title: Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population.
abstract: BACKGROUND
  Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously.
  
  
  RESULTS
  Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%.
  
  
  CONCLUSIONS
  Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.
authors.forename: Ikuko N
authors.initials: IN
authors.lastname: Motoike
authors.forename: Mitsuyo
authors.initials: M
authors.lastname: Matsumoto
authors.forename: Inaho
authors.initials: I
authors.lastname: Danjoh
authors.forename: Fumiki
authors.initials: F
authors.lastname: Katsuoka
authors.forename: Kaname
authors.initials: K
authors.lastname: Kojima
authors.forename: Naoki
authors.initials: N
authors.lastname: Nariai
authors.forename: Yukuto
authors.initials: Y
authors.lastname: Sato
authors.forename: Yumi
authors.initials: Y
authors.lastname: Yamaguchi-Kabata
authors.forename: Shin
authors.initials: S
authors.lastname: Ito
authors.forename: Hisaaki
authors.initials: H
authors.lastname: Kudo
authors.forename: Ichiko
authors.initials: I
authors.lastname: Nishijima
authors.forename: Satoshi
authors.initials: S
authors.lastname: Nishikawa
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Pan
authors.forename: Rumiko
authors.initials: R
authors.lastname: Saito
authors.forename: Sakae
authors.initials: S
authors.lastname: Saito
authors.forename: Tomo
authors.initials: T
authors.lastname: Saito
authors.forename: Matsuyuki
authors.initials: M
authors.lastname: Shirota
authors.forename: Kaoru
authors.initials: K
authors.lastname: Tsuda
authors.forename: Junji
authors.initials: J
authors.lastname: Yokozawa
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Igarashi
authors.forename: Naoko
authors.initials: N
authors.lastname: Minegishi
authors.forename: Osamu
authors.initials: O
authors.lastname: Tanabe
authors.forename: Nobuo
authors.initials: N
authors.lastname: Fuse
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
authors.forename: Kengo
authors.initials: K
authors.lastname: Kinoshita
authors.forename: Jun
authors.initials: J
authors.lastname: Yasuda
authors.affiliation: Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan. masiyamamoto@med.tohoku.ac.jp.
authors.forename: Masayuki
authors.initials: M
authors.lastname: Yamamoto
mesh_terms: D001482:Base Composition; D059472:Exome / Q000235:genetics*; D005260:Female; D015894:Genome, Human / Q000235:genetics; D023281:Genomics / Q000295:instrumentation*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D012666:Semiconductors; D017422:Sequence Analysis, DNA / Q000295:instrumentation*
references.citation: Bioinformatics. 2009 Jul 15;25(14):1754-60
references.pmid: 19451168
references.citation: Nature. 2012 Nov 1;491(7422):56-65
references.pmid: 23128226
references.citation: PLoS One. 2013 Jul 04;8(7):e67744
references.pmid: 23861798
references.citation: Genome Biol. 2011 Sep 29;12(9):R97
references.pmid: 21958622
references.citation: PLoS Comput Biol. 2013 Apr;9(4):e1003031
references.pmid: 23592973
references.citation: Nat Rev Genet. 2013 Jul;14(7):460-70
references.pmid: 23752795
references.citation: Nat Genet. 2011 May;43(5):491-8
references.pmid: 21478889
references.citation: Genome Biol. 2011 Sep 28;12(9):R95
references.pmid: 21955857
references.citation: Nat Biotechnol. 2012 May;30(5):434-9
references.pmid: 22522955
references.citation: Eur J Hum Genet. 2013 Aug;21(8):864-70
references.pmid: 23249957
references.citation: Nature. 2011 May 12;473(7346):174-80
references.pmid: 21508958
references.citation: Am J Hum Genet. 2013 Jan 10;92(1):52-66
references.pmid: 23290073
references.citation: J Mol Diagn. 2012 Nov;14(6):602-12
references.pmid: 22921312
references.citation: Brief Bioinform. 2013 Mar;14(2):178-92
references.pmid: 22517427
references.citation: Nature. 2010 Oct 28;467(7319):1061-73
references.pmid: 20981092
references.citation: J Biomol Tech. 2012 Apr;23(1):24-30
references.pmid: 22468138
references.citation: Nat Biotechnol. 2011 Sep 25;29(10):908-14
references.pmid: 21947028
references.citation: J Clin Microbiol. 2012 Dec;50(12):3831-7
references.pmid: 22972833
references.citation: Genet Med. 2011 Jun;13(6):499-504
references.pmid: 21558861
references.citation: Genome Res. 2010 Sep;20(9):1297-303
references.pmid: 20644199
references.citation: Hum Genet. 2013 Oct;132(10):1153-63
references.pmid: 23757002
references.citation: PLoS One. 2012;7(9):e45798
references.pmid: 23029247
references.citation: Mod Pathol. 2014 Feb;27(2):314-27
references.pmid: 23907151
references.citation: Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12348-53
references.pmid: 21709235
references.citation: Clin Chem. 2013 Oct;59(10):1481-8
references.pmid: 23775370
references.citation: Virchows Arch. 2013 Feb;462(2):249-54
references.pmid: 23262782
references.citation: Nature. 2008 Nov 6;456(7218):53-9
references.pmid: 18987734
references.citation: PLoS One. 2013 Jun 28;8(6):e67539
references.pmid: 23840736
references.citation: PLoS One. 2012;7(8):e41606
references.pmid: 22870235
references.citation: Genome Biol. 2011 Nov 08;12(11):R112
references.pmid: 22067484
references.citation: Nat Genet. 2010 Nov;42(11):931-6
references.pmid: 20972442
references.citation: Annu Rev Med. 2012;63:35-61
references.pmid: 22248320
references.citation: J Mol Diagn. 2013 Mar;15(2):234-47
references.pmid: 23321017
references.citation: PLoS One. 2013;8(2):e55089
references.pmid: 23405114
references.citation: Nat Biotechnol. 2011 Jan;29(1):24-6
references.pmid: 21221095
references.citation: Genome Biol. 2013 May 29;14(5):R51
references.pmid: 23718773
references.citation: BMC Genomics. 2012 Jul 24;13:341
references.pmid: 22827831
references.citation: Am J Hum Genet. 2007 Sep;81(3):559-75
references.pmid: 17701901
references.citation: Bioinformatics. 2009 Aug 15;25(16):2078-9
references.pmid: 19505943
references.citation: BMC Bioinformatics. 2012 Jan 12;13:8
references.pmid: 22239737
references.citation: Bioinformatics. 2010 Mar 15;26(6):841-2
references.pmid: 20110278
references.citation: Nature. 2011 Jul 20;475(7356):348-52
references.pmid: 21776081
references.citation: J Mol Diagn. 2013 Sep;15(5):607-22
references.pmid: 23810757