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Volumn 25, Issue 7, 2017, Pages 869-876

Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ADULT; ARTICLE; CONTROLLED STUDY; ESTONIAN (CITIZEN); GENETIC IMPUTATION; GENETIC VARIATION; GENOTYPE; HAPLOTYPE; HUMAN; POPULATION GENETICS; PRIORITY JOURNAL; STATISTICAL ANALYSIS; WHOLE GENOME SEQUENCING; DNA SEQUENCE; FEMALE; GENE FREQUENCY; GENOME-WIDE ASSOCIATION STUDY; HUMAN GENOME; MALE; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARD; STANDARDS;

EID: 85017438205     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2017.51     Document Type: Article
Times cited : (139)

References (50)
  • 1
    • 77953808087 scopus 로고    scopus 로고
    • Genotype imputation for genome-wide association studies
    • Marchini J, Howie B: Genotype imputation for genome-wide association studies. Nat Rev Genet 2010; 11: 499-511.
    • (2010) Nat Rev Genet , vol.11 , pp. 499-511
    • Marchini, J.1    Howie, B.2
  • 3
    • 79959217817 scopus 로고    scopus 로고
    • International HapMap 3 Consortium Integrating common and rare genetic variation in diverse human populations
    • HapMap C, Altshuler DM, Gibbs RA et al: International HapMap 3 Consortium Integrating common and rare genetic variation in diverse human populations. Nature 2010; 467: 52-58.
    • (2010) Nature , vol.467 , pp. 52-58
    • HapMap, C.1    Altshuler, D.M.2    Gibbs, R.A.3
  • 4
    • 35348983887 scopus 로고    scopus 로고
    • A second generation human haplotype map of over 3.1 million SNPs
    • International HapMap Consortium
    • International HapMap Consortium, Frazer KA, Ballinger DG et al: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449: 851-861.
    • (2007) Nature , vol.449 , pp. 851-861
    • Frazer, K.A.1    Ballinger, D.G.2
  • 5
    • 84943171338 scopus 로고    scopus 로고
    • A global reference for human genetic variation
    • 1000 Genomes Project Consortium
    • 1000 Genomes Project Consortium, Auton A, Brooks LD et al: A global reference for human genetic variation. Nature 2015; 526: 68-74.
    • (2015) Nature , vol.526 , pp. 68-74
    • Auton, A.1    Brooks, L.D.2
  • 6
    • 78049337953 scopus 로고    scopus 로고
    • Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index
    • Speliotes EK, Willer CJ, Berndt SI et al: Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet 2010; 42: 937-948.
    • (2010) Nat Genet , vol.42 , pp. 937-948
    • Speliotes, E.K.1    Willer, C.J.2    Berndt, S.I.3
  • 7
    • 77957947562 scopus 로고    scopus 로고
    • Hundreds of variants clustered in genomic loci and biological pathways affect human height
    • Lango Allen H, Estrada K, Lettre G et al: Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 2010; 467: 832-838.
    • (2010) Nature , vol.467 , pp. 832-838
    • Lango Allen, H.1    Estrada, K.2    Lettre, G.3
  • 8
    • 84868337361 scopus 로고    scopus 로고
    • Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes
    • Morris AP, Voight BF, Teslovich TM et al: Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 2012; 44: 981-990.
    • (2012) Nat Genet , vol.44 , pp. 981-990
    • Morris, A.P.1    Voight, B.F.2    Teslovich, T.M.3
  • 9
    • 84862777492 scopus 로고    scopus 로고
    • Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways
    • Stolk L, Perry JR, Chasman DI et al: Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. Nat Genet 2012; 44: 260-268.
    • (2012) Nat Genet , vol.44 , pp. 260-268
    • Stolk, L.1    Perry, J.R.2    Chasman, D.I.3
  • 10
    • 68449086236 scopus 로고    scopus 로고
    • Common polygenic variation contributes to risk of schizophrenia and bipolar disorder
    • International Schizophrenia Consortium
    • International Schizophrenia Consortium, Purcell SM, Wray NR et al: Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 2009; 460: 748-752.
    • (2009) Nature , vol.460 , pp. 748-752
    • Purcell, S.M.1    Wray, N.R.2
  • 11
    • 84904804929 scopus 로고    scopus 로고
    • Biological insights from 108 schizophrenia-associated genetic loci
    • Schizophrenia Working Group of the Psychiatric Genomics Consortium: Biological insights from 108 schizophrenia-associated genetic loci. Nature 2014; 511: 421-427.
    • (2014) Nature , vol.511 , pp. 421-427
  • 12
    • 84963837739 scopus 로고    scopus 로고
    • Meta-analysis of 49 549 individuals imputed with the 1000 Genomes Project reveals an exonic damaging variant in ANGPTL4 determining fasting TG levels
    • van Leeuwen EM, Sabo A, Bis JC et al: Meta-analysis of 49 549 individuals imputed with the 1000 Genomes Project reveals an exonic damaging variant in ANGPTL4 determining fasting TG levels. J Med Genet 2016; 53: 441-449.
    • (2016) J Med Genet , vol.53 , pp. 441-449
    • Van Leeuwen, E.M.1    Sabo, A.2    Bis, J.C.3
  • 13
    • 84949293492 scopus 로고    scopus 로고
    • Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation
    • Soler Artigas M, Wain LV, Miller S et al: Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation. Nat Commun 2015; 6: 8658.
    • (2015) Nat Commun , vol.6 , pp. 8658
    • Soler Artigas, M.1    Wain, L.V.2    Miller, S.3
  • 14
    • 84937399367 scopus 로고    scopus 로고
    • Meta-analysis of genome-wide association studies for neuroticism, and the polygenic association with major depressive disorder
    • Genetics of Personality Consortium
    • Genetics of Personality Consortium, de Moor MH, van den Berg SM et al: Meta-analysis of genome-wide association studies for neuroticism, and the polygenic association with major depressive disorder. JAMA Psychiatry 2015; 72: 642-650.
    • (2015) JAMA Psychiatry , vol.72 , pp. 642-650
    • De Moor, M.H.1    Van Den Berg, S.M.2
  • 15
    • 84975318713 scopus 로고    scopus 로고
    • Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine
    • Gormley P, Anttila V, Winsvold BS et al: Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine. Nat Genet 2016; 48: 856-866.
    • (2016) Nat Genet , vol.48 , pp. 856-866
    • Gormley, P.1    Anttila, V.2    Winsvold, B.S.3
  • 17
    • 84861598099 scopus 로고    scopus 로고
    • Extremely low-coverage sequencing and imputation increases power for genome-wide association studies
    • Pasaniuc B, Rohland N, McLaren PJ et al: Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet 2012; 44: 631-635.
    • (2012) Nat Genet , vol.44 , pp. 631-635
    • Pasaniuc, B.1    Rohland, N.2    McLaren, P.J.3
  • 18
    • 84867898425 scopus 로고    scopus 로고
    • Effect of genome-wide genotyping and reference panels on rare variants imputation
    • Zheng HF, Ladouceur M, Greenwood CM, Richards JB: Effect of genome-wide genotyping and reference panels on rare variants imputation. J Genet Genomics 2012; 39: 545-550.
    • (2012) J Genet Genomics , vol.39 , pp. 545-550
    • Zheng, H.F.1    Ladouceur, M.2    Greenwood, C.M.3    Richards, J.B.4
  • 19
    • 84943182742 scopus 로고    scopus 로고
    • The UK10K project identifies rare variants in health and disease
    • UK10K Consortium
    • UK10K Consortium, Walter K, Min JL et al: The UK10K project identifies rare variants in health and disease. Nature 2015; 526: 82-90.
    • (2015) Nature , vol.526 , pp. 82-90
    • Walter, K.1    Min, J.L.2
  • 20
    • 84983479616 scopus 로고    scopus 로고
    • A reference panel of 64,976 haplotypes for genotype imputation
    • McCarthy S, Das S, Kretzschmar W et al: A reference panel of 64,976 haplotypes for genotype imputation. Nat Genet 2016; 48: 1279-1283.
    • (2016) Nat Genet , vol.48 , pp. 1279-1283
    • McCarthy, S.1    Das, S.2    Kretzschmar, W.3
  • 21
    • 84930868547 scopus 로고    scopus 로고
    • Rare variant genotype imputation with thousands of study-specific whole-genome sequences: Implications for cost-effective study designs
    • Pistis G, Porcu E, Vrieze SI et al: Rare variant genotype imputation with thousands of study-specific whole-genome sequences: implications for cost-effective study designs. Eur J Hum Genet 2015; 23: 975-983.
    • (2015) Eur J Hum Genet , vol.23 , pp. 975-983
    • Pistis, G.1    Porcu, E.2    Vrieze, S.I.3
  • 22
    • 84929132687 scopus 로고    scopus 로고
    • Large-scale whole-genome sequencing of the Icelandic population
    • Gudbjartsson DF, Helgason H, Gudjonsson SA et al: Large-scale whole-genome sequencing of the Icelandic population. Nat Genet 2015; 47: 435-444.
    • (2015) Nat Genet , vol.47 , pp. 435-444
    • Gudbjartsson, D.F.1    Helgason, H.2    Gudjonsson, S.A.3
  • 23
    • 84908551473 scopus 로고    scopus 로고
    • Improved imputation quality of lowfrequency and rare variants in European samples using the 'Genome of the Netherlands'
    • Deelen P, Menelaou A, van Leeuwen EM et al: Improved imputation quality of lowfrequency and rare variants in European samples using the 'Genome of The Netherlands'. Eur J Hum Genet 2014; 22: 1321-1326.
    • (2014) Eur J Hum Genet , vol.22 , pp. 1321-1326
    • Deelen, P.1    Menelaou, A.2    Van Leeuwen, E.M.3
  • 24
    • 84945370533 scopus 로고    scopus 로고
    • Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers
    • Sidore C, Busonero F, Maschio A et al: Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers. Nat Genet 2015; 47: 1272-1281.
    • (2015) Nat Genet , vol.47 , pp. 1272-1281
    • Sidore, C.1    Busonero, F.2    Maschio, A.3
  • 25
    • 84941702459 scopus 로고    scopus 로고
    • Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel
    • Huang J, Howie B, McCarthy S et al: Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel. Nat Commun 2015; 6: 8111.
    • (2015) Nat Commun , vol.6 , pp. 8111
    • Huang, J.1    Howie, B.2    McCarthy, S.3
  • 26
    • 84923648340 scopus 로고    scopus 로고
    • A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans
    • Timpson NJ, Walter K, Min JL et al: A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans. Nat Commun 2014; 5: 4871.
    • (2014) Nat Commun , vol.5 , pp. 4871
    • Timpson, N.J.1    Walter, K.2    Min, J.L.3
  • 27
    • 55549115654 scopus 로고    scopus 로고
    • Genes mirror geography within Europe
    • Novembre J, Johnson T, Bryc K et al: Genes mirror geography within Europe. Nature 2008; 456: 98-101.
    • (2008) Nature , vol.456 , pp. 98-101
    • Novembre, J.1    Johnson, T.2    Bryc, K.3
  • 28
    • 65549126774 scopus 로고    scopus 로고
    • Genetic structure of Europeans: A view from the North-East
    • Nelis M, Esko T, Magi R et al: Genetic structure of Europeans: a view from the North-East. PLoS ONE 2009; 4: e5472.
    • (2009) PLoS ONE , vol.4 , pp. e5472
    • Nelis, M.1    Esko, T.2    Magi, R.3
  • 29
    • 84947461238 scopus 로고    scopus 로고
    • Genetic heritage of the balto-slavic speaking populations: A synthesis of autosomal, mitochondrial and Y-chromosomal data
    • Kushniarevich A, Utevska O, Chuhryaeva M et al: Genetic heritage of the balto-slavic speaking populations: a synthesis of autosomal, mitochondrial and Y-chromosomal data. PLoS ONE 2015; 10: e0135820.
    • (2015) PLoS ONE , vol.10 , pp. e0135820
    • Kushniarevich, A.1    Utevska, O.2    Chuhryaeva, M.3
  • 30
    • 84874691202 scopus 로고    scopus 로고
    • A genome-wide analysis of populations from European Russia reveals a new pole of genetic diversity in northern Europe
    • Khrunin AV, Khokhrin DV, Filippova IN et al: A genome-wide analysis of populations from European Russia reveals a new pole of genetic diversity in northern Europe. PLoS ONE 2013; 8: e58552.
    • (2013) PLoS ONE , vol.8 , pp. e58552
    • Khrunin, A.V.1    Khokhrin, D.V.2    Filippova, I.N.3
  • 31
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 32
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li H, Handsaker B, Wysoker A et al: The sequence alignment/map format and SAMtools. Bioinformatics 2009; 25: 2078-2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3
  • 33
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna A, Hanna M, Banks E et al: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20: 1297-1303.
    • (2010) Genome Res , vol.20 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3
  • 34
    • 84896009017 scopus 로고    scopus 로고
    • From FastQ data to high confidence variant calls: The Genome Analysis Toolkit best practices pipeline
    • 11.10.1-33
    • Van der Auwera GA, Carneiro MO, Hartl C et al: From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 2013; 43: 11.10.1-33.
    • (2013) Curr Protoc Bioinformatics , vol.43
    • Van Der Auwera, G.A.1    Carneiro, M.O.2    Hartl, C.3
  • 35
    • 84913546864 scopus 로고    scopus 로고
    • Toward better understanding of artifacts in variant calling from high-coverage samples
    • Li H: Toward better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics 2014; 30: 2843-2851.
    • (2014) Bioinformatics , vol.30 , pp. 2843-2851
    • Li, H.1
  • 36
    • 84871952176 scopus 로고    scopus 로고
    • Improved whole-chromosome phasing for disease and population genetic studies
    • Delaneau O, Zagury JF, Marchini J: Improved whole-chromosome phasing for disease and population genetic studies. Nat Methods 2013; 10: 5-6.
    • (2013) Nat Methods , vol.10 , pp. 5-6
    • Delaneau, O.1    Zagury, J.F.2    Marchini, J.3
  • 37
    • 84976331409 scopus 로고    scopus 로고
    • Fast and accurate long-range phasing in a UK Biobank cohort
    • Loh PR, Palamara PF, Price AL: Fast and accurate long-range phasing in a UK Biobank cohort. Nat Genet 2016; 48: 811-816.
    • (2016) Nat Genet , vol.48 , pp. 811-816
    • Loh, P.R.1    Palamara, P.F.2    Price, A.L.3
  • 38
    • 84989838868 scopus 로고    scopus 로고
    • Reference-based phasing using the Haplotype Reference Consortium panel
    • Loh P-R, Danecek P, Palamara PF et al: Reference-based phasing using the Haplotype Reference Consortium panel. Nat Genet 2016; 48: 1443-1448.
    • (2016) Nat Genet , vol.48 , pp. 1443-1448
    • Loh, P.-R.1    Danecek, P.2    Palamara, P.F.3
  • 40
    • 67651222400 scopus 로고    scopus 로고
    • A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    • Howie BN, Donnelly P, Marchini J: A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009; 5: e1000529.
    • (2009) PLoS Genet , vol.5 , pp. e1000529
    • Howie, B.N.1    Donnelly, P.2    Marchini, J.3
  • 41
    • 84973338712 scopus 로고    scopus 로고
    • The ensembl variant effect predictor
    • McLaren W, Gil L, Hunt SE et al: The ensembl variant effect predictor. Genome Biol 2016; 17: 122.
    • (2016) Genome Biol , vol.17 , pp. 122
    • McLaren, W.1    Gil, L.2    Hunt, S.E.3
  • 42
    • 84943759545 scopus 로고    scopus 로고
    • Cohort profile: Estonian biobank of the Estonian genome center, university of Tartu
    • Leitsalu L, Haller T, Esko T et al: Cohort Profile: Estonian Biobank of the Estonian Genome Center, University of Tartu. Int J Epidemiol 2015; 44: 1137-1147.
    • (2015) Int J Epidemiol , vol.44 , pp. 1137-1147
    • Leitsalu, L.1    Haller, T.2    Esko, T.3
  • 43
    • 84864417548 scopus 로고    scopus 로고
    • Fast and accurate genotype imputation in genome-wide association studies through pre-phasing
    • Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR: Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet 2012; 44: 955-959.
    • (2012) Nat Genet , vol.44 , pp. 955-959
    • Howie, B.1    Fuchsberger, C.2    Stephens, M.3    Marchini, J.4    Abecasis, G.R.5
  • 44
    • 84863845193 scopus 로고    scopus 로고
    • Genotype imputation with thousands of genomes
    • Howie B, Marchini J, Stephens M: Genotype imputation with thousands of genomes. G3 2011; 1: 457-470.
    • (2011) G3 , vol.1 , pp. 457-470
    • Howie, B.1    Marchini, J.2    Stephens, M.3
  • 45
    • 84954234248 scopus 로고    scopus 로고
    • Genotype imputation with millions of reference samples
    • Browning BL, Browning SR: Genotype imputation with millions of reference samples. Am J Hum Genet 2016; 98: 116-126.
    • (2016) Am J Hum Genet , vol.98 , pp. 116-126
    • Browning, B.L.1    Browning, S.R.2
  • 46
    • 78649508578 scopus 로고    scopus 로고
    • Mach: Using sequence and genotype data to estimate haplotypes and unobserved genotypes
    • Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR: MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 2010; 34: 816-834.
    • (2010) Genet Epidemiol , vol.34 , pp. 816-834
    • Li, Y.1    Willer, C.J.2    Ding, J.3    Scheet, P.4    Abecasis, G.R.5
  • 47
    • 84929432198 scopus 로고    scopus 로고
    • Loss-of-function variants in ABCA7 confer risk of Alzheimer's disease
    • Steinberg S, Stefansson H, Jonsson T et al: Loss-of-function variants in ABCA7 confer risk of Alzheimer's disease. Nat Genet 2015; 47: 445-447.
    • (2015) Nat Genet , vol.47 , pp. 445-447
    • Steinberg, S.1    Stefansson, H.2    Jonsson, T.3
  • 48
    • 84924363528 scopus 로고    scopus 로고
    • Genome of the Netherlands populationspecific imputations identify an ABCA6 variant associated with cholesterol levels
    • van Leeuwen EM, Karssen LC, Deelen J et al: Genome of The Netherlands populationspecific imputations identify an ABCA6 variant associated with cholesterol levels. Nat Commun 2015; 6: 6065.
    • (2015) Nat Commun , vol.6 , pp. 6065
    • Van Leeuwen, E.M.1    Karssen, L.C.2    Deelen, J.3
  • 49
    • 85009756476 scopus 로고    scopus 로고
    • Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms
    • Guo MH, Nandakumar SK, Ulirsch JC et al: Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms. Proc Natl Acad Sci USA 2017; 114: E327-E336.
    • (2017) Proc Natl Acad Sci USA , vol.114 , pp. E327-E336
    • Guo, M.H.1    Nandakumar, S.K.2    Ulirsch, J.C.3
  • 50
    • 85055643328 scopus 로고    scopus 로고
    • The rate of false polymorphisms introduced when imputing genotypes from global imputation panels
    • Surakka I, Sarin A-P, Ruotsalainen SE et al: The rate of false polymorphisms introduced when imputing genotypes from global imputation panels. bioRxiv 2016. Available at: https://doi.org/10.1101/080770.
    • (2016) BioRxiv
    • Surakka, I.1    Sarin, A.-P.2    Ruotsalainen, S.E.3


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