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Next Generation Sequencing and Human Genome Databases

Next Generation Sequencing and Human Genome Databases. Genomics, Bioinformatics & Medicine http://biochem158.stanford.edu/. Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine. Illumina Solexa Sequencing Technology.

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Next Generation Sequencing and Human Genome Databases

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  1. Next Generation Sequencing andHuman Genome Databases Genomics, Bioinformatics & Medicine http://biochem158.stanford.edu/ Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine

  2. Illumina Solexa Sequencing Technology

  3. Emulsion Based Clonal Amplification Single test tube generation of millions of clonally amplified sequencing templates No cloning and colony picking A + PCR Reagents + Emulsion Oil B Anneal DNA template to capture beads Micro-reactors “Water-in-oil” emulsion Adapter carrying library DNA Break micro-reactors Isolate DNA containing beads Perform emulsion PCR

  4. Pacific Biosciences SMRT Sequencing

  5. Pacific Biosciences Sequencing

  6. Phospholinked Fluorophores

  7. Processive Synthesis

  8. Synthesis of Long Duplex DNA

  9. Circular Templates Gives Redundant Sequencing and Accuracy

  10. Circular Templates Gives RedundantSequencing and Accuracy

  11. Ion Torrent Sequencing

  12. Ion Torrent Sequencing

  13. Ion Torrent Sequencing

  14. The Human GenomeHow fast is the cost going down? • 2006: $ 50 million • 2008: $500,000 • 2009: $50,000 • 2010: $20,000 • 2011: $5,000 • 2012:??? $1,000 Thanks to Serafim Batzoglou

  15. Archon Genomics X-Prize

  16. Archon Genomics X-Prize

  17. TFBS Promoter Exon Intron Exon Intron Exon Terminator Gene Components of a Typical Human Gene

  18. Promoter Exon Terminator Exon Intron Intron Exon Gene Primary Transcript Active Genes are Transcribed into RNA

  19. Promoter Exon Terminator Exon Intron Intron Exon Gene Transcript Splicing mRNA 3’ 5’ Splicing Transcript Yields Mature mRNA

  20. Promoter Exon Terminator Exon Intron Intron Exon Gene 5’UTR 3’UTR Transcript Splicing mRNA 5’ 3’ Coding Region 5’UTR 3’UTR Mature mRNA contains Coding Region and 5’ and 3’ Untranslated Regions

  21. Promoter Exon Terminator Exon Intron Intron Exon Gene 5’UTR 3’UTR Transcript Splicing mRNA Coding Region 5’UTR 3’UTR 7-Me-G-Cap 3’ Poly A Tail Mature mRNA contains7-Methyl-Guanosine 5’ Cap and 3’ Poly A Tail

  22. Promoter Exon Terminator Exon Intron Intron Exon Gene Transcript Splicing mRNA 3’ 5’ 3’ ESTs 5’ ESTs Full Length cDNA ESTs, Full Length cDNAUniGene & RefSeq Databases

  23. Promoter Exon Terminator Exon Intron Intron Exon Gene Transcript Splicing mRNA 3’ 5’ 3’ ESTs 5’ ESTs Full Length cDNA Proteins ESTs, Full Length cDNAUniGene & RefSeq Databases 5’ UTR 3’ UTR 5’ UTR 3’ UTR Protein

  24. GENSCAN Gene Modelhttp://genes.mit.edu/GENSCAN.html Hidden Markov models of gene structure

  25. Genomic DNA Assembled contigs uniSTS dbSNP A Mapping GrailEXP GenScan FGENESH FGENESH+ GeneMark BGene Prediction Human ESTs UniGene Human RefSeq Human Ensembl cDNA C Expression Data Mouse ESTs Entrez Gene Mouse RefSeq Mouse pFAM Motifs nrPRO DProtein Similarity Promoters E Additional Data Genome Databases Entrez Gene UCSC Browser Ensembl F Summary

  26. Inclusive Exon Prediction NR-Pro UniGene ESTs GrailEXP FGENESH Genscan Entrez Gene Loci http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene Entrez Gene

  27. Alternative Splicing GeneratesDistinct Proteins in Different Tissues Promoter Exon Terminator Exon Intron Intron Exon Gene Transcript Splicing mRNA-1 3’ 5’ Alternate Splicing Transcript mRNA-2 5’ 3’

  28. NCBI Genomeshttp://www.ncbi.nlm.nih.gov/sites/entrez?db=genome

  29. Eukaryote Genome Projectshttp://www.ncbi.nlm.nih.gov/genomes/leuks.cgi

  30. Canis lupus familiaris Genomehttp://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=Retrieve&dopt=Overview&list_uids=10726

  31. NCBI Entrez Genehttp://www.ncbi.nlm.nih.gov/sites/entrez?db=gene

  32. NCBI Entrez Gene: Human Opsinhttp://www.ncbi.nlm.nih.gov/gene?term=human%20opsin

  33. Entrez Gene: Human Opsin OPN1MWhttp://www.ncbi.nlm.nih.gov/gene/2652

  34. Entrez Gene: Human Opsin OPN1MWhttp://www.ncbi.nlm.nih.gov/gene/2652

  35. MapViewer: Human Opsin OPN1MWhttp://www.ncbi.nlm.nih.gov/gene/2652

  36. Evidence Viewer for OPN1MWhttp://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&contig=NT_167198.1&gene=OPN1MW&lid=2652&from=4366022&to=4380289

  37. OMIM Home Pagehttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

  38. Colorblindness in OMIM

  39. Colorblindness in OMIMhttp://omim.org/entry/303800

  40. Human Genome Resourceshttp://www.ncbi.nlm.nih.gov/genome/guide/human/

  41. RefSeqhttp://www.ncbi.nlm.nih.gov/RefSeq/

  42. RefSeq Genehttp://www.ncbi.nlm.nih.gov/refseq/rsg/

  43. NCBI UniGenehttp://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene

  44. NCBI Homologene Databasehttp://www.ncbi.nlm.nih.gov/homologene

  45. Comparative Genomics

  46. Ensembl Home Pagehttp://www.ensembl.org/

  47. EBI Genomes Home Pagehttp://www.ensembl.org/

  48. Ensembl Human Genomehttp://www.ensembl.org/Homo_sapiens/

  49. Ensembl Human Opsin Searchhttp://uswest.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;idx=;q=opsin

  50. Ensembl Human Opsin Geneshttp://uswest.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;idx=;q=opsin

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