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Volumn 15, Issue 1, 2014, Pages

Variant calling in low-coverage whole genome sequencing of a Native American population sample

Author keywords

[No Author keywords available]

Indexed keywords

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; COHORT STUDIES; EXOME; GENE FREQUENCY; GENETIC VARIATION; GENOME, HUMAN; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INDIANS, NORTH AMERICAN; LINKAGE DISEQUILIBRIUM; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE; YOUNG ADULT;

EID: 84893173760     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-85     Document Type: Article
Times cited : (29)

References (33)
  • 1
    • 84969213492 scopus 로고    scopus 로고
    • Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
    • 10.1038/nature05911, 2719288, 17554300, The Wellcome Trust Case Control Consortium
    • The Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007, 447:661-678. 10.1038/nature05911, 2719288, 17554300, The Wellcome Trust Case Control Consortium.
    • (2007) Nature , vol.447 , pp. 661-678
  • 2
    • 67249117049 scopus 로고    scopus 로고
    • Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
    • 10.1073/pnas.0903103106, 2687147, 19474294
    • Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009, 106:9362-9367. 10.1073/pnas.0903103106, 2687147, 19474294.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 9362-9367
    • Hindorff, L.A.1    Sethupathy, P.2    Junkins, H.A.3    Ramos, E.M.4    Mehta, J.P.5    Collins, F.S.6    Manolio, T.A.7
  • 3
    • 84862909349 scopus 로고    scopus 로고
    • Five years of GWAS discovery
    • 10.1016/j.ajhg.2011.11.029, 3257326, 22243964
    • Visscher PM, Brown MA, McCarthy MI, Yang J. Five years of GWAS discovery. Am J Hum Genet 2012, 90:7-24. 10.1016/j.ajhg.2011.11.029, 3257326, 22243964.
    • (2012) Am J Hum Genet , vol.90 , pp. 7-24
    • Visscher, P.M.1    Brown, M.A.2    McCarthy, M.I.3    Yang, J.4
  • 8
    • 78649508578 scopus 로고    scopus 로고
    • MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
    • 10.1002/gepi.20533, 3175618, 21058334
    • 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. 10.1002/gepi.20533, 3175618, 21058334.
    • (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
  • 9
    • 79957951017 scopus 로고    scopus 로고
    • Low-coverage sequencing: implications for design of complex trait association studies
    • 10.1101/gr.117259.110, 3106327, 21460063
    • Li Y, Sidore C, Kang HM, Boehnke M, Abecasis GR. Low-coverage sequencing: implications for design of complex trait association studies. Genome Res 2011, 21:940-951. 10.1101/gr.117259.110, 3106327, 21460063.
    • (2011) Genome Res , vol.21 , pp. 940-951
    • Li, Y.1    Sidore, C.2    Kang, H.M.3    Boehnke, M.4    Abecasis, G.R.5
  • 10
    • 3042824767 scopus 로고    scopus 로고
    • The clinical course of alcoholism in 243 Mission Indians
    • 10.1176/appi.ajp.161.7.1204, 15229052
    • Ehlers CL, Wall TL, Betancourt M, Gilder DA. The clinical course of alcoholism in 243 Mission Indians. Am J Psychiatry 2004, 161:1204-1210. 10.1176/appi.ajp.161.7.1204, 15229052.
    • (2004) Am J Psychiatry , vol.161 , pp. 1204-1210
    • Ehlers, C.L.1    Wall, T.L.2    Betancourt, M.3    Gilder, D.A.4
  • 11
    • 33847302950 scopus 로고    scopus 로고
    • Genomic screen for substance dependence and body mass index in southwest California Indians
    • 10.1111/j.1601-183X.2006.00246.x, 16764678
    • Ehlers CL, Wilhelmsen KC. Genomic screen for substance dependence and body mass index in southwest California Indians. Genes Brain Behav 2007, 6:184-191. 10.1111/j.1601-183X.2006.00246.x, 16764678.
    • (2007) Genes Brain Behav , vol.6 , pp. 184-191
    • Ehlers, C.L.1    Wilhelmsen, K.C.2
  • 15
    • 0036948344 scopus 로고    scopus 로고
    • Enhanced pedigree error detection
    • 10.1159/000067666, 12566741
    • Sun L, Wilder K, McPeek MS. Enhanced pedigree error detection. Hum Hered 2002, 54:99-110. 10.1159/000067666, 12566741.
    • (2002) Hum Hered , vol.54 , pp. 99-110
    • Sun, L.1    Wilder, K.2    McPeek, M.S.3
  • 16
    • 2942655651 scopus 로고    scopus 로고
    • Best linear unbiased allele-frequency estimation in complex pedigrees
    • 10.1111/j.0006-341X.2004.00180.x, 15180661
    • McPeek MS, Wu X, Ober C. Best linear unbiased allele-frequency estimation in complex pedigrees. Biometrics 2004, 60:359-367. 10.1111/j.0006-341X.2004.00180.x, 15180661.
    • (2004) Biometrics , vol.60 , pp. 359-367
    • McPeek, M.S.1    Wu, X.2    Ober, C.3
  • 17
    • 34547756415 scopus 로고    scopus 로고
    • Case-control association testing with related individuals: a more powerful quasi-likelihood score test
    • 10.1086/519497, 1950805, 17668381
    • Thornton T, McPeek MS. Case-control association testing with related individuals: a more powerful quasi-likelihood score test. Am J Hum Genet 2007, 81:321-337. 10.1086/519497, 1950805, 17668381.
    • (2007) Am J Hum Genet , vol.81 , pp. 321-337
    • Thornton, T.1    McPeek, M.S.2
  • 18
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • 10.1038/nature11632, 3498066, 23128226, The 1000 Genomes Project Consortium
    • Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA, The 1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes. Nature 2012, 491:56-65. 10.1038/nature11632, 3498066, 23128226, The 1000 Genomes Project Consortium.
    • (2012) Nature , vol.491 , pp. 56-65
    • Abecasis, G.R.1    Auton, A.2    Brooks, L.D.3    DePristo, M.A.4    Durbin, R.M.5    Handsaker, R.E.6    Kang, H.M.7    Marth, G.T.8    McVean, G.A.9
  • 19
    • 67149095078 scopus 로고    scopus 로고
    • Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip
    • Spencer CCA, Su Z, Donnelly P, Marchini J. Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet 2009, 5:13.
    • (2009) PLoS Genet , vol.5 , pp. 13
    • Spencer, C.C.A.1    Su, Z.2    Donnelly, P.3    Marchini, J.4
  • 20
    • 50949095168 scopus 로고    scopus 로고
    • Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data
    • 10.1016/j.ajhg.2008.06.024, 2842185, 18691683
    • Li B, Leal SM. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 2008, 83:311-321. 10.1016/j.ajhg.2008.06.024, 2842185, 18691683.
    • (2008) Am J Hum Genet , vol.83 , pp. 311-321
    • Li, B.1    Leal, S.M.2
  • 21
    • 80052731371 scopus 로고    scopus 로고
    • A general framework for detecting disease associations with rare variants in sequencing studies
    • 10.1016/j.ajhg.2011.07.015, 3169821, 21885029
    • Lin D-Y, Tang Z-Z. A general framework for detecting disease associations with rare variants in sequencing studies. Am J Hum Genet 2011, 89:354-367. 10.1016/j.ajhg.2011.07.015, 3169821, 21885029.
    • (2011) Am J Hum Genet , vol.89 , pp. 354-367
    • Lin, D.-Y.1    Tang, Z.-Z.2
  • 24
    • 0003992773 scopus 로고    scopus 로고
    • Respondent-driven sampling: a New approach to the study of hidden populations
    • Heckathorn DD. Respondent-driven sampling: a New approach to the study of hidden populations. Soc Probl 1997, 44:174-199.
    • (1997) Soc Probl , vol.44 , pp. 174-199
    • Heckathorn, D.D.1
  • 25
    • 3042824767 scopus 로고    scopus 로고
    • The clinical course of alcoholism in 243 mission indians
    • 10.1176/appi.ajp.161.7.1204, 15229052
    • Ehlers CL. The clinical course of alcoholism in 243 mission indians. Am J Psychiatry 2004, 161:1204-1210. 10.1176/appi.ajp.161.7.1204, 15229052.
    • (2004) Am J Psychiatry , vol.161 , pp. 1204-1210
    • Ehlers, C.L.1
  • 29
    • 84895111835 scopus 로고    scopus 로고
    • GATK | Best practices
    • GATK | Best practices. http://www.broadinstitute.org/gatk/guide/topic?name=best-practices.
  • 31
    • 84895115210 scopus 로고    scopus 로고
    • Samtools-hybrid - genome analysis wiki
    • Samtools-hybrid - genome analysis wiki. http://genome.sph.umich.edu/wiki/Samtools-hybrid.
  • 32
    • 35348817330 scopus 로고    scopus 로고
    • Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
    • 10.1086/521987, 2265661, 17924348
    • Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 2007, 81:1084-1097. 10.1086/521987, 2265661, 17924348.
    • (2007) Am J Hum Genet , vol.81 , pp. 1084-1097
    • Browning, S.R.1    Browning, B.L.2
  • 33
    • 84895186171 scopus 로고    scopus 로고
    • UMAKE - genome analysis wiki
    • UMAKE - genome analysis wiki. http://genome.sph.umich.edu/wiki/UMAKE.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.