Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome ... View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-08-10

AUTHORS

Ikuko N Motoike, Mitsuyo Matsumoto, Inaho Danjoh, Fumiki Katsuoka, Kaname Kojima, Naoki Nariai, Yukuto Sato, Yumi Yamaguchi-Kabata, Shin Ito, Hisaaki Kudo, Ichiko Nishijima, Satoshi Nishikawa, Xiaoqing Pan, Rumiko Saito, Sakae Saito, Tomo Saito, Matsuyuki Shirota, Kaoru Tsuda, Junji Yokozawa, Kazuhiko Igarashi, Naoko Minegishi, Osamu Tanabe, Nobuo Fuse, Masao Nagasaki, Kengo Kinoshita, Jun Yasuda, Masayuki Yamamoto

ABSTRACT

BackgroundValidation 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.ResultsHere, 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%.ConclusionsOur 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. More... »

PAGES

673

References to SciGraph publications

  • 2011-09-29. A comparative analysis of exome capture in GENOME BIOLOGY
  • 2012-04-22. Performance comparison of benchtop high-throughput sequencing platforms in NATURE BIOTECHNOLOGY
  • 2013-06-11. Sequencing studies in human genetics: design and interpretation in NATURE REVIEWS GENETICS
  • 2013-05-29. Characterizing and measuring bias in sequence data in GENOME BIOLOGY
  • 2011-09-28. Comprehensive comparison of three commercial human whole-exome capture platforms in GENOME BIOLOGY
  • 2013-06-12. The new sequencer on the block: comparison of Life Technology’s Proton sequencer to an Illumina HiSeq for whole-exome sequencing in HUMAN GENETICS
  • 2011-11-08. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems in GENOME BIOLOGY
  • 2012-10-31. An integrated map of genetic variation from 1,092 human genomes in NATURE
  • 2011-07-20. An integrated semiconductor device enabling non-optical genome sequencing in NATURE
  • 2012-12-19. Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes in EUROPEAN JOURNAL OF HUMAN GENETICS
  • 2012-12-22. Molecular diagnostics of a single multifocal non-small cell lung cancer case using targeted next generation sequencing in VIRCHOWS ARCHIV
  • 2008-11. Accurate whole human genome sequencing using reversible terminator chemistry in NATURE
  • 2011-09-25. Performance comparison of exome DNA sequencing technologies in NATURE BIOTECHNOLOGY
  • 2012-07-24. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers in BMC GENOMICS
  • 2011-01-01. Integrative genomics viewer in NATURE BIOTECHNOLOGY
  • 2010-10-27. A map of human genome variation from population-scale sequencing in NATURE
  • 2013-08-02. Next-generation sequencing-based multi-gene mutation profiling of solid tumors using fine needle aspiration samples: promises and challenges for routine clinical diagnostics in MODERN PATHOLOGY
  • 2012-01-12. An integrative variant analysis suite for whole exome next-generation sequencing data in BMC BIOINFORMATICS
  • 2010-10-24. Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing in NATURE GENETICS
  • 2011-04-20. Enterotypes of the human gut microbiome in NATURE
  • 2011-04-10. A framework for variation discovery and genotyping using next-generation DNA sequencing data in NATURE GENETICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2164-15-673

    DOI

    http://dx.doi.org/10.1186/1471-2164-15-673

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1046479354

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25109789


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Base Composition", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Exome", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Female", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome, Human", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genomics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "High-Throughput Nucleotide Sequencing", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Male", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Polymorphism, Single Nucleotide", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Reproducibility of Results", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Semiconductors", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sequence Analysis, DNA", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Motoike", 
            "givenName": "Ikuko N", 
            "id": "sg:person.01123743164.98", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01123743164.98"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
                "Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Matsumoto", 
            "givenName": "Mitsuyo", 
            "id": "sg:person.01027201353.74", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01027201353.74"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Danjoh", 
            "givenName": "Inaho", 
            "id": "sg:person.0756307073.37", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0756307073.37"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
                "Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Katsuoka", 
            "givenName": "Fumiki", 
            "id": "sg:person.01256763277.02", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01256763277.02"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kojima", 
            "givenName": "Kaname", 
            "id": "sg:person.01120062535.70", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01120062535.70"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Nariai", 
            "givenName": "Naoki", 
            "id": "sg:person.01366516712.58", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366516712.58"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Sato", 
            "givenName": "Yukuto", 
            "id": "sg:person.01076532462.38", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01076532462.38"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yamaguchi-Kabata", 
            "givenName": "Yumi", 
            "id": "sg:person.0755734750.34", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0755734750.34"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ito", 
            "givenName": "Shin", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kudo", 
            "givenName": "Hisaaki", 
            "id": "sg:person.01143064075.41", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01143064075.41"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Nishijima", 
            "givenName": "Ichiko", 
            "id": "sg:person.015625425445.04", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015625425445.04"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Nishikawa", 
            "givenName": "Satoshi", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Pan", 
            "givenName": "Xiaoqing", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Saito", 
            "givenName": "Rumiko", 
            "id": "sg:person.0630071325.31", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0630071325.31"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Saito", 
            "givenName": "Sakae", 
            "id": "sg:person.01244432017.80", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01244432017.80"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Saito", 
            "givenName": "Tomo", 
            "id": "sg:person.01003705110.36", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01003705110.36"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, -1 Seiryo-machi, Aoba-ku, 980-8575, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
                "Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, 980-8579, Sendai, Miyagi, Japan", 
                "United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, -1 Seiryo-machi, Aoba-ku, 980-8575, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Shirota", 
            "givenName": "Matsuyuki", 
            "id": "sg:person.01337753235.02", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01337753235.02"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Tsuda", 
            "givenName": "Kaoru", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yokozawa", 
            "givenName": "Junji", 
            "id": "sg:person.01151144116.06", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01151144116.06"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
                "Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Igarashi", 
            "givenName": "Kazuhiko", 
            "id": "sg:person.01133436765.75", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01133436765.75"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Minegishi", 
            "givenName": "Naoko", 
            "id": "sg:person.01203447733.32", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01203447733.32"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Tanabe", 
            "givenName": "Osamu", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Fuse", 
            "givenName": "Nobuo", 
            "id": "sg:person.01341300014.21", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01341300014.21"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Nagasaki", 
            "givenName": "Masao", 
            "id": "sg:person.01126167006.24", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01126167006.24"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute of Development, Aging, and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku Sendai, 980-8575, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
                "Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, 980-8579, Sendai, Miyagi, Japan", 
                "Institute of Development, Aging, and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku Sendai, 980-8575, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kinoshita", 
            "givenName": "Kengo", 
            "id": "sg:person.01320210336.24", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01320210336.24"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yasuda", 
            "givenName": "Jun", 
            "id": "sg:person.012210055615.38", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012210055615.38"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan", 
              "id": "http://www.grid.ac/institutes/grid.69566.3a", 
              "name": [
                "Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan", 
                "Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Yamamoto", 
            "givenName": "Masayuki", 
            "id": "sg:person.01074705012.55", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01074705012.55"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/nature07517", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052925719", 
              "https://doi.org/10.1038/nature07517"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/modpathol.2013.122", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000906290", 
              "https://doi.org/10.1038/modpathol.2013.122"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00428-012-1346-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052679792", 
              "https://doi.org/10.1007/s00428-012-1346-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2011-12-9-r95", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027264848", 
              "https://doi.org/10.1186/gb-2011-12-9-r95"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.1975", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039257970", 
              "https://doi.org/10.1038/nbt.1975"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.691", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048495870", 
              "https://doi.org/10.1038/ng.691"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2011-12-11-r112", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027516867", 
              "https://doi.org/10.1186/gb-2011-12-11-r112"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2013-14-5-r51", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034665395", 
              "https://doi.org/10.1186/gb-2013-14-5-r51"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.2198", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043867750", 
              "https://doi.org/10.1038/nbt.2198"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11632", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1000661742", 
              "https://doi.org/10.1038/nature11632"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ejhg.2012.270", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010219922", 
              "https://doi.org/10.1038/ejhg.2012.270"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.1754", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019307928", 
              "https://doi.org/10.1038/nbt.1754"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2011-12-9-r97", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015716722", 
              "https://doi.org/10.1186/gb-2011-12-9-r97"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg3455", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016740058", 
              "https://doi.org/10.1038/nrg3455"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-13-341", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003392841", 
              "https://doi.org/10.1186/1471-2164-13-341"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature09534", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010608717", 
              "https://doi.org/10.1038/nature09534"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature09944", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026204536", 
              "https://doi.org/10.1038/nature09944"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-13-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005761682", 
              "https://doi.org/10.1186/1471-2105-13-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature10242", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007480955", 
              "https://doi.org/10.1038/nature10242"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00439-013-1321-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043621975", 
              "https://doi.org/10.1007/s00439-013-1321-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.806", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010244476", 
              "https://doi.org/10.1038/ng.806"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2014-08-10", 
        "datePublishedReg": "2014-08-10", 
        "description": "BackgroundValidation 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.ResultsHere, 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\u00d7), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109\u00d7). 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%.ConclusionsOur 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.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/1471-2164-15-673", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.6118623", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.6089202", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.6146555", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.6084512", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.6129368", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1023790", 
            "issn": [
              "1471-2164"
            ], 
            "name": "BMC Genomics", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "15"
          }
        ], 
        "keywords": [
          "whole-genome sequencing", 
          "next-generation sequencing platforms", 
          "single nucleotide variations", 
          "sequencing platforms", 
          "single nucleotide polymorphisms", 
          "nucleotide variations", 
          "Illumina HiSeq 2500 platform", 
          "semiconductor sequencer", 
          "HiSeq 2500 platform", 
          "human population genetics", 
          "SNP chip data", 
          "exome sequencing", 
          "disease-related variations", 
          "next-generation sequencer", 
          "population genetics", 
          "multiple sequencing platforms", 
          "individual genomes", 
          "Japanese genomes", 
          "whole-exome sequencing", 
          "chip data", 
          "SNP calls", 
          "sequencing", 
          "nucleotide polymorphisms", 
          "genome", 
          "exome analysis", 
          "human population", 
          "variant calls", 
          "sequencer", 
          "genetics", 
          "large population", 
          "ConclusionsOur results", 
          "variation", 
          "population", 
          "polymorphism", 
          "ResultsHere", 
          "efficient means", 
          "combination", 
          "data", 
          "versatility", 
          "platform", 
          "analysis", 
          "different types", 
          "types", 
          "concordance", 
          "efficient approach", 
          "study", 
          "results", 
          "calls", 
          "samples", 
          "validation", 
          "approach", 
          "means", 
          "reference", 
          "usefulness"
        ], 
        "name": "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", 
        "pagination": "673", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1046479354"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/1471-2164-15-673"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "25109789"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/1471-2164-15-673", 
          "https://app.dimensions.ai/details/publication/pub.1046479354"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-08-04T17:02", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220804/entities/gbq_results/article/article_647.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/1471-2164-15-673"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-15-673'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-15-673'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-15-673'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-15-673'


     

    This table displays all metadata directly associated to this object as RDF triples.

    444 TRIPLES      21 PREDICATES      112 URIs      83 LITERALS      19 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/1471-2164-15-673 schema:about N0992b1b232694ee984b0a68a4c1d444d
    2 N0aa432ea74cb45a5b2722e56fd992f8d
    3 N1ec3b411cda749e295ce405961e992cc
    4 N25aa1aba4f3041369b1ab3b394e70dad
    5 N29f8b3fb0d294d37acdcfbaba828fd20
    6 N4447990bc0654674a6f192ef8a4137ea
    7 N494cdc0abc734a08bb35ad37e53865f8
    8 N4bd94c65d4274164aad2691d648b9e03
    9 N7c3310c4d1f74d8d86c0e458b419f217
    10 N881e4723156747c8b18a9718d703b5a1
    11 Nbcf332f0861a40c08018816c43d50622
    12 Ncfa31f844677408abb94c4b466374a45
    13 anzsrc-for:06
    14 anzsrc-for:0604
    15 schema:author N51785e3aff0b48ea8269916e7e30fad5
    16 schema:citation sg:pub.10.1007/s00428-012-1346-4
    17 sg:pub.10.1007/s00439-013-1321-4
    18 sg:pub.10.1038/ejhg.2012.270
    19 sg:pub.10.1038/modpathol.2013.122
    20 sg:pub.10.1038/nature07517
    21 sg:pub.10.1038/nature09534
    22 sg:pub.10.1038/nature09944
    23 sg:pub.10.1038/nature10242
    24 sg:pub.10.1038/nature11632
    25 sg:pub.10.1038/nbt.1754
    26 sg:pub.10.1038/nbt.1975
    27 sg:pub.10.1038/nbt.2198
    28 sg:pub.10.1038/ng.691
    29 sg:pub.10.1038/ng.806
    30 sg:pub.10.1038/nrg3455
    31 sg:pub.10.1186/1471-2105-13-8
    32 sg:pub.10.1186/1471-2164-13-341
    33 sg:pub.10.1186/gb-2011-12-11-r112
    34 sg:pub.10.1186/gb-2011-12-9-r95
    35 sg:pub.10.1186/gb-2011-12-9-r97
    36 sg:pub.10.1186/gb-2013-14-5-r51
    37 schema:datePublished 2014-08-10
    38 schema:datePublishedReg 2014-08-10
    39 schema:description BackgroundValidation 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.ResultsHere, 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%.ConclusionsOur 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.
    40 schema:genre article
    41 schema:isAccessibleForFree true
    42 schema:isPartOf N1854f8caaf5d4deebd6755f19466366d
    43 N8b78fafede854c929e6935cbf0446a63
    44 sg:journal.1023790
    45 schema:keywords ConclusionsOur results
    46 HiSeq 2500 platform
    47 Illumina HiSeq 2500 platform
    48 Japanese genomes
    49 ResultsHere
    50 SNP calls
    51 SNP chip data
    52 analysis
    53 approach
    54 calls
    55 chip data
    56 combination
    57 concordance
    58 data
    59 different types
    60 disease-related variations
    61 efficient approach
    62 efficient means
    63 exome analysis
    64 exome sequencing
    65 genetics
    66 genome
    67 human population
    68 human population genetics
    69 individual genomes
    70 large population
    71 means
    72 multiple sequencing platforms
    73 next-generation sequencer
    74 next-generation sequencing platforms
    75 nucleotide polymorphisms
    76 nucleotide variations
    77 platform
    78 polymorphism
    79 population
    80 population genetics
    81 reference
    82 results
    83 samples
    84 semiconductor sequencer
    85 sequencer
    86 sequencing
    87 sequencing platforms
    88 single nucleotide polymorphisms
    89 single nucleotide variations
    90 study
    91 types
    92 usefulness
    93 validation
    94 variant calls
    95 variation
    96 versatility
    97 whole-exome sequencing
    98 whole-genome sequencing
    99 schema:name 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
    100 schema:pagination 673
    101 schema:productId Ncf892160069d42c29f24bc446555db7c
    102 Nda0cf14838004a9484ac4e7f3291f066
    103 Ndea6e1fb700f4a4997e45fdceea8d03b
    104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046479354
    105 https://doi.org/10.1186/1471-2164-15-673
    106 schema:sdDatePublished 2022-08-04T17:02
    107 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    108 schema:sdPublisher N4bb5688615d747d2bdb84bae925f580d
    109 schema:url https://doi.org/10.1186/1471-2164-15-673
    110 sgo:license sg:explorer/license/
    111 sgo:sdDataset articles
    112 rdf:type schema:ScholarlyArticle
    113 N02cc0b326329441fa0911496c967838b schema:affiliation grid-institutes:grid.69566.3a
    114 schema:familyName Nishikawa
    115 schema:givenName Satoshi
    116 rdf:type schema:Person
    117 N02d92f3c5abe48ec9c43b63a7635e89a rdf:first sg:person.01341300014.21
    118 rdf:rest N2220304d3373434799ea55543d0e5a92
    119 N034b687e5d7147ab836f482d550923fb rdf:first sg:person.012210055615.38
    120 rdf:rest N752cc8429575426ebe03a844bb1ea467
    121 N0992b1b232694ee984b0a68a4c1d444d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    122 schema:name Humans
    123 rdf:type schema:DefinedTerm
    124 N0aa432ea74cb45a5b2722e56fd992f8d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    125 schema:name Female
    126 rdf:type schema:DefinedTerm
    127 N10cc7be5b5dd45a0b73a65743b09f2d7 rdf:first sg:person.0630071325.31
    128 rdf:rest N9b1cb186d4bc4c9cb5f5baf9ff3b1b2e
    129 N127ea1f3440d494e91b31712f7ad1242 rdf:first sg:person.01337753235.02
    130 rdf:rest N244b259662d94c53bde98ca4a33ab647
    131 N1854f8caaf5d4deebd6755f19466366d schema:volumeNumber 15
    132 rdf:type schema:PublicationVolume
    133 N1c50060eea99425a800933f460bbcc4e rdf:first sg:person.01076532462.38
    134 rdf:rest N5b6e6fb822514be4aa126af0b65886fc
    135 N1ec3b411cda749e295ce405961e992cc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    136 schema:name Polymorphism, Single Nucleotide
    137 rdf:type schema:DefinedTerm
    138 N2220304d3373434799ea55543d0e5a92 rdf:first sg:person.01126167006.24
    139 rdf:rest N3d21b426951c4c31896021f93faaef4a
    140 N244b259662d94c53bde98ca4a33ab647 rdf:first Neb0dfd7e0d104090a6bb5d9ba01c552a
    141 rdf:rest Nfc68724a6b3d40b8874bc47723aab3ce
    142 N248d3e83c0024959b4e0257ab0658211 rdf:first sg:person.01120062535.70
    143 rdf:rest N673415c19cfe40e39a3285b08f752108
    144 N25aa1aba4f3041369b1ab3b394e70dad schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    145 schema:name Reproducibility of Results
    146 rdf:type schema:DefinedTerm
    147 N29f30b91bd514ae589477ba7c7d070e1 schema:affiliation grid-institutes:grid.69566.3a
    148 schema:familyName Pan
    149 schema:givenName Xiaoqing
    150 rdf:type schema:Person
    151 N29f8b3fb0d294d37acdcfbaba828fd20 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    152 schema:name Semiconductors
    153 rdf:type schema:DefinedTerm
    154 N31c21e2009e446eb9b414a29581ae54d schema:affiliation grid-institutes:grid.69566.3a
    155 schema:familyName Ito
    156 schema:givenName Shin
    157 rdf:type schema:Person
    158 N3d21b426951c4c31896021f93faaef4a rdf:first sg:person.01320210336.24
    159 rdf:rest N034b687e5d7147ab836f482d550923fb
    160 N4447990bc0654674a6f192ef8a4137ea schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    161 schema:name High-Throughput Nucleotide Sequencing
    162 rdf:type schema:DefinedTerm
    163 N494cdc0abc734a08bb35ad37e53865f8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    164 schema:name Sequence Analysis, DNA
    165 rdf:type schema:DefinedTerm
    166 N4bb5688615d747d2bdb84bae925f580d schema:name Springer Nature - SN SciGraph project
    167 rdf:type schema:Organization
    168 N4bd94c65d4274164aad2691d648b9e03 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    169 schema:name Male
    170 rdf:type schema:DefinedTerm
    171 N51785e3aff0b48ea8269916e7e30fad5 rdf:first sg:person.01123743164.98
    172 rdf:rest N8cc0ad81262b429eb8639d1d407175f3
    173 N541da59497bf42ce97f1c68cfbd56f0e rdf:first sg:person.01256763277.02
    174 rdf:rest N248d3e83c0024959b4e0257ab0658211
    175 N55c61b1b6e55418dad888d19d64d9895 rdf:first sg:person.015625425445.04
    176 rdf:rest Ncc7c3624bf6241fd8a518396704e4721
    177 N5b6e6fb822514be4aa126af0b65886fc rdf:first sg:person.0755734750.34
    178 rdf:rest Ndcd465788c5144dbb79062716919529a
    179 N673415c19cfe40e39a3285b08f752108 rdf:first sg:person.01366516712.58
    180 rdf:rest N1c50060eea99425a800933f460bbcc4e
    181 N752cc8429575426ebe03a844bb1ea467 rdf:first sg:person.01074705012.55
    182 rdf:rest rdf:nil
    183 N7c3310c4d1f74d8d86c0e458b419f217 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    184 schema:name Genomics
    185 rdf:type schema:DefinedTerm
    186 N881e4723156747c8b18a9718d703b5a1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    187 schema:name Exome
    188 rdf:type schema:DefinedTerm
    189 N8b78fafede854c929e6935cbf0446a63 schema:issueNumber 1
    190 rdf:type schema:PublicationIssue
    191 N8cc0ad81262b429eb8639d1d407175f3 rdf:first sg:person.01027201353.74
    192 rdf:rest Ndf322dc08fe84ebe93962caa2291c841
    193 N90415a22f32e46f49370d107536f1e67 rdf:first sg:person.01203447733.32
    194 rdf:rest N9654fc98ca1e4e958f19d06225afaf86
    195 N9654fc98ca1e4e958f19d06225afaf86 rdf:first Nbd6149a415584c239b935a4297c48c9c
    196 rdf:rest N02d92f3c5abe48ec9c43b63a7635e89a
    197 N9b1cb186d4bc4c9cb5f5baf9ff3b1b2e rdf:first sg:person.01244432017.80
    198 rdf:rest Nd93278be2b6745d6b86fc6ed2621b335
    199 Nbcf332f0861a40c08018816c43d50622 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    200 schema:name Base Composition
    201 rdf:type schema:DefinedTerm
    202 Nbd6149a415584c239b935a4297c48c9c schema:affiliation grid-institutes:grid.69566.3a
    203 schema:familyName Tanabe
    204 schema:givenName Osamu
    205 rdf:type schema:Person
    206 Ncc7c3624bf6241fd8a518396704e4721 rdf:first N02cc0b326329441fa0911496c967838b
    207 rdf:rest Ncd069dc9302343d7ab579d3291a9ae62
    208 Ncd069dc9302343d7ab579d3291a9ae62 rdf:first N29f30b91bd514ae589477ba7c7d070e1
    209 rdf:rest N10cc7be5b5dd45a0b73a65743b09f2d7
    210 Ncf892160069d42c29f24bc446555db7c schema:name dimensions_id
    211 schema:value pub.1046479354
    212 rdf:type schema:PropertyValue
    213 Ncfa31f844677408abb94c4b466374a45 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    214 schema:name Genome, Human
    215 rdf:type schema:DefinedTerm
    216 Nd93278be2b6745d6b86fc6ed2621b335 rdf:first sg:person.01003705110.36
    217 rdf:rest N127ea1f3440d494e91b31712f7ad1242
    218 Nda0cf14838004a9484ac4e7f3291f066 schema:name pubmed_id
    219 schema:value 25109789
    220 rdf:type schema:PropertyValue
    221 Ndcd465788c5144dbb79062716919529a rdf:first N31c21e2009e446eb9b414a29581ae54d
    222 rdf:rest Ne9b6c5a1269a4512a5e929dd498be4f6
    223 Nddb7e58198274c989ef0547f00682b9b rdf:first sg:person.01133436765.75
    224 rdf:rest N90415a22f32e46f49370d107536f1e67
    225 Ndea6e1fb700f4a4997e45fdceea8d03b schema:name doi
    226 schema:value 10.1186/1471-2164-15-673
    227 rdf:type schema:PropertyValue
    228 Ndf322dc08fe84ebe93962caa2291c841 rdf:first sg:person.0756307073.37
    229 rdf:rest N541da59497bf42ce97f1c68cfbd56f0e
    230 Ne9b6c5a1269a4512a5e929dd498be4f6 rdf:first sg:person.01143064075.41
    231 rdf:rest N55c61b1b6e55418dad888d19d64d9895
    232 Neb0dfd7e0d104090a6bb5d9ba01c552a schema:affiliation grid-institutes:grid.69566.3a
    233 schema:familyName Tsuda
    234 schema:givenName Kaoru
    235 rdf:type schema:Person
    236 Nfc68724a6b3d40b8874bc47723aab3ce rdf:first sg:person.01151144116.06
    237 rdf:rest Nddb7e58198274c989ef0547f00682b9b
    238 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    239 schema:name Biological Sciences
    240 rdf:type schema:DefinedTerm
    241 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    242 schema:name Genetics
    243 rdf:type schema:DefinedTerm
    244 sg:grant.6084512 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-15-673
    245 rdf:type schema:MonetaryGrant
    246 sg:grant.6089202 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-15-673
    247 rdf:type schema:MonetaryGrant
    248 sg:grant.6118623 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-15-673
    249 rdf:type schema:MonetaryGrant
    250 sg:grant.6129368 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-15-673
    251 rdf:type schema:MonetaryGrant
    252 sg:grant.6146555 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-15-673
    253 rdf:type schema:MonetaryGrant
    254 sg:journal.1023790 schema:issn 1471-2164
    255 schema:name BMC Genomics
    256 schema:publisher Springer Nature
    257 rdf:type schema:Periodical
    258 sg:person.01003705110.36 schema:affiliation grid-institutes:grid.69566.3a
    259 schema:familyName Saito
    260 schema:givenName Tomo
    261 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01003705110.36
    262 rdf:type schema:Person
    263 sg:person.01027201353.74 schema:affiliation grid-institutes:grid.69566.3a
    264 schema:familyName Matsumoto
    265 schema:givenName Mitsuyo
    266 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01027201353.74
    267 rdf:type schema:Person
    268 sg:person.01074705012.55 schema:affiliation grid-institutes:grid.69566.3a
    269 schema:familyName Yamamoto
    270 schema:givenName Masayuki
    271 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01074705012.55
    272 rdf:type schema:Person
    273 sg:person.01076532462.38 schema:affiliation grid-institutes:grid.69566.3a
    274 schema:familyName Sato
    275 schema:givenName Yukuto
    276 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01076532462.38
    277 rdf:type schema:Person
    278 sg:person.01120062535.70 schema:affiliation grid-institutes:grid.69566.3a
    279 schema:familyName Kojima
    280 schema:givenName Kaname
    281 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01120062535.70
    282 rdf:type schema:Person
    283 sg:person.01123743164.98 schema:affiliation grid-institutes:grid.69566.3a
    284 schema:familyName Motoike
    285 schema:givenName Ikuko N
    286 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01123743164.98
    287 rdf:type schema:Person
    288 sg:person.01126167006.24 schema:affiliation grid-institutes:grid.69566.3a
    289 schema:familyName Nagasaki
    290 schema:givenName Masao
    291 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01126167006.24
    292 rdf:type schema:Person
    293 sg:person.01133436765.75 schema:affiliation grid-institutes:grid.69566.3a
    294 schema:familyName Igarashi
    295 schema:givenName Kazuhiko
    296 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01133436765.75
    297 rdf:type schema:Person
    298 sg:person.01143064075.41 schema:affiliation grid-institutes:grid.69566.3a
    299 schema:familyName Kudo
    300 schema:givenName Hisaaki
    301 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01143064075.41
    302 rdf:type schema:Person
    303 sg:person.01151144116.06 schema:affiliation grid-institutes:grid.69566.3a
    304 schema:familyName Yokozawa
    305 schema:givenName Junji
    306 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01151144116.06
    307 rdf:type schema:Person
    308 sg:person.01203447733.32 schema:affiliation grid-institutes:grid.69566.3a
    309 schema:familyName Minegishi
    310 schema:givenName Naoko
    311 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01203447733.32
    312 rdf:type schema:Person
    313 sg:person.012210055615.38 schema:affiliation grid-institutes:grid.69566.3a
    314 schema:familyName Yasuda
    315 schema:givenName Jun
    316 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012210055615.38
    317 rdf:type schema:Person
    318 sg:person.01244432017.80 schema:affiliation grid-institutes:grid.69566.3a
    319 schema:familyName Saito
    320 schema:givenName Sakae
    321 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01244432017.80
    322 rdf:type schema:Person
    323 sg:person.01256763277.02 schema:affiliation grid-institutes:grid.69566.3a
    324 schema:familyName Katsuoka
    325 schema:givenName Fumiki
    326 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01256763277.02
    327 rdf:type schema:Person
    328 sg:person.01320210336.24 schema:affiliation grid-institutes:grid.69566.3a
    329 schema:familyName Kinoshita
    330 schema:givenName Kengo
    331 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01320210336.24
    332 rdf:type schema:Person
    333 sg:person.01337753235.02 schema:affiliation grid-institutes:grid.69566.3a
    334 schema:familyName Shirota
    335 schema:givenName Matsuyuki
    336 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01337753235.02
    337 rdf:type schema:Person
    338 sg:person.01341300014.21 schema:affiliation grid-institutes:grid.69566.3a
    339 schema:familyName Fuse
    340 schema:givenName Nobuo
    341 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01341300014.21
    342 rdf:type schema:Person
    343 sg:person.01366516712.58 schema:affiliation grid-institutes:grid.69566.3a
    344 schema:familyName Nariai
    345 schema:givenName Naoki
    346 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366516712.58
    347 rdf:type schema:Person
    348 sg:person.015625425445.04 schema:affiliation grid-institutes:grid.69566.3a
    349 schema:familyName Nishijima
    350 schema:givenName Ichiko
    351 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015625425445.04
    352 rdf:type schema:Person
    353 sg:person.0630071325.31 schema:affiliation grid-institutes:grid.69566.3a
    354 schema:familyName Saito
    355 schema:givenName Rumiko
    356 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0630071325.31
    357 rdf:type schema:Person
    358 sg:person.0755734750.34 schema:affiliation grid-institutes:grid.69566.3a
    359 schema:familyName Yamaguchi-Kabata
    360 schema:givenName Yumi
    361 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0755734750.34
    362 rdf:type schema:Person
    363 sg:person.0756307073.37 schema:affiliation grid-institutes:grid.69566.3a
    364 schema:familyName Danjoh
    365 schema:givenName Inaho
    366 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0756307073.37
    367 rdf:type schema:Person
    368 sg:pub.10.1007/s00428-012-1346-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052679792
    369 https://doi.org/10.1007/s00428-012-1346-4
    370 rdf:type schema:CreativeWork
    371 sg:pub.10.1007/s00439-013-1321-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043621975
    372 https://doi.org/10.1007/s00439-013-1321-4
    373 rdf:type schema:CreativeWork
    374 sg:pub.10.1038/ejhg.2012.270 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010219922
    375 https://doi.org/10.1038/ejhg.2012.270
    376 rdf:type schema:CreativeWork
    377 sg:pub.10.1038/modpathol.2013.122 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000906290
    378 https://doi.org/10.1038/modpathol.2013.122
    379 rdf:type schema:CreativeWork
    380 sg:pub.10.1038/nature07517 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052925719
    381 https://doi.org/10.1038/nature07517
    382 rdf:type schema:CreativeWork
    383 sg:pub.10.1038/nature09534 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010608717
    384 https://doi.org/10.1038/nature09534
    385 rdf:type schema:CreativeWork
    386 sg:pub.10.1038/nature09944 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026204536
    387 https://doi.org/10.1038/nature09944
    388 rdf:type schema:CreativeWork
    389 sg:pub.10.1038/nature10242 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007480955
    390 https://doi.org/10.1038/nature10242
    391 rdf:type schema:CreativeWork
    392 sg:pub.10.1038/nature11632 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000661742
    393 https://doi.org/10.1038/nature11632
    394 rdf:type schema:CreativeWork
    395 sg:pub.10.1038/nbt.1754 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019307928
    396 https://doi.org/10.1038/nbt.1754
    397 rdf:type schema:CreativeWork
    398 sg:pub.10.1038/nbt.1975 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039257970
    399 https://doi.org/10.1038/nbt.1975
    400 rdf:type schema:CreativeWork
    401 sg:pub.10.1038/nbt.2198 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043867750
    402 https://doi.org/10.1038/nbt.2198
    403 rdf:type schema:CreativeWork
    404 sg:pub.10.1038/ng.691 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048495870
    405 https://doi.org/10.1038/ng.691
    406 rdf:type schema:CreativeWork
    407 sg:pub.10.1038/ng.806 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010244476
    408 https://doi.org/10.1038/ng.806
    409 rdf:type schema:CreativeWork
    410 sg:pub.10.1038/nrg3455 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016740058
    411 https://doi.org/10.1038/nrg3455
    412 rdf:type schema:CreativeWork
    413 sg:pub.10.1186/1471-2105-13-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005761682
    414 https://doi.org/10.1186/1471-2105-13-8
    415 rdf:type schema:CreativeWork
    416 sg:pub.10.1186/1471-2164-13-341 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003392841
    417 https://doi.org/10.1186/1471-2164-13-341
    418 rdf:type schema:CreativeWork
    419 sg:pub.10.1186/gb-2011-12-11-r112 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027516867
    420 https://doi.org/10.1186/gb-2011-12-11-r112
    421 rdf:type schema:CreativeWork
    422 sg:pub.10.1186/gb-2011-12-9-r95 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027264848
    423 https://doi.org/10.1186/gb-2011-12-9-r95
    424 rdf:type schema:CreativeWork
    425 sg:pub.10.1186/gb-2011-12-9-r97 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015716722
    426 https://doi.org/10.1186/gb-2011-12-9-r97
    427 rdf:type schema:CreativeWork
    428 sg:pub.10.1186/gb-2013-14-5-r51 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034665395
    429 https://doi.org/10.1186/gb-2013-14-5-r51
    430 rdf:type schema:CreativeWork
    431 grid-institutes:grid.69566.3a schema:alternateName Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan
    432 Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan
    433 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan
    434 Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan
    435 Institute of Development, Aging, and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku Sendai, 980-8575, Sendai, Japan
    436 United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, -1 Seiryo-machi, Aoba-ku, 980-8575, Sendai, Japan
    437 schema:name Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, 980-8579, Sendai, Miyagi, Japan
    438 Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan
    439 Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan
    440 Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, 980-8573, Sendai, Japan
    441 Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, 980-8575, Sendai, Japan
    442 Institute of Development, Aging, and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku Sendai, 980-8575, Sendai, Japan
    443 United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, -1 Seiryo-machi, Aoba-ku, 980-8575, Sendai, Japan
    444 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...