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Whole Genome Analysis

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Presentation about whole genome analysis.

Presentation about whole genome analysis.

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  • 1. Whole Genome AnalysisBone-Net Workshop - 21 January 2012 Ir Stéphane Wenric – s.wenric@dnavision.be
  • 2. Whole Genome Analysis Whole genome analysis: why is it such a hot topic today?
  • 3. Whole Genome Analysis
  • 4. Whole Genome Analysis human whole genome sequencing Price Time
  • 5. Whole Genome Analysis Microarray Exome Whole Genome Only known SNPs Only the coding regions The complete DNA (~ 900 000) of the genome sequencesUp to 0.0003 % of the ~ 1 % of the human ~ 80 % of the human human genome genome genome
  • 6. Whole Genome Analysis What are the technologies involved ? • Illumina (Solexa) • ABI SOLiD • Ion Proton (2013)
  • 7. Whole Genome Analysis Illumina (Solexa) : • cluster generation by bridge amplification • sequencing by synthesis
  • 8. Whole Genome Analysis
  • 9. Whole Genome Analysis ABI SOLiD : • amplification on magnetic beads • ligation + fluorescence detection • 2-base color encoding
  • 10. Whole Genome Analysis
  • 11. Whole Genome Analysis Ion semiconductor sequencing : • PCR amplification • dNTP incorporation w/ H+ release
  • 12. Whole Genome Analysiswhole genome analysis = whole genome sequencing + bioinformatics
  • 13. Whole Genome Analysis What kind of bioinformatics analyses are best suited for whole genome data? • SNP • Indels • CNV • SV
  • 14. Whole Genome AnalysisSingle Nucleotide Polymorphisms • What? • How? • Impact?
  • 15. Whole Genome Analysis
  • 16. Whole Genome AnalysisSNPs : easy to detect 1. Map sequenced reads to reference sequence 2. See how the consensus sequence differs from the reference 3. 1-base difference between consensus sequence and reference = SNP
  • 17. Whole Genome Analysis SNPs: impact? • Public databases: • DbSNP (ncbi) • OMIM (Johns Hopkins University School of Medicine) • SIFT (Craig Venter Institute) • … • Manual annotation
  • 18. Whole Genome AnalysisInsertions and Deletions • What? • How? • Impact?
  • 19. Whole Genome Analysis Insertion or deletion of a sequence of DNA of arbitrary length
  • 20. Whole Genome Analysis Indels detection Small Indels : • Detection of small gaps in the alignment • Combination of the gapped alignments based on proximity • Filtering (read pos., coverage, quality) Large Indels : • Use of the reads pairing info (Illumina and SOLiD only)
  • 21. Whole Genome Analysis Indels: impact? • Public databases: • dbSNP for small indels (ncbi) • dbVar for large indels (ncbi) • Manual annotation
  • 22. Whole Genome AnalysisCopy Number Variations • What? • How? • Impact?
  • 23. Whole Genome AnalysisCNV:• variation in terms of copy number of a sequence• >= 1 kb• up to n Mb
  • 24. Whole Genome Analysis CNV detection methods • Statistical models: • Depth-of-reads/coverage • Pairing information
  • 25. Whole Genome Analysis CNVs: impact? • Public databases: • Database of Genomic Variants (Center for Applied genomics, Canada) • CNV Project (Sanger) • ... • Manual annotation
  • 26. Whole Genome AnalysisStructural Variations • What? • How? • Impact?
  • 27. Whole Genome AnalysisStructural Variations • >= 1 kb • Inversions • Translocations • (Large indels) • (CNVs)
  • 28. Whole Genome AnalysisInversions
  • 29. Whole Genome AnalysisTranslocations
  • 30. Whole Genome Analysis SVs: detection methods • Geometric approach (GASV) • Takes pairing info into account • Compares potential variants to geometric models
  • 31. Whole Genome Analysis SVs: impact? • Public databases: • Database of Genomic Variants (Center for Applied genomics, Canada) • dbVar (ncbi) • ... • Manual annotation
  • 32. Whole Genome Analysis Questions?