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  • Sample & Assay Technologies

    Your Best Data: Teaming QIAGEN Chemistry & Bioinformatics to Drive

    Samples to Insight

    Aysel Heckel Director Clinical Solutions Sales

    Dr. Anne Arens

    Field Application Scientist

    Course on Variant Detection and Interpretation in a Diagnostic Context

    RS Erasmus MC Course 2014

  • Sample & Assay Technologies Sample to Insight

    SSample Prep

    Assay Data

    Sequence- Level

    Statistics

    Biology of Interest (Genes, Variants,

    etc)

    Comparative Statistical Analysis

    Biological Interpretation

    Upstream Analysis “primary”

    Streamline Integration and Workflow Embedding

    “secondary” “tertiary”

    Better Results With Any Platform

    Erasmus MC Course 2014

  • Sample & Assay Technologies Universal NGS workflow: from sample to insight

    Overcome NGS challenges

    Sample Isolation

    Targeted Enrichment

    Library Construction

    NGS Run

    Data Analysis

    Interpretation

    Sample Insight

    Library QC

    Sample QC

    Variant Confirmation

    Turnaround time, and limited

    amounts of DNA

    Library yield Platform specific

    Amplification and

    Sequencing

    Data

    processing & Variant calling

    Isolation of high- quality DNA

    samples

    Quantifying amplifiable (not

    bulk) amounts of DNA

    Clinical & Biological

    interpretation of data

    RS Erasmus MC Course 2014

  • Sample & Assay Technologies Universal NGS workflow: from sample to insight

    Integrated solutions to address NGS challenges

    Sample Isolation

    Targeted Enrichment

    Library Construction

    NGS Run

    Data Analysis

    Interpretation

    Sample Insight

    Library QC

    Sample QC

    Variant Confirmation

    GeneRead DNAseq Targeted Panels V2

    GeneRead DNAseq PCR Kit V2

    GeneRead DNA Library Core & Amp Kits

    GeneRead Adapter 12-plex GeneRead Size selection Kit GeneRead DNASeq Library Quant Array

    Platform specific Amplification and Sequencing

    CLC Cancer Research Workbench

    GeneRead DNAseq V2 Data analysis

    GeneRead DNA FFPE kit

    GeneRead DNA QuantiMIZE kit

    Ingenuity Variant

    Analysis

      Ingenuity Clinical

    Decision Support

    RS Erasmus MC Course 2014

  • Sample & Assay Technologies GeneRead DNA FFPE Kit

      The use of DNA isolated from FFPE tissues remains challenging

      Low DNA quality   Presence of base damage leading to artifactual single nucleotide

    changes –  >50% of artifacts are C>T changes resulting from deamination

      Increase false positive rate

      GeneRead DNA FFPE Kit

      Enzymatically remove artifacts during DNA isolation step and provide more confidence in SNP calling

      Automate on QIAcube

    5

    Targeted high throughput sequencing in clinical cancer Settings: formaldehyde fixed- paraffin embedded (FFPE) tumor tissue, input amount and tumor heterogeneity

    See also: Williams et al., 1999. A high frequency of sequence alterations is due to formalin fixation of archival specimens. Am J Pathol 155(5): 1467-1571 Yost et al., 2012. Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. NAR 40(14): e108

  • Sample & Assay Technologies GeneRead DNA QuantiMIZE kits

    Overcome the challenges of DNA quantification & qualification

    Control and sample gDNA

    Multi-copy qPCR assays +

    Master Mix

    Amount of input DNA and number of targeted

    enrichment cycles

      Uses Innovative multi-copy qPCR assays to increase accuracy

      Two qPCR assays to query 40 genomic loci that are randomly distributed in the genome

      Quantifies only PCR-amplifiable DNA

      Provides guidance to rescue low-quality DNA samples

      Appropriate amount of input DNA

      Number of targeted enrichment cycles

      Generates libraries from low-quality FFPE samples

    Need to quantify amplifiable “functional”, not bulk, DNA….. Why?

    RS Erasmus MC Course 2014

  • Sample & Assay Technologies Universal NGS workflow: from sample to insight

    Overcoming the challenges of targeted enrichment prior to NGS

    Sample Isolation

    Targeted Enrichment

    Library Construction

    NGS Run

    Data Analysis

    Interpretation

    Sample Insight

    Library QC

    Sample QC

    Variant Confirmation

    GeneRead DNAseq Panel V2

    GeneRead DNAseq PCR Kit V2

    Gene 1 Gene 2 Multiplex PCR-based approach that enriches genes of interest to enable targeted DNA sequencing

    RS Erasmus MC Course 2014

  • Sample & Assay Technologies GeneRead DNAseq Targeted Panels V2

    Minimal DNA input; Wet-bench validated panels

    Actionable Mutations

    Clinically- relevant

    Tissue-specific

    Comprehensive

    Breast Cancer

    Colorectal Cancer

    Myeloid Neoplasms

    Liver Cancer

    Lung Cancer

    Ovarian Cancer

    Prostate Cancer

    Gastric Cancer

    Cardiomyopathy

    Cancer

    Carrier Testing

    Cancer Predisposition

    Only 40 ng DNA needed per panel (except Actionable Mutations panel which needs a total of 20 ng)

    Largest collection of pre-designed panels suitable for a wide range of needs

    RS

    Mix-n-Match &

    Custom

    Erasmus MC Course 2014

  • Sample & Assay Technologies Compatibility with major sequencing platforms

    Same panel for different platforms

    GeneRead® DNAseq Panels V2

    HiSeq 2500 MiSeq

    NextSeq

    PGM Proton

    RS

      Outstanding experimental performance   150 bp amplicons; FFPE-compatible   Enrichment in 3 hours   One library per sample   Customization tools to fit unique customer requirements

    Booth

    Erasmus MC Course 2014

  • Sample & Assay Technologies GeneRead DNAseq Targeted Panels V2

    Applications

    Bone marrow samples

    Single cells & circulating tumor cells

    Biopsies & FFPE samples

    Cell-free DNA

    Liquid Biopsies

    Abstract (Mon; 3384M): Single cell mutation detection with multiplex PCR-based targeted enrichment sequencing (Copies in back)

    Presentation & Abstract (Sunday; 3353S) Evaluation of a multiplex PCR targeted enrichment approach for the detection of actionable mutations in FFPE samples via Next-Generation Sequencing Dr. Francine de Abreu Dartmouth-Hitchcock Medical Center (Copies in back)

    RS Erasmus MC Course 2014

  • Sample & Assay Technologies Universal NGS workflow: from sample to insight

    To overcome NGS challenges

    Sample Isolation

    Targeted Enrichment

    Library Construction

    NGS Run

    Data Analysis

    Interpretation

    Sample Insight

    Library QC

    Sample QC

    Variant Confirmation

    Turnaround time, and limited

    amounts of DNA

    Library yield Platform specific

    Amplification and

    Sequencing

    Data

    processing & Variant calling

    Isolation of high- quality DNA

    samples

    Quantifying amplifiable (not

    total) amounts of DNA

    Clinical & Biological

    interpretation of data

    RS Erasmus MC Course 2014

  • Sample & Assay Technologies

    Workflow

    Sample & Assay Technologies

    Interpretation Annotation Variant calling Assembly

    Raw DNA sequence data

    Sequencing

    Report with valuable insights

    Offering bioinformatics gold standards

    QIAGEN has strong solutions for all worksteps

    Strengthening leadership in offering universal bioinformatics solutions

    Alignment to reference genome

    Variant database & mutation content

    Curated knowledge databases

    Disease/Biological models

    Reporting

    CLC bio Ingenuity

    Analysis & visualization

    Erasmus MC Course 2014

  • Sample & Assay Technologies

    QIAGEN Bioinformatics Products for data analysis and interpretation of cancer and other human diseases

    Erasmus MC Course 2014

  • Sample & Assay Technologies Sample to Insight

    Streamline Integration and Workflow Embedding

    QIAGEN NGS solutions

    Sample preparation

    Data analysis Library construction Target

    enrichment Sample

    technologies Sequencing

    •  CLC Cancer Research Workbench

    •  Ingenuity Variant Analysis •  Ingenuity Clinical •  HGMD, PGMD, GenomeTrax •  Ingenuity Pathway Analysis

    Erasmus MC Course 2014

  • Sample & Assay Technologies CLC Cancer Research Workbench

      Easy to use   Human- and cancer-specific da