尊敬的 微信汇率：1円 ≈ 0.046078 元 支付宝汇率：1円 ≈ 0.046168元 [退出登录]
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Aug2015 analysis team spiral genetics

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GenomeInABottle
GenomeInABottle

1. The document describes a method called Anchored Assembly for detecting structural variants from short-read sequencing data using read overlap assembly and reference removal. 2. The method was validated against other SV detection tools using validated SVs from fosmid/PacBio sequencing, detecting 15 previously undetected SVs with high sensitivity and specificity. 3. Examples are given of validated deletions and insertions detected in an Ashkenazi Jewish trio that were identical in the offspring and followed expected inheritance patterns from parents.

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ANCHORED ASSEMBLY Accurate StructuralVariant Detection Using Short-Read Data AA Bruestle, J.J. and Shekar, S.N.
Methodology Anchoring AA Anchor Assemblies 7 7 7 7 8 89 9 7 8 7 R1 R2 R3 R5 R8R7 R3 R6 R9 Read overlap assembly Read Overlap Assembly Remove Reference ReadsRead Correction 0 0 200 400 600 800 1000 1200 10002000300040005000 K-merCount Total K-mer Quality Score K-mer Quality Score Distribution A* error correction
SV Comparison Baylor College of Medicine, against Illumina, PacBio, Array, Nextera and BioNano Program FDR Sensitivity CNVnator 80.46% 22.62% BreakDancer 58.89% 42.39% Delly 55.13% 31.18% Crest 14.87% 35.29% Pindel 31.81% 56.70% SVStat 1.79% 16.36% Tiresias 69.04% 7.79% Spiral 3.03% 42% English et al. (2015), updated AA
Fosmid/PacBio validated SVsAA Validated in collaboration by Malig, M, Eichler, EE et al. Selected 15 high confidence SVs not previously detected in the 1000 Genomes Project
PacBio validated SVs deleteAA Chr Call  Size  (bp) Clones  seq  with   PacBio Validated  by   Micropeats Validated  by   Dotplots Call  validated? 1 1026 2 2 2 yes 1 6375 2 2 2 yes 2 26838 2 2 2 yes 3 4184 1 1 1 yes 5 9507 2 2 2 yes 7 3013 1 1 1 yes 8 5157 2 1 1 yes 9 2883 1 1 1 yes 15 6051 2 2 2 yes Malig,  M,  Eichler,  EE  et  al.  (Manuscript  in  preparation)
PacBio validated SVs InsertsAA Malig,  M,  Eichler,  EE  et  al.  (Manuscript  in  preparation) Chr Call  Size  (bp) Clones  seq  with   PacBio Validated  by   Micropeats Validated  by   Dotplots Call  validated? 1 1755 2 2 2 yes 1 3865 2 2 2 yes 8 2457 2 2 2 yes 8 1508 2 2 2 yes 13 2142 2 2 2 yes X 1548 2 2 2 yes
PacBio validation dotplotsAA Malig,  M,  Eichler,  EE  et  al.   (Manuscript  in  preparation) Chromosome  1   3.8kb  insertion
Chromosome  1   6.4kb  deletion PacBio validation dotplotsAA Malig,  M,  Eichler,  EE  et  al.   (Manuscript  in  preparation)
Chromosome  2   26.8kb  deletion PacBio validation dotplotsAA Malig,  M,  Eichler,  EE  et  al.   (Manuscript  in  preparation)
Ashkenazi Jewish TrioAA Validated by Noah Spies using his program SVViz Chr2 Deletion Chr8 Insertion
Reference Chr 2 Deletion - FatherAA Alternative
Chr 2 Deletion - MotherAA Alternative Reference
Chr 2 Deletion - OffspringAA Alternative Reference
Chr 2 Deletion - VCF IdenticalAA HG002 - Offspring chr2 34695829 T <DEL> 100 PASS NS=1;DP=51;SVTYPE=DEL;END=34736567;SVLEN=-40730 DP:AD 51:21,30 HG003 - Father chr2 34695829 T <DEL> 100 PASS NS=1;DP=55;SVTYPE=DEL;END=34736567;SVLEN=-40730; DP:AD 55:0,55
Chr 8 Insertion - FatherAA Alternative Reference
Chr 8 Insertion - MotherAA Alternative Reference
Chr 8 Insertion - OffspringAA Alternative Reference
HG0004 chr8 129739066 AATAAA 100 masking_present NS=1;DP=41;SVTYPE=INS; END=129739071;SVLEN=3404; DP:AD 41:28,13 Chr 2 Insertion - VCF IdenticalAA GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGGCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAAC TTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGC AAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTC TTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTAC TTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACT TTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAG ATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTG TAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCC TATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCA AAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAG CGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTG ACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTG ATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGG GTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTAC CACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAAACT Mother
GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAAGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAACAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCCATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAA CTTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATG CAAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCT CTTTAGAAAAGAAATTGTACGATCGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTA CTTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAAC TTTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCA GATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCT GTAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTC CTATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGC AAGAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCA GCGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTT GACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTT GATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGG GGTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTA CCACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT Chr 2 Insertion - VCF IdenticalAA FatherHG003 chr8 129739066 AATAAA 100 masking_present NS=1;DP=47;SVTYPE=INS; END=129739071;SVLEN=3405;DP:AD 47:32,15
Chr 2 Insertion - VCF IdenticalAA HG002 chr8 129739066 AATAAA 100 masking_present NS=1;DP=18;SVTYPE=INS; END=129739071;SVLEN=3405;DP:AD 18:0,18 GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAA CTTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATG CAAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCT CTTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTA CTTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAAC TTTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCA GATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCT GTAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTC CTATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGC AAAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCA GCGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTT GACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTT GATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGG GGTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTA CCACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT Offspring
Chr 2 Insertion - VCF IdenticalAA GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGGCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAAC TTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGC AAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTC TTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTAC TTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACT TTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAG ATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTG TAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCC TATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCA AAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAG CGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTG ACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTG ATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGG GTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTAC CACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAAACT Overlay - SNPs from both parents are present in the Offspring GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAAGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAACAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCCATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAAC TTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGC AAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTC TTTAGAAAAGAAATTGTACGATCGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTAC TTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACT TTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAG ATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTG TAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCC TATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCA AGAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAG CGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTG ACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTG ATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGG GTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTAC CACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAAC TTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGC AAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTC TTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTAC TTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACT TTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAG ATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTG TAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCC TATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCA AAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAG CGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTG ACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTG ATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGG GTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTAC CACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT A
What is GraphBWT?
Core Technology to Make Anchored Assembly Feasible • Needed a way to represent the read data that was graph based • Fast search for variation from reference directly from the reads in a whole genome dataset • Small enough footprint to store a read overlap graph of whole human genome in memory 23
GraphBWT • Technology for storing all of the reads that comprise the variation graph of a whole human genome • Very compact to fit into memory (1.5 bytes per base) • In memory, allows for extremely fast searches via subsequence 24
Resulting technologies that use GraphBWT
SpEC SV and Query • SpEC: A lossless compression format that reduces BAM files to 50% of their original size and that can be analyzed with existing bioinformatics tools while compressed • SpEC SV: SpEC that also includes a compact sequence index, known as a GraphBWT (3GB), which is a graph based representation of genomic variation • SpEC Query: an API that reads SpEC SV files to enable rapid queries of sequence data via location or by a subsequence 26
27 Create a SpEC SV File Spiral’s SpEC SV File
Query Times 28 Samples,  Variant  calls SpEC  Query  using  SpEC SpEC  Query  using  SpEC  SV 1  sample,  1  variant Milliseconds Milliseconds 1  sample,  1M  variants 10  Minutes 5  Minutes 1000  samples,  1  variant 10-­‐20  Minutes 10-­‐20  Minutes 1000  samples,  1M  variants 4  Days 2  Days Variant  types SNPs  and  Indels SNPs,  Indels  and  SVs
GraphBWT Technical Details • Constant time traversal of k-mer graph for any sized k-mer • Subsequence search linear with size of sequence • Storage requirements grow linearly with size of novel sequence (i.e. variation) 29
Use Cases for SpEC SV • Search for evidence of variation in read data • Compare graphs between individuals for unique variation • Compare combined graphs of two groups • Store variation, for example a reference genome 30
Questions? Niranjan Shekar - VP of Bioinformatics niranjan@spiralgenetics.com

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Aug2015 analysis team spiral genetics

  • 1. ANCHORED ASSEMBLY Accurate StructuralVariant Detection Using Short-Read Data AA Bruestle, J.J. and Shekar, S.N.
  • 2. Methodology Anchoring AA Anchor Assemblies 7 7 7 7 8 89 9 7 8 7 R1 R2 R3 R5 R8R7 R3 R6 R9 Read overlap assembly Read Overlap Assembly Remove Reference ReadsRead Correction 0 0 200 400 600 800 1000 1200 10002000300040005000 K-merCount Total K-mer Quality Score K-mer Quality Score Distribution A* error correction
  • 3. SV Comparison Baylor College of Medicine, against Illumina, PacBio, Array, Nextera and BioNano Program FDR Sensitivity CNVnator 80.46% 22.62% BreakDancer 58.89% 42.39% Delly 55.13% 31.18% Crest 14.87% 35.29% Pindel 31.81% 56.70% SVStat 1.79% 16.36% Tiresias 69.04% 7.79% Spiral 3.03% 42% English et al. (2015), updated AA
  • 4. Fosmid/PacBio validated SVsAA Validated in collaboration by Malig, M, Eichler, EE et al. Selected 15 high confidence SVs not previously detected in the 1000 Genomes Project
  • 5. PacBio validated SVs deleteAA Chr Call  Size  (bp) Clones  seq  with   PacBio Validated  by   Micropeats Validated  by   Dotplots Call  validated? 1 1026 2 2 2 yes 1 6375 2 2 2 yes 2 26838 2 2 2 yes 3 4184 1 1 1 yes 5 9507 2 2 2 yes 7 3013 1 1 1 yes 8 5157 2 1 1 yes 9 2883 1 1 1 yes 15 6051 2 2 2 yes Malig,  M,  Eichler,  EE  et  al.  (Manuscript  in  preparation)
  • 6. PacBio validated SVs InsertsAA Malig,  M,  Eichler,  EE  et  al.  (Manuscript  in  preparation) Chr Call  Size  (bp) Clones  seq  with   PacBio Validated  by   Micropeats Validated  by   Dotplots Call  validated? 1 1755 2 2 2 yes 1 3865 2 2 2 yes 8 2457 2 2 2 yes 8 1508 2 2 2 yes 13 2142 2 2 2 yes X 1548 2 2 2 yes
  • 7. PacBio validation dotplotsAA Malig,  M,  Eichler,  EE  et  al.   (Manuscript  in  preparation) Chromosome  1   3.8kb  insertion
  • 8. Chromosome  1   6.4kb  deletion PacBio validation dotplotsAA Malig,  M,  Eichler,  EE  et  al.   (Manuscript  in  preparation)
  • 9. Chromosome  2   26.8kb  deletion PacBio validation dotplotsAA Malig,  M,  Eichler,  EE  et  al.   (Manuscript  in  preparation)
  • 10. Ashkenazi Jewish TrioAA Validated by Noah Spies using his program SVViz Chr2 Deletion Chr8 Insertion
  • 11. Reference Chr 2 Deletion - FatherAA Alternative
  • 12. Chr 2 Deletion - MotherAA Alternative Reference
  • 13. Chr 2 Deletion - OffspringAA Alternative Reference
  • 14. Chr 2 Deletion - VCF IdenticalAA HG002 - Offspring chr2 34695829 T <DEL> 100 PASS NS=1;DP=51;SVTYPE=DEL;END=34736567;SVLEN=-40730 DP:AD 51:21,30 HG003 - Father chr2 34695829 T <DEL> 100 PASS NS=1;DP=55;SVTYPE=DEL;END=34736567;SVLEN=-40730; DP:AD 55:0,55
  • 15. Chr 8 Insertion - FatherAA Alternative Reference
  • 16. Chr 8 Insertion - MotherAA Alternative Reference
  • 17. Chr 8 Insertion - OffspringAA Alternative Reference
  • 18. HG0004 chr8 129739066 AATAAA 100 masking_present NS=1;DP=41;SVTYPE=INS; END=129739071;SVLEN=3404; DP:AD 41:28,13 Chr 2 Insertion - VCF IdenticalAA GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGGCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAAC TTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGC AAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTC TTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTAC TTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACT TTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAG ATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTG TAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCC TATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCA AAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAG CGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTG ACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTG ATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGG GTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTAC CACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAAACT Mother
  • 19. GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAAGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAACAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCCATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAA CTTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATG CAAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCT CTTTAGAAAAGAAATTGTACGATCGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTA CTTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAAC TTTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCA GATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCT GTAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTC CTATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGC AAGAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCA GCGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTT GACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTT GATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGG GGTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTA CCACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT Chr 2 Insertion - VCF IdenticalAA FatherHG003 chr8 129739066 AATAAA 100 masking_present NS=1;DP=47;SVTYPE=INS; END=129739071;SVLEN=3405;DP:AD 47:32,15
  • 20. Chr 2 Insertion - VCF IdenticalAA HG002 chr8 129739066 AATAAA 100 masking_present NS=1;DP=18;SVTYPE=INS; END=129739071;SVLEN=3405;DP:AD 18:0,18 GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAA CTTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATG CAAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCT CTTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTA CTTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAAC TTTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCA GATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCT GTAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTC CTATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGC AAAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCA GCGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTT GACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTT GATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGG GGTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTA CCACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT Offspring
  • 21. Chr 2 Insertion - VCF IdenticalAA GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGGCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAAC TTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGC AAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTC TTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTAC TTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACT TTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAG ATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTG TAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCC TATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCA AAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAG CGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTG ACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTG ATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGG GTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTAC CACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAAACT Overlay - SNPs from both parents are present in the Offspring GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAAGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAACAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCCATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAAC TTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGC AAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTC TTTAGAAAAGAAATTGTACGATCGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTAC TTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACT TTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAG ATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTG TAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCC TATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCA AGAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAG CGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTG ACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTG ATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGG GTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTAC CACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT GAAAGTTGTGCACAATATAAAAATTATAATTTTATATTTCAAAACAAATTAAATATCTTAAAATTATAGAAGACATTAAAGAACTATATAAATCAAAGTTAGAAAAAAACCCAGATGTGAGTTGGGAAATCT GAAGAAAATTTAAAAGAGAAATTTAAAAATATTAATATAAAAAATGAAGACTAAACTGGAAAGATACACTAGAGTGAATAAACAAAATAGAAAATACTCAGATGTTTTGTTTTAACTTCCTATTGTATGAGT TTTGGAGACCAACATAAGATAATGACTTGCCTCTGGATATGAAGGTAAAAAAACAGACACAGGCCTATGTAGTGATTTCTTACAGAACAACACAGCAGAAAGCAAATCCCTAAAAAACCATGTGGACGTGGC TTTTACAGATGGTTGTCCAATCCCTGCATGCTATTGCTTGCTTATGGATGAGTGAAAGGAATAAAAATTTTAAGTTATAGCTACAGTTTCTCTACCTGTACATTCCAATACTGACCTTGCATGGTTTCTTTG AGGGCTAAGTATGACAAAAGGATGCAGTGATTTCGAACTTAGATTTTAAAAAACAAATATGACTCTTTTGAACTGTGTGAACATAGGCACATTGCTGGATCTGAGTAATTTCATGTGCTAAGAGGGAATAAT AGCATCAGCCTTAATGCTGCATTATTGCATTTAGCATTATTTCTTTCTGAAGATGAAAGAAGACAGACATCATTATATTTAACAAAGTGCCTGGCACATATAAAATAGTCAATAAATGTTATCTATCATTGC TATTATTACCTAATACTGCGCATAGTAAGCCCTGAACCTGTTCCTGGCATGTGGAGCTATGTACTATGTTCATGACATTAAACAAAGTAGTAGCTATATAATGAATATATAAATGTGACTTTTATTATTACA TCCCTGTAGTTTTGGCAAGTAGTTTACTAAAAGGAAGTTCCAATTTTGACTTAGCATGGAGTTTGTTTTTATCCTGGGCATGTTATCTACCCAGCTTACCTTATTCTTCCTTTCTTCGAAACAGGAATCATG CTTGTTAATTGACTGGGATGTTGCAAGGCCTTATATCTGAGAAGTATATCATCAAGGAATAGAGAAGATGAGTCTTAGAGAGGAAATGGAAGCCCCTGTCAATTAGGAGAGGCAAAGGCTCTATGATACAGC ATAGCCTAAGAATTTCGTTGATACAGAATTCTAAGTGTGAAACGAATGAATGGAGTGACCACTCCTCCCTACTAAAGAATCTTGTAAACACTAGTTTTAAAAGCACAAACGTATTATATCATATACCTATGT ATAATGTCATTTTGCTACTTTTCTCTTCCAACTTCTCAAATCTTTGAATGCAGGGGTTTTTGGAGTTATTCCCTGTGTATTATTTCGACTGATATGTAATAGCTGCTCAGCGAATGTGTGTTGCTAAATAAG AGATGGAGTACAGACAAGCTGAAATTGCACATTTATGTTGCCATTGTACTGCTCAAAAAAAAAAAAAATTAGAATTAGGGTTAAAGAGAGTGCTCAGGCCCTAGACTAGGATTTATTTGCTGTATAATAAAC TTTATGCAAACAATTAACCTCCCTGCTTCTCAATTTTCTCCTCTATAAAATTGGGTTATTACAAAATTCTTTGTAACATATTATGGAGTTCAATTAGGATAAGTTAAATATTGGAAATCTGAAGCATTATGC AAATATGAGGCATTATTATAATAATTATAACAATATTGTTTTTATTCTTAATTGCTACTCTTGAGTACTCTGTTGCTCTGCAGATATCTCTCTCCCTGCCTTCCCCAGGGTGTTGGCATACCAGGATGCCTC TTTAGAAAAGAAATTGCACGATGGACCTAAGGAAACAGAATTTTCCATCCTGGCATTTGCATAAAGGCCACACATGCATAGCCATATGCTGATTTAACCAACAGCTTTCACACTTATAATCGAGTTTGCTAC TTGTTCTGCGATATCTACTCTCCCTCTATTTCTTATTAATAGAACAAAATTTTAGTTGGGAATATGGCTACTGAGAATAAAGATTACCTTTCTCAGCTTCTTTGCGGCTAACTCTGATTATGTGTCTAAACT TTGGTGCATATTTTGGTAAACGGAAATTCTTAAAGGGAGATTCTCTACTTTCTTCCTGCTTGCTGGAATGCAAACATGATTGTTGGATTTGAGCAGCCATCTTATGCCAGGAGTTGGAAACCATGCAGGCAG ATCCTGGTCATTAGCACTACAGACCTCTATACCAAACTGGATTTCTGTGAGACTCCAGAAGAAAGTAAGCAGCACAAGGAGTTTCTTCATGTATTCTTCATTTCCCACACCCCATTATACGTGCTTTTGCTG TAATCTGGAATCAGTTGTACTAATCTACTGCACATACCTAGATTCTATTGATAGTCTATTCCAGGATTGATAACTTTGAGCCCAGATAACTTGCAGTAAGATTTATAACAAGATTTCAAAAATATTCTTTCC TATACACCAAATAGTTTTGGTTAGAGAAAACAAAACTTTTGGCATAGCAACTTCATTTGTAGGAAGTTACCTTCTTAAAATTGTTTATCTGTGGACAGCTATGCTGCTATTAGTAGGGAATGGTTTCAGGCA AAAGGTTACAGAAGGATGGAGAGGGCCTGGGCTTTGGGGTTCCAGGGGTATGGAAGTCAGCAGAGCTGAGAGTAGTTCCCAACAGCCAGAGTGTCCATGGATCAAGCCCTTTTGTGAAGCTGGAGGTACCAG CGCTGGTCCAGGATGCGCAGCTGTAAAGTTGTGAATATATGTATTTGGTCTTTTTCCTTGTTTGCTGGCCTACAACTCTTAAAATCCTTGGAATCTTCAAAGTGATGTGTCTTTTTGTATGCTAATGAGTTG ACTAATGGCTGGCAGCCTCTAGGTGGCTTCTGGATAAGAGCTGGTCACCAGGAAGACCAAGGCCAGATTAGAGGGTTGGGACATTCGGTCCTACTCCGCAACCACCATGGAGACAGTCTGAAGGTTAACTTG ATCACCAATGGCCAATAATTTCATCAATCATGCCAGTGTAATGAAGCCAGCATAAAAACTCAAAAGGACAGGGCTCAGAGAGTTCCATTAGCTGAACATTGGAGGTTCCCACAAGTGGCATGCCCGGAGGGG GTTATGGAAGCTTCACACCCTTTCCCCATACCTCACCCTGTGCATCTCTTCATCTGTATCTTCTGTAATATCCTTTATAATACGCCATTAAATATAAGGAAGTATTTCTCTGAGTTCTGTGAGCCACTCTAC CACATTAATCGAACCCCATGGGGAAGCTGAGTAAAGTTTCAAGTGGAGTAAAATTGCTGATACCGTGACCATCAGGTCAATGTTGCTGGAAGCACAGGTAAAACAACCT A
  • 23. Core Technology to Make Anchored Assembly Feasible • Needed a way to represent the read data that was graph based • Fast search for variation from reference directly from the reads in a whole genome dataset • Small enough footprint to store a read overlap graph of whole human genome in memory 23
  • 24. GraphBWT • Technology for storing all of the reads that comprise the variation graph of a whole human genome • Very compact to fit into memory (1.5 bytes per base) • In memory, allows for extremely fast searches via subsequence 24
  • 26. SpEC SV and Query • SpEC: A lossless compression format that reduces BAM files to 50% of their original size and that can be analyzed with existing bioinformatics tools while compressed • SpEC SV: SpEC that also includes a compact sequence index, known as a GraphBWT (3GB), which is a graph based representation of genomic variation • SpEC Query: an API that reads SpEC SV files to enable rapid queries of sequence data via location or by a subsequence 26
  • 27. 27 Create a SpEC SV File Spiral’s SpEC SV File
  • 28. Query Times 28 Samples,  Variant  calls SpEC  Query  using  SpEC SpEC  Query  using  SpEC  SV 1  sample,  1  variant Milliseconds Milliseconds 1  sample,  1M  variants 10  Minutes 5  Minutes 1000  samples,  1  variant 10-­‐20  Minutes 10-­‐20  Minutes 1000  samples,  1M  variants 4  Days 2  Days Variant  types SNPs  and  Indels SNPs,  Indels  and  SVs
  • 29. GraphBWT Technical Details • Constant time traversal of k-mer graph for any sized k-mer • Subsequence search linear with size of sequence • Storage requirements grow linearly with size of novel sequence (i.e. variation) 29
  • 30. Use Cases for SpEC SV • Search for evidence of variation in read data • Compare graphs between individuals for unique variation • Compare combined graphs of two groups • Store variation, for example a reference genome 30
  • 31. Questions? Niranjan Shekar - VP of Bioinformatics niranjan@spiralgenetics.com
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