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Doug Brutlag 2011 Next Generation Sequencing and Human Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University.

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Presentation on theme: "Doug Brutlag 2011 Next Generation Sequencing and Human Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University."— Presentation transcript:

1 Doug Brutlag 2011 Next Generation Sequencing and Human Genome Databases Doug Brutlag Professor Emeritus of Biochemistry & Medicine Stanford University School of Medicine Genomics, Bioinformatics & Medicine http://biochem158.stanford.edu/

2 Doug Brutlag 2011 Illumina Solexa Sequencing Technology

3 Doug Brutlag 2011 Emulsion Based Clonal Amplification Micro-reactors Adapter carrying library DNA Anneal DNA template to capture beads Break micro-reactors Isolate DNA containing beads Single test tube generation of millions of clonally amplified sequencing templates No cloning and colony picking “Water-in-oil” emulsion + PCR Reagents + Emulsion Oil Perform emulsion PCR A B

4 Doug Brutlag 2011 Pacific Biosciences SMRT Sequencing

5 Doug Brutlag 2011 Pacific Biosciences Sequencing

6 Doug Brutlag 2011 Phospholinked Fluorophores

7 Doug Brutlag 2011 Processive Synthesis

8 Doug Brutlag 2011 Synthesis of Long Duplex DNA

9 Doug Brutlag 2011 Highly Parallel Optics System

10 Doug Brutlag 2011 Circular Templates Gives Redundant Sequencing and Accuracy

11 Doug Brutlag 2011 Circular Templates Gives Redundant Sequencing and Accuracy

12 Doug Brutlag 2011 Ion Torrent Sequencing

13 Doug Brutlag 2011 Ion Torrent Sequencing

14 Doug Brutlag 2011 Ion Torrent Sequencing

15 Doug Brutlag 2011 The Human Genome How 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

16 Doug Brutlag 2011 Archon Genomics X-Prize

17 Doug Brutlag 2011 Archon Genomics X-Prize

18 Doug Brutlag 2011 Components of a Typical Human GeneGene IntronIntronExonExonExonPromoterTerminator TFBS

19 Doug Brutlag 2011 Active Genes are Transcribed into RNA PrimaryTranscript Gene IntronIntronExon Exon Exon PromoterTerminator

20 Doug Brutlag 2011Transcript mRNA Gene IntronIntronExon Exon Exon PromoterTerminator 5’5’5’5’ 3’3’3’3’ Splicing Splicing Transcript Yields Mature mRNA

21 Doug Brutlag 2011 Mature mRNA contains Coding Region and 5’ and 3’ Untranslated Regions Transcript mRNA Gene IntronIntronExon Exon Exon PromoterTerminator 5’5’5’5’ 3’3’3’3’ Splicing Coding Region 5’UTR 3’UTR 5’UTR 3’UTR

22 Doug Brutlag 2011 Mature mRNA contains 7-Methyl-Guanosine 5’ Cap and 3’ Poly A Tail Transcript mRNA Gene IntronIntronExon Exon Exon PromoterTerminator Splicing Coding Region 5’UTR 3’UTR 5’UTR 3’UTR 7-Me-G-Cap 3’ Poly A Tail

23 Doug Brutlag 2011 ESTs, Full Length cDNA UniGene & RefSeq Databases UniGeneRefSeq Transcript mRNA Gene Intron Exon PromoterTerminator 5’5’ 3’3’ 3’ ESTs 5’ ESTs Full Length cDNA Splicing

24 Doug Brutlag 2011 ESTs, Full Length cDNA UniGene & RefSeq Databases UniGeneRefSeq Transcript mRNA Gene Intron Exon PromoterTerminator 5’5’ 3’3’ 3’ ESTs 5’ ESTs Full Length cDNA Splicing Proteins 5’ UTR 3’ UTR Protein

25 Doug Brutlag 2011 GENSCAN Gene Model http://genes.mit.edu/GENSCAN.html http://genes.mit.edu/GENSCAN.html Hidden Markov models of gene structure

26 Doug Brutlag 2011 Promoters E Additional Data Genomic DNA Assembled contigs A Mapping uniSTS dbSNP Mouse ESTs Human ESTs C Expression Data Entrez Gene Mouse RefSeq Mouse UniGene Human RefSeq Human Ensembl cDNA Genome Databases nrPRO D Protein Similarity pFAM Motifs GrailEXP B Gene Prediction GenScanFGENESH FGENESH+ GeneMark F Summary Entrez Gene UCSC Browser Ensembl

27 Doug Brutlag 2011Inclusive Exon Prediction Entrez Gene Loci http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene NR-Pro Genscan GrailEXP FGENESH Entrez Gene UniGene ESTs

28 Doug Brutlag 2011 Alternative Splicing Generates Distinct Proteins in Different Tissues Transcript mRNA-1 Gene Intron Exon PromoterTerminator 5’5’ 3’3’ Transcript mRNA-2 5’5’3’3’ Alternate Splicing Splicing

29 Doug Brutlag 2011 Alternative Splicing Detected in EST Libraries

30 Doug Brutlag 2011 NCBI Genomes http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome

31 Doug Brutlag 2011 Eukaryote Genome Projects http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi

32 Doug Brutlag 2011 Canis lupus familiaris Genome http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=Retrieve&dopt=Overv iew&list_uids=10726 http://www.ncbi.nlm.nih.gov/sites/entrez?db=bioproject&cmd=Retrieve&dopt=Overv iew&list_uids=10726

33 Doug Brutlag 2011 NCBI Entrez Gene http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene

34 Doug Brutlag 2011 NCBI Entrez Gene: Human Opsin http://www.ncbi.nlm.nih.gov/gene?term=human%20opsin http://www.ncbi.nlm.nih.gov/gene?term=human%20opsin

35 Doug Brutlag 2011 Entrez Gene: Human Opsin OPN1MW http://www.ncbi.nlm.nih.gov/gene/2652 http://www.ncbi.nlm.nih.gov/gene/2652

36 Doug Brutlag 2011 Entrez Gene: Human Opsin OPN1MW http://www.ncbi.nlm.nih.gov/gene/2652 http://www.ncbi.nlm.nih.gov/gene/2652

37 Doug Brutlag 2011 MapViewer: Human Opsin OPN1MW http://www.ncbi.nlm.nih.gov/gene/2652 http://www.ncbi.nlm.nih.gov/gene/2652

38 Doug Brutlag 2011 Evidence Viewer for OPN1MW http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&contig=NT_167198.1&gene=OPN1MW& lid=2652&from=4366022&to=4380289 http://www.ncbi.nlm.nih.gov/sutils/evv.cgi?taxid=9606&contig=NT_167198.1&gene=OPN1MW& lid=2652&from=4366022&to=4380289

39 Doug Brutlag 2011 OMIM Home Page http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

40 Doug Brutlag 2011 Colorblindness in OMIM

41 Doug Brutlag 2011 Colorblindness in OMIM http://omim.org/entry/303800 http://omim.org/entry/303800

42 Doug Brutlag 2011 Human Genome Resources http://www.ncbi.nlm.nih.gov/genome/guide/human/ http://www.ncbi.nlm.nih.gov/genome/guide/human/

43 Doug Brutlag 2011 RefSeq http://www.ncbi.nlm.nih.gov/RefSeq/ http://www.ncbi.nlm.nih.gov/RefSeq/

44 Doug Brutlag 2011 RefSeq Gene http://www.ncbi.nlm.nih.gov/refseq/rsg/ http://www.ncbi.nlm.nih.gov/refseq/rsg/

45 Doug Brutlag 2011 NCBI UniGene http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene

46 Doug Brutlag 2011 NCBI Homologene Database http://www.ncbi.nlm.nih.gov/homologene http://www.ncbi.nlm.nih.gov/homologene

47 Doug Brutlag 2011 Comparative Genomics

48 Doug Brutlag 2011 Ensembl Home Page http://www.ensembl.org/ http://www.ensembl.org/

49 Doug Brutlag 2011 EBI Genomes Home Page http://www.ensembl.org/ http://www.ensembl.org/

50 Doug Brutlag 2011 Ensembl Human Genome http://www.ensembl.org/Homo_sapiens/ http://www.ensembl.org/Homo_sapiens/

51 Doug Brutlag 2011 Ensembl Human Opsin Search http://uswest.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;id x=;q=opsin http://uswest.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;id x=;q=opsin

52 Doug Brutlag 2011 Ensembl Human Opsin Genes http://uswest.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;id x=;q=opsin http://uswest.ensembl.org/Homo_sapiens/Search/Results?species=Homo_sapiens;id x=;q=opsin

53 Doug Brutlag 2011 Ensembl Human OPN1MW Gene http://uswest.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000 147380;r=X:153448107-153461633 http://uswest.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000 147380;r=X:153448107-153461633

54 Doug Brutlag 2011 Ensembl Opsin OPN1MW Gene Location http://uswest.ensembl.org/Homo_sapiens/Location/View?h=Havana%20gene;r=X:1 53448107-153461633#r=X:153448109-153461632 http://uswest.ensembl.org/Homo_sapiens/Location/View?h=Havana%20gene;r=X:1 53448107-153461633#r=X:153448109-153461632

55 Doug Brutlag 2011 Ensembl OPN1MW Transcripts http://uswest.ensembl.org/Homo_sapiens/Location/View?h=Havana%20gene;r=X:1 53448107-153461633#r=X:153448109-153461632 http://uswest.ensembl.org/Homo_sapiens/Location/View?h=Havana%20gene;r=X:1 53448107-153461633#r=X:153448109-153461632

56 Doug Brutlag 2011 Ensembl OPN1MW Opsin Protein http://uswest.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000 147380;r=X:153448107-153461633;t=ENST00000369935 http://uswest.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000 147380;r=X:153448107-153461633;t=ENST00000369935

57 Doug Brutlag 2011 Ensembl Tutorials http://uswest.ensembl.org/info/website/tutorials/index.html http://uswest.ensembl.org/info/website/tutorials/index.html

58 Doug Brutlag 2011 UCSC Genome Home Page http://genome.ucsc.edu/ http://genome.ucsc.edu/

59 Doug Brutlag 2011 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgGateway http://genome.ucsc.edu/cgi-bin/hgGateway

60 Doug Brutlag 2011 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgGateway http://genome.ucsc.edu/cgi-bin/hgGateway

61 Doug Brutlag 2011 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203- 153499469&hgsid=216983641&knownGene=pack&hgFind.matches=uc004fkd.2, http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203- 153499469&hgsid=216983641&knownGene=pack&hgFind.matches=uc004fkd.2,

62 Doug Brutlag 2011 UCSC Genome Browser http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203- 153499469&hgsid=216983641&knownGene=pack&hgFind.matches=uc004fkd.2, http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153485203- 153499469&hgsid=216983641&knownGene=pack&hgFind.matches=uc004fkd.2,

63 Doug Brutlag 2011 UCSC Proteome Browser http://genome.ucsc.edu/cgi-bin/pbGateway http://genome.ucsc.edu/cgi-bin/pbGateway

64 Doug Brutlag 2011 UCSC Proteome Browser http://genome.ucsc.edu/cgi-bin/pbGateway http://genome.ucsc.edu/cgi-bin/pbGateway

65 Doug Brutlag 2011 UCSC Help File http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html

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