RNA structure prediction Practical: • Assignment homology modelling • Assignment immunocomplex modelling

form of tuition 13 Lectures (2 two-hour lectures per week), Assignment introductions, Computer practicals, Hands-on support

literature • E-course material: http://ibivu.cs.vu.nl • Carl Branden & John Tooze, Introduction to Protein Structure, 2nd

Edition or higher. Garland Science, ISBN 0815323050, 1998. mode of assessment Assignment results and oral or written exam (depending on number of course

students). entry requirements Bachelor Physics, Chemistry, Mathematics, Computer Science,

Biology, Medical Natural Sciences,. A completed course Sequence Analysis is a strong advantage.

target audience Students with Bachelor Physics, Chemistry, Mathematics, Computer Science, Biology, Medical Natural Sciences or Medicine, with a strong interest and some basic knowledge in Bioinformatics.

remarks The course is taught in English.

subject Genome Analysis code 430047

coördinator prof.dr. J. Heringa lecturers prof.dr. J. Heringa; Gastdocenten

credits 6 period 1

aim A 1-month practical course about genome analysis. The corse provides an introduction to the algorithmic and biological principles of genome analysis, as well as practical implications.

content Goals • At the end of the course, the student will be aware of the major issues,

methodology and available algorithms in genome analysis. • At the end of the course, the student will have hands-on experience in

tackling biological problems in genome analysis. Theory:• Sequence alignment, dynamic programming, database searching, and

further appropriate downstream genomics analysis techniques. Practical: A choice between assignments: • Phylogenetic profiling of a selected bacterial gene • Prediction of function of unknown ORF's in selected viruses or bacteria • Function prediction through interpolation of distances from Clusters of

Orthologous Groups (COGs) form of tuition • One-to-one assignment introductions

• Hand-on support • If necessary: parts of bachelor course Genomics

literature • E-course material and overheads • Gibson G and Muse, A primer of genome science, SV, Sinauer

Associates Inc Publishers, 2002, ISBN 0878932348 (pbk).

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• Durbin, R., Eddy, Sean R., e.a., biological Sequence Analysis, Cambridge University Press, 350 pp., ISBN 0521629713.

• Extra: Parts from the book; Claverie & Notrdame, Bioinformatics for Dummies, Wiley Publishing, Inc., 2003, ISBN 0764516965

mode of assessment Assignment results and oral or written examination (depending on number of course students).

entry requirements Bachelor course Genomics. target audience Third or fourth year students Computer Science, Mathematics, Chemistry or

Physics Masterstudents Biomolecular Sciences, Biology en Bio-Medical Sciences, all with a strong interest in Bioinformatics.

remarks Active participation is required. The course will be taught in English (master level) and Dutch (bachelor level).

subject Bioinformatic Data Analysis and Tools code 430048

coördinatoren prof.dr. J. Heringa; dr. E. Marchiori lecturers prof.dr. J. Heringa; dr. E. Marchiori (and other lectures)

credits 6 period 5

aim A theoretical and practical bioinformatics course on the fundamentals of bioinformatics tools and tool creation for biological data mining. Goals: • At the end of the course, students will be aware of the issues,

methodology and available bioinformatics tools. • At the end of the course, students will have hands-on experience in

molecular modeling and studying structure-function relationships. content Theory:

Introduction to statistical thermodynamics, inverse protein folding, genetic algorithm, repeat recognition tools and concepts (e.g. transitivity), molecular mechanics simulations, (hidden) Markov models, pattern recognition, machine learning techniques. Practical: • Assignment Statistical Thermodynamics • Assignment hidden Markov modelling

form of tuition 13 Lectures (2 two-hour lectures per week), Assignment introductions, Computer practicals, Hands-on support

literature • E-course material (slides, assignment material, papers): http://ibivu.cs.vu.nl

• Nelson, P., Biological Physics. Energy, Information, Life, W H Freeman & Co., (July 2003), ISBN: 0716743728

• Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT Press, 2004, ISBN: 0262101068.

mode of assessment Assignment results and oral or written exam (depending on number of course students)

entry requirements A completed course Sequence Analysis and DNA/Protein Structure-Function Analysis and Prediction is a strong advantage. Some experience in programming is required.

target audience Students with Bachelor Physics, Chemistry, Mathematics, Computer Science,

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Medical Biology, with a strong interest and some basic knowledge in Bioinformatics.

remarks Active participation is required. The course is taught in English.

naam Genomics code 470076

coördinator prof.dr. M. Verhage (matthijs@cncr.vu.nl) docenten dr. J.M. Kooter; prof.dr. M. Verhage; dr A.S. Groffen; prof dr P. Heutink;

prof.dr. A.B. Smit; dr. R.J.M. van Spanning studiepunten 6

periode 03.09.2007-28.09.2007 doel De hoofddoelen zijn:

• het verkrijgen van inzicht in de samenstelling en organisatie van het genoom en de benaderingen om dat te analyseren.

• het analyseren van verschillen en overeenkomsten binnen het genoom en tussen genomen van verschillende individuen of species en het inzichtelijk maken hoe die verschillen en overeenkomsten de basis vormen voor verschillen en overeenkomsten in het funktioneren van cellen en het gedrag van organismen en in het ontstaan van ziekte

• het verkrijgen van inzicht in hoe genoom-elementen bijdragen tot complexe biologische funkties of het ontstaan van ziektes.

Voor deze hoofddoelen worden de volgende vaardigheden bijgebracht: • het gebruiken van de bioinformatica in genoomanalyse, bij het vinden en

gebruiken van de verschillende databases voor DNA sequenties, transcriptomics profielen, proteomics en metabolomics en het vergelijken van deze verschillende genoomsequenties,

• het identificeren van genetische diversiteit en variaties die bijdragen tot het onstaan van ziekte of de kwetsbaarheid hiervoor.

• het vergelijken van de funktie van orthologe genen in verschillende organismen

Ten slotte heeft de cursus het doel de student te laten kennismaken met een aantal belangrijkse toepassingen en afgeleiden van genoomanalyse: • de transcriptomics, de proteomics en de metabolomics, ook voor

diagnostische doeleinden • methodes om in model organismen in te grijpen in hun genoom, om

daarmee de basis van fysiologisch, biotechnologisch en pathologisch functioneren te onderzoeken (tuneable promoters, transgenese, knock-out technologie, RNA-interferentie)

• de genetische basis van gedrag en gedragsafwijkingen • medische toepassingen van genomics (vergelijken zieke en gezonde

weefsels, diagnose; uitzicht op therapie, pharmacogenomics) • biotechnologische toepassingen van genomics • ecologische toepassingen van genomics • ethische aspecten aan genomics en genetische modificatie

inhoud De cursus bestaat uit twee kort 'opfris' colleges afgerond met een toets om een goed ingangsniveau te garanderen. Het hoofdbestanddeel van de cursus zijn 14 modules die elk bestaan uit hoorcolleges en een computerpracticum. Tenslotte is er tijd voor het afronden van opdrachten en voorbereiden van het tentamen.

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werkwijze Hoorcolleges, (computer)werkcolleges, zelfstudie literatuur Syllabus Genomics

toetsing Tentamen en ingeleverde werkopdrachten. Het eindcijfer wordt bepaald uit het gewogen gemiddelde van de scores voor het tentamen (60%) en de werkopdrachten (samen 40%) Studenten kunnen alleen slagen nadat zij alle computerpraktica hebben volbracht.

doelgroep Verplicht voor tweedejaars en derdejaars bachelorstudenten Biomedische wetenschappen. Keuze voor derdejaars bachelorstudenten Biologie. Keuzecursus voor tweedejaars BSc Gezondheid en Leven. De cursus staat open voor belangstellenden uit andere opleidingen. Studenten uit andere studierichtingen moeten vooraf contact opnemen met de docent en goedkeuring vragen bij de examencommissie van hun eigen opleiding.

subject Philosophy of Systems Biology and its Relation to Society code 470121

co-ordinator dr. F.C. Boogerd lecturers guest lecturers; dr. F.C. Boogerd; prof.dr. H.V. Westerhoff

credits 3 period 26.05.2008-06.06.2008

aim An intensive course to acquaint students with the philosophical background of Systems Biology. The aim is to get insight into the following topics: • Holism versus reductionism • The potential of Systems Biology to bridge the above gap • Mechanistic and functional explanation • Emergence in the Life Sciences • Merites and drawbacks of the reductionist view of life

content The philosophy of Systems Biology and its position relative to various other disciplines will be dealt with in five sessions of 1.5 day each. Every session consists of three parts: preparing for the lectures, listening to the lectures and participating in the discussion, and studying the reader. At the end of the second week, 2.5 days are to be spent on further selfstudy and making the final examination.

form of tuition Self-preparation, Lectures, Discussion groups, Self-study. literature Reader (ca.10 euro), selected articles

mode of assessment The grading is based on active participation during the lectures and the discussion groups and on the final examination.

target audience Students with Bachelor Physics, Chemistry, Mathematics, Biology, Medical Biology or an equivalent degree with a strong interest in the interface between these disciplines.

remarks The course is taught in the English language

subject Caput Epigenetics code 470606

co-ordinator dr. J.M. Kooter lecturer dr. J.M. Kooter credits 6 period In consultation, contact the co-ordinator

aim Acquire knowledge of the biochemistry and dynamics of DNA Modification and Chromatin Modification (DM&CM) and of the role these epigenetic mechanisms have on gene expression and inheritance of traits. Important is

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the insight students will get about the role of epigenetics in various biological processes in human, animals, plants, fungi, and bacteria.

content • Non-mendelian inheritance of traits • Biochemistry of DNA methylation • Biochemistry of histone modifications and chromatin structure • Composition of chromatin and chromatin remodeling • Somatic and gametic cell inheritance of epigenetic information • Cellular memory by means of polycomb-group proteins • Role of DM&CM in gene expression • Role of epigenetics in cancer and other diseases • Role of DM&CM in sex-chromosome inactivation and activation • Role of DM&CM in gene-dosage compensation • Role of DM&CM in genomic / parental imprinting • Cloning of animals and epigenetics • Impact of non-coding RNAs / RNA interference on DM&CS

modifications • DNA methylation as genomic defense mechanism • Epigenomics • Epigenetic effects of diet and environmental factors • Genetically identical but epigenetically different individuals • Transgenerational effects • Role of epigenetics in evolution • Methods to analyze DM&CM

form of tuition Self-study combined with discussions with lecturer. literature Review and Research articles which will be provided. It is advised to study

the chapters on DM&CM and gene expression of the book, Molecular Biology of the Cell by Alberts et al.

mode of assessment Written exam entry requirements Bachelor courses: Genetics (Genetica) and Molecular Developmental

Biology (Moleculaire ontwikkelingsbiologie) target audience Master students: Biomolecular Sciences, Biology, Bio-Medical Sciences,

Oncology, and Biochemistry

subject Biological fluorescence code 470609

co-ordinator dr.ir. Y.J.M. Bollen lecturers dr.ir. Y.J.M. Bollen; guest lecturers; prof.dr. A.J.W.G. Visser

credits 6 period 04.02.2008-29.02.2008

aim Goals: To introduce students into the application of various fluorescent methods to tackle biochemical problems. Students should be able to • plan and conduct experiments utilizing fluorescent techniques • evaluate results on the basis of theory and recent literature • present their results in short reports and one journal-style paper. Students should know • theoretical principles and application of different fluorescence methods

content Theory: Theoretical fundaments and practical applications of (time-resolved)

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fluorescence spectroscopy and microscopy will be covered. Practical: • background is briefly discussed with the instructor prior to the

experiment. • laboratory work is carried out using several different fluorescent

methods, including a unique one (PEFFLS) which has been developed within the department of Structural Biology

• results are interpreted and a short report is written. form of tuition • Lectures

• Tutorials/discussions of book material, lecture notes • Laboratory work: students work in small groups within the departments

labs literature • Reader (ca 5 Euro)

• Papers available on blackboard mode of assessment Active participation and written reports. entry requirements Bachelor Physics, Chemistry, Mathematics, Biology, Medical Biology plus

topmaster portal course, or equivalent target audience Students with Bachelor Physics, Chemistry, Mathematics, Biology, Medical

Biology with a strong interest in the interface between these disciplines remarks Taught in English and much direct contact with the professors and associate

professors is involved.

subject Wetenschapsjournalistiek (science journalism) code 471014

co-ordinator drs. B.J. Regeer lecturers drs. B.J. Regeer; drs L. Bonaparte

credits 6 period 03.09.2007-28.09.2007

aim • Gaining insight in popularization of the beta sciences in print and digital media;

• Learning how to write popular science articles for newspapers, magazines and websites;

• Learning how to write specific genres like interviews, book reviews and opinion articles.

content This module consists of lectures about practical and theoretical aspects of science journalism. Topics are the role of science journalism in constructing relations between science and society, images of science in the press, ethical aspects of science journalism and communication barriers between scientists and journalists. Guest speakers give insight into their profession as science journalists, working for news-papers, magazines, internet or broadcasting media. Moreover, students receive training in all aspects of writing popular science articles, such as data collection (interviewing), writing techniques, target groups and genres.

form of tuition Lectures and seminars on theory and practice of science journalism and writing skill training. A large amount of time is set aside for writing popular science articles. The assignments are assessed by lecturers and fellow students.

literature Donkers, H. & Willems, J. (2002). Journalistiek schrijven. Bussum: Coutinho (2nd edition).

mode of assessment Assessment is based on the last assignment (possibly adjusted on the basis of

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the other assignments): a popular scientific article for a newspaper or magazine.

target audience Master's students in the Health, Life and Natural sciences remarks Course is taught in Dutch.

For more information: mark.bos@falw.vu.nl

4.3 Practical training

4.3.1 Short description In total a student has to spend 69 ECTS credit points to two practical training periods: two periods with the same length or one longer (corresponding to maximal 40 ECTS credit points ~ ca. 27 weeks) and a shorter one (corresponding to minimal 29 ECTS credit points ~ ca.19 weeks). For more information see chapter 5.

4.4 Study of literature

4.4.1 Short description The study of literature will be carried out under supervision, yet highly independent. There will be the possibility that the student proposes his or her own subject and presents an own question. For more information see chapter 5.

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5 Options to placements and studies of literature

5.1 Regulation for placements and literature surveys 2007-2008 General This manual was composed under responsibility of the Board of Governors of the VUmc. It is a result of the academic "stage- en scriptieregeling" as determined by the Board of Governors on the 22nd of October 1998, ex art. 5.7 of the "Statuut VU". Because of the fact that a study of literature is relatively short (usually 9 ECTS credit points), not all of the stated components can be of use. This manual is declared applicable to students of the Master's Programme in Oncology. Other students cannot make use of this application. Course of events Teachers and students have to do the following: 1. Before initiation of a placement or a literature study: Before starting a placement, a student always has to ask for approval of the examination board of the Master's Programme in Oncology via a "form for approval of an internal placement" / a "form for approval of an external placement". 2. During the placement, within 6 weeks: A student has to write a research proposal. The research proposal and a completed list of appointments made between the student and the department at which the student is working has to be handed in to the examination board. An interim assessment has to be made using the form of an assessment of a placement. 3. At the end of a placement: A "credits registration form" has to be filled in including the total mark. This form has to be handed in with the coordinator of the Master's Programme in Oncology. In addition a copy of the written report has to be handed in. All forms necessary for internal and external placements can be downloaded via the website of the master's in Oncology, or can be picked up at the office of the Master's Programme in Oncology’s coordinator. Approval and Supervision Before starting a placement or a study of literature, a student always has to ask for approval of the examination board of the Master's Programme in Oncology via a "form for approval of an internal placement" / a "form for approval of an external placement". The examination board meets once a month. Decisions and data will be announced on the blackboard site "Communication site Master Oncology". Correctly filled in forms for approval have to be handed over to the coordinator of the Master's Programme in Oncology one week before the meeting of the examination board. Within the Master’s Programme in Oncology two types of placements and studies of literature are being distinguished. • Internal placement / study of literature: to be carried out within the VUmc or the

VU faculty of Earth and Life Sciences. • External placement / study of literature: to be carried out outside the VUmc or the

VU faculty of Earth and Life Sciences. Within the Master’s Programme in Oncology several types of supervisors are being distinguished.

Options to placements and studies of literature 43

• Internal supervisor: supervisor appointed at VUmc or the VU faculty of Earth and Life Sciences.

• External supervisor: supervisor appointed at an institute outside the VU/VUmc. • Supervisor 1: day-to-day supervisor of the placement or study of literature. In case

of an external placement supervisor 1 is appointed at the institute outside the VU/Vumc and is the external supervisor.

• Supervisor 2: qualified academic teacher (UD, UHD or professor) with a permanent appointment at the VU/VUmc. Supervisor 2 is examiner of the placement or study of literature, is responsible for the final mark and will sign the credits registration form. In case of an external placement / study of literature supervisor 2 is the internal supervisor.

About the site and the supervision of placement the examination board has set up the following regulations for approval. • It is not allowed to do two external placements, one placement should be done

within the VU/VUmc. • It is not allowed to do two internal placements under supervision of the same

supervisors. • It is allowed to do two placements within the same department, but with different

supervisors. • It is allowed to do an internal and an external placement under the supervision of

the same examiner. • It is allowed to do one placement and the study of literature under the same

supervisor / examiner. • It is not allowed to do two placements and the study of literature under the same

supervisor /examiner. An external placement has to be discussed with the internal supervisor before starting the placement: the internal supervisor will not give always his approval. The form for approval has to be signed by both supervisors. A letter or e-mail of commitment from the external supervisor is valid also. List of appointments Within 6 weeks after the initiation of a placement, a list of appointments made between the student and the department at which the student is working has to be filled in. A copy of this list has to be handed in to the coordinator of the Master's Programme in Oncology. On the list of appointments things like date of initiation and of termination (including writing of the final report and registration of a final mark)of the placement, coaching, oral presentations, facilities to be used and possible interruptions of the period due to optional courses/holiday have to be registered. It is possible that for certain placements the department wants a student to have done a specific optional course before starting the placement, e.g. "working with radioactivity". If this course is finished successfully with an examination "stralingshygiëne deskundigheidsniveau 5B", this course will also count as an optional course for 3 ECTS credit points. If the student doesn't take the examination, the course will be included into the placement, including the study load. During a placement a student has to have a work discussion with his day-to-day supervisor on a weekly basis, but the possibility to have contact on a daily basis is assumed to be possible. It is also requested to have work discussions with the head of the department to make up the final mark. If the daily supervisor is inexperienced (e.g. a PhD

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student), it is demanded for the student to have a work discussion with the supervisor of his/her supervisor once or twice a month. At least two oral presentations are requested for a placement: one to practise and one in a later stadium to give a mark for. For a study of literature only one oral presentation is demanded. Facilities to be used: in principal all facilities will be taken care of by the department (apparatus, working space, materials, trips on behalf of the placement, costs for oral presentations and the final report). Research proposal Within 6 weeks after initiation of a placement, a research proposal containing a plan of investigation has to be written and handed in to the coordinator of the Master's Programme in Oncology. This research proposal has to include: the title and aim of the study, background information, materials and methods, expected results and a time scheme. A format for the research proposal can be downloaded from the website. Trial period, interim assessment and success of a placement Within 6 weeks (trial period) after initiation of a placement, an interim assessment has to be made the day-to-day supervisor and a second supervisor if it is possible to conclude the placement successfully. For this interim assessment the form for the assessment of a placement has to be used. After the assessment a decision will be made explicitly about the continuation of the placement. If the placement can be continued with consent of both parties, there is an agreement with which the student can count on a successful termination of the placement, providing that the student is dedicated to his/her research and that he/she meets his/her commitments. If there is no reasonable prospect on success, the supervisor will contact the coordinator of the Master's Programme in Oncology. The coordinator will then contact the student and will act as an intermediary for possible continuation of the placement or to credit the spent time with ECTS credit points. With problems concerning failure of the student or supervisor, the coordinator of the Master's Programme in Oncology will act as an intermediary. The student can protest by contacting the examination board of the Master's Programme in Oncology. Obtaining scientific results does not mean that a placement will necessarily be terminated successfully. An important condition for success is an academic attitude. Of course, also the final report and the oral presentation have to meet the conditions of success. The final report includes a period of work, not a well-rounded research project. A study of literature does not include a trial period. Norm of a placement A student is expected to learn and carry out scientific research under supervision and in a later stadium more independently. Hypotheses and problems have to be clear to the student from the start. A placement has to include time for the student to perform research independently and it is not allowed to use a student just for routine analysis. Also it needs to be clear to the student how the research has to be performed, with the use of an outlined phasing and planning of activities. Also included in the scientific research are theoretical preparation, literature search, writing of the final report, work discussions and participating in scientific activities at the department. Office hours are 8 hours per day, as worked at the department, e.g. 9.00-17.30 including one half hour-break.

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Duration and elongation of a placement The duration for both placements and the study of literature is determined in the programme of examination. Norm for a final report and an oral presentation during a placement is 2-4 weeks, extension will not be rewarded with credit points. Writing of the final report is totally included in the duration of a placement. A placement can be elongated up to a maximum of 40 ECTS credit points, providing that it strokes with the planning and the combination of courses of a student. This placement then counts as the longest one of the two. This means that the student is not allowed to spend more than 29 ECTS credit points on the other placement. A student has to have a written consent of approval of the coordinator of the Master's Programme in Oncology for elongation of a placement. Furthermore, a placement can also be elongated with 6 ECTS credit points at once, coming from credits to use either for an once-only elongation of a placement or an extra optional course. This elongation has to be approved of separately via a form of approval for the filling in of credit points out of free space. The mark for the extension is the same as the mark for the placement. Elongation will only be accepted if this will lead to more scientific results and if it strokes with the student's planning. Elongation to compensate low quality will not be tolerated. Final report, oral presentation and accessibility of a placement or study of literature A final report of a placement will have the format of a scientific publication, common in the field of research. The report will be written in English. The report will consist of the following subjects: introduction with the aim of the study, materials and methods, results, conclusions, discussion and recommendations and references. When necessary detailed information can be described in appendices. Agreements have to be made concerning criticism, judging the report and the time of handing in the report. The supervisor will receive a concept report, and he/she should give it back to the student complete with written critics within a few days. Afterwards, the critics will be discussed with the student. The concept report can only be corrected once, maximal twice, before the final handing in. The performed research and the final report are intellectually owned by the department at which the placement is performed. When necessary agreements about confidentiality can be made between internal and external supervisors. Internal supervisors are obliged to read and assess the full report. The student is co-author at the time of publication of is/her results, only if the results are sufficient. The final report is printed and handed in at the department at least in duplicate. A copy of the final report is handed over to the coordinator of the Master's Programme in Oncology for central registration. An oral presentation concerning the placement and the results will be given to the research group of the department. As stated above, there is a central registration, archive and accessibility to reports of placements and studies of literature. These documents will be filed at a central place, to be viewed in by next-generation Master's Programme in Oncology students. It is possible to not offer a report to view in, only on request of a teacher/ supervisor to consider that report confidential. This request has to be provided with a clear motivation. The final mark for the placement will not be registered when the student fails to submit a copy of the written report to the coordinator of the Master's in Oncology.

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Structure of a study of literature Preferably, a study of literature is written in the format of a scientific review article. The study of literature has to be written in English, and the period will always be terminated with an oral presentation. Assessment report An assessment report has to be filled in by the day-to-day supervisor. For each part a partial mark will be given. The final mark is calculated, using the norm 50-25-25% for respectively laboratory practise, final report and oral presentation. If a student hasn’t performed laboratory practise and in case of a study of literature, the norm will be 75-25% for respectively final report and oral presentation. The final judgement will be executed in the presence of the supervisor-2, head of the department and the student. The final mark will be filled in on a credits registration form and handed over to the coordinator of the Master's Programme in Oncology. Evaluations Evaluation of placements, studies of literature etc. are decreed in the "Onderwijs- en examenregeling" (OER). It is important to tell the coordinator of the Master's Programme in Oncology about problems concerning a placement or a study of literature; these problems will be handled confidentially. Supplementary conditions The tasks performed by a student during a period of placement cannot be considered as a replacement of an employee of the teacher's/supervisor's department. The department has to accept responsibility for injury, accidents or damage to the student during his/her presence or during the performance of practical tasks at that department, only if the injury, accidents or damage come with the legal responsibility of the department and/or its employees. A student needs to have a private "WA"-insurance, covering for possible costs of events that can happen during a placement, of which the student is legally responsible

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5.2 Options for a placement at departments of the VUmc

5.2.1 Department of Radiation Oncology Coordinator: prof. dr. B.J. Slotman, radiation oncologist, phone: (020) 444 0414, email: bj.slotman@vumc.nl Prof.dr. S. Senan, radiation oncologist; Dr. M.V.M. Lafleur, radiobiologist; Dr. P. Sminia, radiobiologist; Mw.dr. G. Kuipers, radiobiologist; Mw.dr. B. van Triest, radiation oncologist; Dr. F. Lagerwaard, radiation oncologist; Dr.ir. J.P. Cuijpers, clinical physicist. Summary: The department of Radiotherapy / Radiation Oncology consists of a clinical, a biological and physics division. The research at the department focuses on the use of new radiation techniques and new multi modal treatment methods in the treatment of (mostly malignant) tumours. Research is focussed on tumors of the brain, head&neck, thorax and abdomen, and aims to improve both cure rates and quality of life. Besides clinical topics, research on physics and tumor bioiology is performed. The radiobiological laboratory in particular is relevant for master students. IMAGE-GUIDED RADIOTHERAPY This research line explores the use of 4-dimensional and respiratory gated radiotherapy to reduce the toxicity of clinical treatments, and enable radiation dose-escalation. Respiratory gated radiotherapy involves treatment during only phases of respiration in which the target volume is relatively immobile, or when a normal organ is maximally displaced from the target volume. Evaluation of 4-dimensional (4D) CT scans has allowed for the identification of patients who derive maximal benefit from gating for stage I and III lung cancer. 4D approaches are now routinely applied in patients with locally advanced lung cancer and abdominal tumors, using respiratory coaching in order to increase the efficiency of gated radiotherapy for conventional chemo-radiotherapy. Coordinator: Prof.dr. S. Senan STEREOTACTIC RADIOTHERAPY OF CNS LESIONS Intracranial stereotactic radiosurgery focuses on treatment of arteriovenous malformations (AVM), brain metastases and vestibular schwannomas. Research lines on AVMs deal with improvements of target definition for radiosurgery using a combination of available diagnostic imaging techniques such as angiography, magnetic resonance angiography. Clinical results of stereotactic radiosurgery as a sole modality for treatment of brain metastases are currently being evaluated. For vestibular schwannomas, a prospective evaluation of outcome parameters (local control, loss of hearing and other side-effects) is being performed. Finally, improvements of dose delivery using intensity-modulated radiosurgery (IMRS) have been implemented in order to allow safe dose-escalation for small primary brain tumors.Coordinator: Dr. F.J. Lagerwaard COMBINED MODALITY RADIOTHERAPY Preclinical and clinical studies are being carried out to investigate the combination of radiotherapy and chemotherapeutic drugs and novel targeted agents. These studies aim at achieving radiosensitization and improved clinical outcome. In particular,

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translational research might elucidate signaling pathways involved in resistance to (radio)therapy and uncover underlying mechanisms and candidate targets for treatment optimization. Apart from clinical studies, this research includes biological studies, including 2D and 3D cell cultures, flow-cytometry, immunohistochemistry; micro-array techniques and proteomics. Coordinators: Dr. B. van Triest (clinical part), Dr. M.V.M. Lafleur (biological part) For more information visit the website: http://www.vumc.nl/radiother

Options to placements and studies of literature 49

5.2.2 Department of Molecular Cell Biology and Immunology At the Department of MCBI research is performed on fundamental immunological processes involved in infection, chronic inflammatory diseases and cancer. Different research topics are addressed that involve tumour immunology (headed by prof. dr. Rob Beelen), immune regulation (headed by prof dr G.Kraal), neuro-immunology (headed by prof dr CD Dijkstra), and dendritic cell immunobiology (headed by prof dr van Kooyk). The MCBI houses over 120 people including PhD-students, post-docs and undergraduate students generating a good collaborative atmosphere with lively scientific discussions. The MCBI has outstanding facilities to perform state-of-the-art research. Approaches that are applied range from well validated in vitro and in vivo models with the possibility to validate findings in patient material. Advanced cellular identification and imaging systems are operational (like FACS sorting and analysis, confocal microscopy, life cell imaging). Well characterized in vivo and in vitro models assist us in the identification of a number of crucial molecules and processes involved in the development of chronic inflammatory diseases. Within the MCBI, internships are regularly available for students. During their internship, students will receive training in various aspects required for performing high quality research, including access to various techniques and models necessary for their research, and documenting and presentation of their data. Students receive specific education in critically reading literature through journal clubs organized for students. Moreover, at the end of the internship students are invited to present their research data on the special symposium organized for and by students. If you are interested to join the MCBI for your internship please contact me for further information: Elga de Vries, 020 – 4448077, he.devries@vumc.nl

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5.2.3 Department of Pediatric Oncology/Hematology Coordinator: Prof. dr. G.J.L. Kaspers, email: gjl.kaspers@vumc.nl, dr. J. Cloos (laboratory research coordinator, email: j.cloos@vumc.nl), dr. E. van Dulmen-den Broeder (research coordinator quality of life and late effects, email: eline.vandulmen-denbroeder@vumc.nl). Summary: Research in this department is focused on targeted therapy for childhood cancer. Especially for children side-effects of treatment are largely influencing their quality of life during therapy but also many years thereafter. Specifically targeting the tumor cells and protecting the normal tissue are currently the most promising approaches. New drugable targets are being identified and novel drugs are tested as single drug, but also in combination with conventional chemotherapeutics and radiation. Besides acute leukemia, which is the most common cancer in children, we are also working on brain tumors (in particular medulloblastoma and gliomas) and the eye tumor retinoblastoma. Gertjan Kaspers is leading the projects from the clinical point of view while Jacqueline Cloos is research coordinator of the laboratory research. Eline van Dulmen-den Broeder coordinates research on the late effects of childhood cancer and its treatment, including quality of life projects. With increasing survival in childhood cancer, it is estimated that in the year 2010 one out of every 250 young adults will be a survivor of childhood cancer. Studies have shown that more than 50% of survivors have at least 1 late effect, 15 years after completion of therapy. These physical and/or psychosocial late side effects of cancer and its treatment may severely debilitate quality of life. This emphasizes the need for research in this area with maximum (100%!) survival with a minimum of side-effects and late effects as our goal. Main research lines in our department on late effects of treatment are 1) the female reproductive system and 2) neurocognitive functioning and quality of life. Specific projects: Glucocorticoid resistance in acute lymphoblastic leukemia (ALL). Glucocorticoids (GC) are the first line treatment in ALL and response to these drugs largely determines treatment outcome. Resistance to GC either intrinsically or drug-induced is one of the reasons of treatment failure. We are investigating possible mechanisms underlying GC resistance in order to find ways to circumvent it. Currently we are focusing on NFkB inhibition and changes in the GC receptor, which is crucial for GC action. This research is performed in close collaboration with the Department of Rheumatology (Dr. G. Jansen). Targeted therapy in acute myeloid leukemia (AML). Treatment outcome for AML is worse as compared to ALL due to apoptosis resistance and presence of increased cell proliferation inducing mutations such as in receptor tyrosine kinases. Research currently focuses on identifying new treatment targets and determining the anti-leukemic properties of novel targeted drugs. Role of tyrosine phosphatases in AML. It has already been established that tyrosine kinases play an important role in AML development. However, not all patient samples harbor mutations in those genes. Currently we are investigating the role of phosphatases (the kinases counterparts) as new treatment targets. This work is in collaboration with the Department of Cell Biology (Dr. T. van den Berg).

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Relapsed AML. We investigate which factors play an important role in the development of relapses. For this, we study differences between relapse and initial AML samples and look for markers in the initial samples that might already predict the high risk of developing relapse. In addition, we look for these markers in the minimal residual disease cells that remain after first course treatment. Ultimately, leukemic stem cells will be investigated. Novel treatment modalities for childhood brain tumors. The most important factor hampering treatment of brain tumors is the adverse side-effects of radiation. Therefore our aim is to find drugs that can specifically target brain tumor cells and/or sensitize the tumor cells to radiation and to find novel approaches for neuroprotection. In addition, one research project is focussing on diffuse brain stem tumors, which are lethal in nearly all patients. Convection-enhanced delivery will be studied in preclinical, animal and finally clinical studies. Preclinical studies will focus on good candidate antitumor drugs which ideally also act as radiosensitizer. Identification of risk factors for the development of retinoblastoma in young children and secondary primary tumors later on in life. The Department of Ophtalmology is the referral center for all retinoblastoma children in the Netherlands, which concerns 15-20 children per year. Although it has been well established that double inactivation of the Rb-gene is associated with retinoblastoma development the exact carcinogenesis pathway is unknown. About 95% of patients survive the retinoblastoma but many are at high risk of developing osteosarcoma just after puberty, or melanoma and other epithelial tumors later in adult life. Together with the Department of Ophtalmology (A. Moll and S. Imhof) and Human Genetics (H. Meijers) we want to unravel retinoblastoma carcinogenesis and identify risk factors involved in the development of retinoblastoma and subsequent second primary tumors. Reproductive function, ovarian reserve and risk of premature menopause in female survivors of childhood cancer. Many female survivors of childhood cancer are currently in the reproductive age and have questions about their fertility. A nationwide study, coordinated by the VU university medical center, has therefore been set up to evaluate in adult female childhood cancer survivors in the Netherlands, the effects of treatment in general, and the effects of different types of treatment, doses of drugs, radiation sites and doses, and age at time of treatment on: 1) ovarian function and actual fertility; 2) ovarian reserve and premature menopause; 3) uterine function and pregnancy outcome. Approximately 1250 female survivors will be approached for participation in the study, which consists of a questionnaire, blood sample and ultrasound of the reproductive organs. (Project leaders: Dr. E. van Dulmen-den Broeder (Dept. of pediatrics), Dr. CB Lambalk (Dept. of Gynaecology) and Prof. Dr. FE van Leeuwen (Dept of Epidemiology, Netherlands Cancer Institute)). The price of treatment: effects on the central nervous system in adult survivors of ALL: neurocognitive function, brain morphology and quality of life. The psychosocial and neurocognitive profile of long-term adult survivors of childhood ALL is hardly known. This multicenter cross-sectional study therefore aims to examine neurocognitive functions (i.e. attention, information processing, and

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memory) structural and functional morphology indices of brain damage, and quality of life (i.e. academic achievement, professional career, self reported cognitive functioning) in approximately 250 adult survivors of ALL from the VU university medical center and the Academic Medical Center. Results may help identify patients at risk of developing problems and may serve to develop follow-up guidelines and intervention strategies for adequate support of survivors of ALL. In addition, results will help improve future treatment protocols in aiming to optimize cognitive development and quality of life of survivors of ALL. (Principal Investigators: Dr. ir. LMJ de Sonneville (VUmc), Prof. Dr. AJP Veerman (VUmc), and Dr. C van den Bos (AMC). Quality of Life in children with acute lymphoblastic leukaemia In 2 cohorts of patients (one treated according to the so-called ALL9 protocol, now closed for patient accrual, the other treated according to the ongoing ALL10 protocol) we are investigating quality of life in children treated for acute lymphoblastic leukaemia. Together with investigators from Nijmegen, and within a nationwide collaboration, quality of life issues are being studied using questionnaires. We will also study factors that influence quality of life as experienced by parents and by patients. An add-on study will look at the effect of dexamethasone on sleep. (principal investigators: Prof. dr R. Gemke and Prof. dr. G.J.L. Kaspers). Methods & Techniques: Cell culture (suspension cells, adherent cells and primary patient cells), drug sensitivity assays (MTT, growth inhibition, clonogenic assays), DNA damage induction and repair (sandwich ELISA), chromosomal instability test, Western blotting, quantitative PCR (TaqMan and Lightcycler), mRNA expression micro arrays, flow cytometry, immuno histo- and cyto chemistry, cloning of PCR products, cDNA transfections, MLPA, methylation specific PCR and bisulphate sequencing, mutation analysis. Data extraction from patient files; questionnaires, blood samples, ultrasound measurements, neuropsychological tasks, MRI. Statistical analyses For more information visit the website: http://www.vumc.nl/hoi/onderzoek/index.html (in the future, the website will be called www.vumc.nl/kinderoncologie-hematologie)

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5.2.4 Department of Medical Oncology Coordinator: prof. dr. G.J. Peters, head of the laboratory, phone: (020) 444 2633, e-mail: gj.peters@vumc.nl and for each division their division heads, prof. dr. E. Boven, phone: (020) 444 4336, email: e.boven@vumc.nl, dr. V.W. van Beusechem, phone: (020) 444 8423, email: vw.vanbeusechem@vumc.nl, prof. dr. R. Scheper, phone: (020) 444 4031, email: rj.scheper@vumc.nl. Summary: Research in the department is mainly focused on translational research. Next to this, pure clinical research and fundamental research are also important research activities in the department. Research in the Clinical Research Laboratory of the Department (head: Prof. dr. G.J. Peters, PhD), takes place in four divisions: the Division of Angiogenesis, the Division of Gene Therapy, the Division of Immunotherapy and the Division of Pharmacology. Each division is directed by a division head and a head of the laboratory. The division head has the responsibility for the direction of the investigations, whereas the head of the laboratory has the responsibility regarding the practical realization of the research. Each division holds regular scientific meetings, and every week Ph.D. students and post-docs present the progress of their research to the whole department. Another weekly meeting is devoted to presentation of clinical research. Projects: Division of Angiogenesis The evidence that the growth of primary tumors beyond 2-3 mm3, and the development of tumor metastases are dependent on neovascularisation is well-established. The number of identified growth factors, enzymes, adhesion molecules and conditions which stimulate angiogenesis in physiological situations and in cancer is still rapidly growing. Recently the first definitive demonstration has been reported, that the combination of an anti-angiogenesis compound (anti-VEGF) with classical chemotherapy improves the anti-tumor response and survival of cancer patients. The Division of Angiogenesis, established in 1997, is involved in clinical and pre-clinical studies. An important aim of our group is the investigation of novel angiogenesis inhibiting agents in the laboratory and understanding fundamental mechanisms of tumor neoangiogenesis and to translate this knowledge into clinical studies of novel agents (translational research). (prof. dr. E. Boven, prof. dr. V. van Hinsbergh, prof. dr. J. Lankelma, dr. K. Hoekman, dr. H.J. Broxterman) Division of Gene therapy We explore the utility of recombinant viruses, primarily adenoviruses, in new anti-cancer therapies. We investigate two types of therapies, i.e., gene therapy and virotherapy. For gene therapy, we use virus-derived gene transfer vectors to introduce anti-cancer genes into cancer cells. For virotherapy, we exploit the inherent capacity of viruses to kill cancer cells by viral replication. As for any kind of anti-cancer treatment, the main issues in cancer gene therapy and virotherapy are efficacy and selectivity. Therefore, our main research aims are to selectively target treatment to cancer cells and to provide most effective cancer cell killing. In this regard, we also investigate combination treatments with chemotherapy or radiotherapy. The ultimate goal is to translate new gene-based treatment modalities into clinical applications for cancer patients. (dr. V.W. van Beusechem, dr. W.R. Gerritsen)

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Division of Pharmacology Research in the Division of Pharmacology focuses on two major topics: –Pharmacodynamics and pharmacogenomics dynamics of cancer drugs, focusing on translational research to individualise treatment, mechanisms of resistance (antimetabolites, platinum derivatives, topoisomerase inhibitors and multidrug-resistance related proteins, targeted agents. Another line of research is focused on the elucidation of the molecular mechanisms underlying cell death activation (apoptosis) by conventional therapies and novel targeted cancer agents in order to improve current cancer therapies and to develop new strategies. (prof. dr. G.J. Peters, dr. F.A.E. Kruyt) Division of Immunotherapy The division immunotherapy is an intensive collaboration between the Department of Medical Oncology, under the supervision of dr. A.J.M. van den Eertwegh and dr. T.D. de Gruijl and the Department of Pathology, under the supervision of Prof. dr. R.J. Scheper. Lines of research within the division of immunotherapy: • Tumor cell vaccination • Dendritic Cell based therapies • NKT cell based therapies Many different techniques are being used. The technology varies from cell culture (various tumor cells as monolayers, suspensions, spheroids, endothelial cells, various hemopoitic precursors, fibroblasts), molecular biological techniques (real-time PCR, sequencing, cloning, transfection, modification of adenovirus, siRNA, methylation), protein work (western blotting, enzyme assays, protein function, phosphorylation), many immunlogical techniques (characterization of subtypes, vaccination, FACS, interaction with other cells), immunohistochemistry, cell biology, etc. For more information visit the website: www.vu-medicaloncology.org/

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5.2.5 Department of Otolaryngology/ Head and Neck Surgery Coordinator: prof. dr. C.R. Leemans, dr. B.J. M. Braakhuis (students contact), phone: (020) 444 0905, email: bjm.braakhuis@vumc.nl, prof. dr. R.H. Brakenhoff, phone: (020) 444 0953, email: rh.brakenhoff@vumc.nl, prof. dr. G.A.M.S. van Dongen, phone: (020) 444 0953, email: gams.vandongen@vumc.nl, prof. dr. R. de Bree, email: r.bree@vumc.nl. Summary: The head and neck department consists of a clinical division and a research division (section Tumor Biology). In the latter division we study head and neck squamous cell carcinoma (HNSCC) aimed at improving the diagnostic and therapeutic possibilities. Unfortunately, 50% of HNSCC patients die of their carcinoma within 5 years. Poor survival is related to recurrent cancer 1) at the primary site, 2) in the regional lymph nodes, 3) at distant metastatic sites and to second primary cancer. Recurrent cancer can develop from occult tumor cells, that can not be detected with the now available standard techniques. Also, we have discovered that cancer can develop in large premalignant fields that remain unnoticed after surgery. Early stage disease is usually successfully managed with surgery or radiotherapy. Although nowadays advanced stage disease is treated with a combination of surgery, radiotherapy and/or chemotherapy, survival rates have only increased marginally. The research of the department is focusing on molecular and genetic methods to improve the prognosis of patients. Projects: Development of novel antibody-based diagnostics and therapies for the treatment of head and neck squamous cell carinoma. Labeling of specific monoclonal antibodies with various (radioactive) imaging or therapeutic agents for selective tumor-targeting. Genetic analysis of the multi-step process of head and neck carcinogenesis. (Braakhuis et al, Cancer Res 63, 1727, 2003 and Semin Cancer Biol, 15, 113, 2005).Various methods are used to characterize tissues with an increasing level of progression. Sensitive detection of residual cancer cells with molecular markers (DNA/RNA) in patient material to improve staging and early diagnosis. Viral therapy of fields with preneoplastic cells. Adenoviral constructs are generated to specifically target preneoplastic cells. Generation of an in vitro progression model for head and neck cancer. Normal cells are genetically manipulated by ectopic expression and RNAi mediated inhibition of expression in order to mimic in vivo carcinogenesis. Methods & Techniques: 3D-cell culture; apoptosis; cell culture attached cells; cell culture floating cells; comparative genomic hybridisation (array); DNA index measurements; expression arrays; flow-cytometry; immune histochemistry; immune precipitation; in vitro carcinogenesis models; loss of heterozygosity analysis; mutation detection; PCR methods; proliferation assays; protein conjugation; RNAi screens; sequencing For more information visit the website: www.vumc.nl/kno/onderzoek/index.html

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5.2.6 Department of Opthalmology Coordinator: prof. dr. P.J. Ringens, phone: (020) 444 4795, email: oogheelk@vumc.nl Summary: Relevant oncological research is focused on children’s eye surgery and eye tumours during childhood and on diagnostics, treatment and epidemiology mainly concerning retinoblastoma. Descriptions of projects are available through the secretary of the department (mrs. N. van der Geugten, room 4A84). For more information visit the website: www.vumc.nl/oogheelkunde/onderzoek/index.html

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5.2.7 Department of Clinical Genetics Coordinator: mw. prof. dr. M.C. Cornel, phone: (020) 444 8910, email: mc.cornel@vumc.nl. Researchers involved: mw. prof. dr. H. Meijers-Heijboer, phone: (020) 444 0786, email: h.meijers@vumc.nl; prof. dr. H. Joenje, phone: (020) 444 8273, email: h.joenje@vumc.nl; dr. J.P. de Winter, phone: (020) 444 8423, email: j.dewinter@vumc.nl; mw. dr. J.C. Dorsman, phone: (020) 444 8424, email: jc.dorsman@vumc.nl; dr. Q. Waisfisz, phone: (020) 444 9986, email: q.waisfisz@vumc.nl. Summary: The department of Clinical Genetics is divided in seven sections: • Outpatients’ clinic on Clinical Genetics • Laboratory for Chromosome diagnostics • Laboratory for DNA and protein diagnostics • Section Community Genetics • Section Functional Genome Analysis • Section Medical Genome Analysis • Section Oncogenetics Information about the research performed in these sections can be found on the departments website. Especially the research of the section Oncogenetics is relevant for students of the Master's Programme in Oncology. Research of this section is focussed on genetic instability and cancer and embedded in the V-ICI research program Oncogenesis. Projects: The section Oncogenetics plays a leading role in the identification of gene defects leading to the genetic instability syndrome Fanconi anemia (FA). Patients suffering from this disease are characterized by chromosomal instability (chromatid breaks), especially seen upon treatment with DNA crosslinking agents (e.g. mitomycin C and cisplatin), to which FA cells are extremely sensitive. In addition, these patients are prone to develop cancer, in particular acute myeloid leukaemia (AML) and squamous cell carcinomas of the head and neck region. The FA genes encode proteins that function in a DNA damage response network, which is probably involved in stabilizing the replication fork after replication has been stalled by roadblocks in the DNA. The breast cancer predisposition genes BRCA1 and BRCA2 are part of this network and defects in BRCA2 and its associated protein PALB2 lead to an extremely severe form of FA, with AML, medulloblastomas and Wilms tumours developing during childhood. The research of the section Oncogenetics is focussed on the unravelling of the role of the FA/BRCA network in replication coupled DNA maintenance. To this aim we try to identify novel FA genes and breast cancer susceptibility genes and investigate their interrelationship. We also study the role of the FA/BRCA network in sporadic tumours and aim to explore the FA/BRCA pathway in cancer therapy. Another genetic instability syndrome that we are focussing on is Roberts syndrome. In this disease the cohesion between the daughter strands generated after DNA replication is disturbed due to a mutation in the putative acetyltransferase ESCO2. This leads to crosslinker sensitivity and may result in aneuploidy. We are

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investigating the role of ESCO2 in chromatid cohesion and try to relate this function to aneuploidy and cancer. Methods & Techniques: In the various projects many different techniques are being used. The technology varies from cell culture (lymphoblasts, fibroblasts and tumour cells), molecular biological techniques (generation of fusion proteins, transfection, siRNA, MLPA, real-time PCR, sequencing, genetic linkage analysis), protein work (western blotting, immunoprecipiations, immunofluorescence), flow cytometry, chromosomal breakage assays. For more information visit the website: http://www.vumc.nl/klgen/professionals/org_functgen.html http://prod-internet-staging.vumc.nl/afdelingen/klinischegenetica

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5.2.8 Department of Nuclear Medicine & PET Research Coordinators: Prof. dr. O.S. Hoekstra, head of department, Phone (020) 444 4214, email: OS.Hoekstra@VUmc.nl; Prof. dr. A.A. Lammertsma, head of department, Phone (020) 444 4214, email : AA.Lammertsma@VUmc.nl The Department of Nuclear Medicine & PET Research is a multi-disciplinary department in which nuclear medicine physicians, biologists, pharmacologists, pharmacists, computer scientists, physicists and chemists work together. Research of the department is focused on both development and application of molecular imaging procedures with an emphasis on PET, as is highlighted by the name of the department. As such, the activities of the department cover the entire process from biological hypotheses to implementation of technologies into clinical practice. Nearly all research of the Department of Nuclear Medicine & PET Research is embedded within four VUmc based research institutes (V-ICI, ICEN, IcaR-VU, MOVE) and one VU/UL (University of Leiden) research institute (LACDR), the latter primarily covering radiochemistry research. Most scientific research is carried out in collaboration with other groups, both from within and outside VUmc. Research themes of the department are • Chemical development of new PET radiotracers • Development of new quantitative tracer kinetic PET procedures • Use of PET in drug development and evaluation • Use of PET for preclinical and clinical pathophysiological studies • Use of PET tracers for both diagnosis and monitoring response to treatment • Medical technology assessment of PET procedures. There is ample scope for student projects. Interested students should contact one of the coordinators. In a personal interview various potential projects will be discussed and, wherever possible, actual projects will be tailored to the interest of each student individually.

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5.2.9 Department of Heamatology Coordinator: dr. J.W. van Oostveen, phone: (020) 4447409 / 42604, email: HansJW.vanOostveen@vumc.nl Research in the department of Haematology is aimed firstly at the identification and detection of malignant cells in the context of minimal residual disease (MRD). As a consequence stem cell research is a main effort of research and concerns both normal and malignant cells and their interaction with the stromal matrix. Malignant stem cell research is focussing on CML and AML. To improve common cancer therapies leukemiavaccins are developed for myeloid malignancies. Related to the clinic, investigations in the fields of supportive care, anticancertherapies and nuclear detection techniques are developed and improved. For more information visit the website: www.vumc.nl/hema/

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5.2.10 Department Obstetrics and Gynaecology Coordinator: prof. dr. R.H.M. Verheijen, phone: (020) 4444813, email: r.verheijen@vumc.nl Oncological research themes of the department of Obstetrics and Gynecology are • Genetics and cancer • Monoclonal antibodies and vaccination • Sentinel node • HPV and cervixcarcinoma For more information visit the website: www.vumc.nl/veng/index.html

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5.2.11 Department of Pathology Coordinator: prof. dr. R.J. Scheper tel: (020) 444 4031, email: rj.scheper@vumc.nl Web page: http://www.vumc.nl/pathologie/onderzoek/index.html Research themes: The research lines within the Department of Pathology of the VU Medical Center are focused on the theme "Morphological, functional and molecular biological aspects of cells in tumors". Using the knowledge obtained and techniques developed the ultimate goal is in daily practice: to improve the early diagnosis of cancer, to develop new prognostic markers useful for the clinical management of patients, to develop new screening strategies for the early detection of cancer, and to develop new immunotherapeutic strategies. The Department of Pathology is currently introducing molecular techniques into clinical medicine and the expectation is that the introduction of these techniques in the detection, prognostication and measurement of therapy sensitivity of tumors will not only revolutionize the early detection and prognostication of tumors but also greatly influence and individualize the clinical management of patients. Research lines focus on genomics and viral factors in the development of cancer, chromosomal instability, immune regulation in cancer and autoimmunity, and novel tumor vaccination approaches. The VUmc microarray facility is embedded within the Department of Pathology. All oncological and immunological research is carried out within the framework of the VUmc Research Institute V-ICI. Other research lines within the Department of Pathology on neurological and vascular diseases are carried out in conjunction with the respective Institutes ICEN (Neurosciences) and IcarVU (Cardio-vascular research). Many research groups within the Department of Pathology act in close collaboration with clinical disciplines within VUmc like the departments of Medical Oncology, Gastroenterology, Gynecology, Surgery, etc. Numerous collaborations exist with national and internationally renowned groups, in both European and transatlantic networks. Researchers frequently exchange between these groups, boosting the quality and international competitiveness of the research. Qualified students frequently benefit from this network for arranging internships in excellent international research institutes abroad. Leading scientists of the Department of Pathology successfully compete in fundraising from University, governmental (NWO), charity (KWF etc) and industrial sources, and are amongst the most productive (PubMed publications, scientation scores etc) within the field. In brief, major research topics are: Oncogenesis, with one of the focuses on malignancies caused by viruses such as human papillomavirus- (HPV-) induced cervical cancer (see for example www.zelftest.nl; www.humavac.nl) and Epstein-Barr virus- (EBV-) induced lymphomas and nasopharyngeal carcinomas. Hereto, virus-induced oncogenic progression is investigated using both in vitro models and clinically well-defined patient material, and the genes involved in this process are being identified and characterized at the functional level. Some viral and host markers are currently being tested in screening and clinical trials for their capability to assess risk of malignant

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disease and high-grade precursor stages with an increased sensitivity and specificity compared to currently existing methods, and newly identified markers will be investigated likewise. Special attention is also given to molecular events that lead to colorectal and lung cancer, and current research in these areas focuses on translating the results of this genomic research into molecular early diagnosis of colorectal and lung cancer, e.g. by stool and sputum based DNA tests, respectively. The above mentioned research lines studies make use of the most state-of-the art technology available today, such as RNAi technology, microarray expression and arrayCGH analysis, proteomics approaches, and methylation and miRNA assays. Closely related research in the area of Tumor Profiling focuses on gene expression and DNA copy number (i.e. high resolution chromosomal) profiles, as revealed by microarray analyses, in relation to clinical behaviour (e.g. prognosis or response to therapy) of tumors of the stomach, colon, lungs, head and neck region, as well as neurological tumors. (see: www.tumorprofiling.org ; www.gameijer.nl; www.darmkankerpreventie.nl). In the field of Tumorimmunology, preclinical and clinical tumor vaccination studies focus on DC (dendritic cell)-targeting approaches, immuno-gene therapies, adoptive transfers of (immortalized) NKT and tumor-specific T cells, and immunological monitoring of effector functions. The translational, therapy-directed research within the Dept of Pathology is carried out in close collaboration with clinical departments, notably the Dept of Medical Oncology (for further details see also www.vu-medicaloncology.org/ under Research, Immunotherapy).

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6 List of addresses and telephone numbers

Student Administration Instituut of Medical Education B. Oulad Youssef Secretariaat, Kamer A-114 PO Box 7057 1007 MB Amsterdam The Netherlands Phone: + 31-20-4448013 Fax: +31-20-4448427 E-mail: b.ouladyoussef@vumc.nl office hours 9.00-17.00 monday till friday Programme Coordinator dr. R.A. Puras PO Box 7057 1007 MB Amsterdam The Netherlands Phone: + 31-20-4446345 Fax: +31-20-4448427 E-mail: masteroncology@vumc.nl Visiting address: Van der Boechorststraat 7 Room: MF/D-227 Name Beelen Beliën Boven Braakhuis Brakenhoff Cloos Cornel Die, van Fijneman Hoekstra Hooijberg Kaspers Keblusek Kooter Lafleur Lammertsma Lankelma Leemans Meijer Middeldorp Oderwald Oostveen, van Oudejans Oulad Youssef Peters Puras Ringens Scheper Slotman Sminia Snijders Verheijen Visser Winter, de

Title prof.dr. dr. dr. dr. prof.dr. dr. prof.dr. dr. dr. prof.dr. dr dr. dr. dr. dr. prof.dr. prof.dr. prof.dr. prof.dr. prof.dr. dr. dr. dr. prof.dr. dr. prof.dr. prof.dr. prof.dr. dr. prof.dr. prof.dr. dr. dr.

Initials R.H.J. J.A.M. E. B.J.M. R.H.A. J. M.C. I.M. R.J.A. O.S. E. G.J.L. P. J. M.V.M. A.A. J. C.R. G.A. J.J.M. A.K. J.W. J.J. B. G.J. R.A. P.J. R.J. B.J. P. P.J.F. R.H.M. G.W.M. J.

Department mol.cell. biol. pathology med.oncology otolaryngology otolaryngology paediatrics clin/antrop.gen. mol.cell.biol. pathology nuclear med. Pathology paediatrics V-ICI/OOA develop.gen. radiotherapy nuclear med. med.oncology otolaryngology pathology pathology metamedica haematology pathology onderwijsinstituut med.oncology onderwijsinstituut obstr./gyneac. pathology radiotherapy radiotherapy pathology obstr./gyneac. nucl-pet clin/antrop.gen.

Telephone 4448055 4444025 4444336 4440905 4440953 4442645 4448910 4448157 4442405 4444442 4444041 4442420 4444054 4444360 4448349 4444214 4442603 4443690 4444772 4444052 4448215 4447409 4444771 4448013 4442633 4446345 4444741 4444031 4440415 4448355 4443852 4444591 4449710 4448423

Email rhj.beelen@vumc.nl jam.belien@vumc.nl e.boven@vumc.nl bjm.braakhuis@vumc.nl rh.brakenhoff@vumc.nl j.cloos@vumc.nl mc.cornel@vumc.nl im.vandie@vumc.nl rja.fijneman@vumc.nl os.hoekstra@vumc.nl Erik.hooijberg@vumc.nl gjl.kaspers@vumc.nl p.keblusek@vumc.nl kooter@bio.vu.nl mvm.lafleur@vumc.nl aa.lammertsma@vumc.nl j.lankelma@vumc.nl chr.leemans@vumc.nl ga.meijer@vumc.nl j.middeldorp@vumc.nl ak.oderwald@vumc.nl hansjw.vanoostveen@vumc.nl jj.oudejans@vumc.nl b.ouladyoussef@vumc.nl gj.peters@vumc.nl ra.puras@vumc.nl oogheelk@vumc.nl rj.scheper@vumc.nl bj.slotman@vumc.nl p.sminia@vumc.nl pjf.snijders@vumc.nl r.verheijen@vumc.nl gwm.visser@vumc.nl j.dewinter@vumc.nl

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Examination board (status April 2007): prof. dr. G.J. Peters, chairman prof. dr. R.H.J. Beelen, vice chairman prof.dr. R.J. Scheper, secretary dr. R.A. Puras, official secretary Programme committee (status April 2007): prof. dr. G.A. Meijer, chairman prof. dr. P.J.F. Snijders, vice chairman Z. Euler, student J. van Meerloo, student L. Fitoury, student T. de Gunst, student prof. dr. J. Lankelma, advisor dr. R.A. Puras, official secretary

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Appendices

Appendix 1 Important websites Blackboard site "Communication site Master Oncology" Information for current students; course information, course documents, forms, announcements, placements, scholarships, career opportunities…etc www.bb.vu.nl TISVU Credit registration system www.tisvu.vu.nl Master’s Programme in Oncology General information for prospective students www.masteroncology.nl VU www.vu.nl Information for current students (international students: www.vuamsterdam.com) VUmc www.vumc.nl Cancer Center Amsterdam www.cancercenteramsterdam.nl VUmc Research Institute for Immunology and Cancer Research (V-ICI) Announcements for lectures and www.v-ici.org

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Appendix 2 Programme & Procedures; Master Courses

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Appendix 3 Programme & Procedures; Research Training (Placement)

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Appendix 4 Programme & Procedures; Study of Literature

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Form 1

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Form 2

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Form 3

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Form 4

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Form 5

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Form 6

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Form 7

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Form 8

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Form 9

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Index subject Animal experimentation (Proefdierkunde voor onderzoekers), 33 Bioinformatic Data Analysis and Tools, 37 Biological fluorescence, 40 Caput Epigenetics, 39 Clinical Oncology, 28 DNA Protein Structure-Function Analysis and Prediction, 35 Genome Analysis, 36 Genomics, 38 Glycoimmunology, 30 In the footsteps of Antoni van Leeuwenhoek, 32 Macroscopic, microscopic & pathological anatomy of the mouse, 28 Mastercourse Immunity, 23 Mastercourse Innovative Tumortherapies, 24 Mastercourse Oncogenesis, 21 Mastercourse Tumor Biology and Clinical Behaviour, 22 Philosophy of Systems Biology and its Relation to Society, 39 Radiation Oncology, 28 Radiation Protection Course, level 5B, 29 Scientific Writing in English, 25 Sequence Analysis, 34 Systems Biology of Cancer, 34 The Symbolic and Cultural Meanings of Cancer, 32 Viral Oncogenesis, 31 Wetenschapsjournalistiek (science journalism), 41

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