Genomics and Personalized Care

Genomics and Personalized CareLeming Zhou, PhDAssistant ProfessorDepartment of Health Information Management School of Health and Rehabilitation SciencesUniversity of PittsburghHuman Genome Project1990 2003Goals:identify all the approximately 20,000-25,000 genes in human DNA determine the sequences of the 3 billion chemical base pairs that make up human DNA store this information in databases improve tools for data analysistransfer related technologies to the private sector address the ethical, legal, and social issues (ELSI) that may arise from the project http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

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Eukaryotic Gene OrganizationGene: A stretch of DNA containing the information necessary for coding a protein / polypeptide / RNAtranscription factor binding sitesPromoter regionSp1C/EBPOct1TATA boxInitiatorGeneDNA coding strandTranslation startSplicingmRNA5 UTR3 UTRATGTGAExon 1Intronprimary transcript5 UTR3 UTRAAUAAATranscription(A)ncapGTAGExon 2protein(peptide)Translation

ProteinA molecule comprising a long chain of amino acids connected by peptide bondsThere are 20 standard amino acids encoded by the universal genetic code

Protein 3D StructureProtein structure is closely related to its biological function/activityOne protein may have multiple domains (structural or functional blocks) which may have functional interactions with different molecules

Human P53 core domain, MMDB ID: 69151, PDB ID: 3D0ADNA VariationsDNA mutationsSynonymous mutations: mutations do not lead to protein modificationNon-synonymous mutationMutations lead to protein modification

9GenomicsGenomics is the study of the genomes of organisms.

Genomics involves large data sets (whole genome sequences) and high-throughput methods (DNA sequencing technologies)Genetics research focuses on one or a set of genesDNA Sequencing TechnologiesDNA sequencing: The process of determining the order of the nucleotide bases along a DNA strandTechnologies: Sanger method, 1977Used in Human Genome ProjectSlow, and expensive ($300m/genome)Whole Genome Shotgun sequencing (1990s)Break the genome into short pieces Sequence all the pieces in parallelPut all the pieces back together (sequence assembly)Faster and cheaper (~$10m/genome)Next generation sequencing technologies (2000s)Much faster speed & lower cost (