메뉴 건너뛰기




Volumn 27, Issue 21, 2011, Pages 2987-2993

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; DNA SEQUENCE; GENE FREQUENCY; GENETIC ASSOCIATION; GENOTYPE; HUMAN; METHODOLOGY; MUTATION; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

EID: 80054915847     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr509     Document Type: Article
Times cited : (4356)

References (38)
  • 1
    • 84975742565 scopus 로고
    • A map of human genome variation from population-scale sequencing
    • Genomes Project Consortium (2010)
    • 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
    • (1000) Nature , vol.467 , pp. 1061-1073
    • Jayanthi, J.1
  • 2
    • 80051732262 scopus 로고    scopus 로고
    • Accurate and comprehensive sequencing of personal genomes
    • Ajay,S.S. et al. (2011) Accurate and comprehensive sequencing of personal genomes. Genome Res., 21, 1498-1505.
    • (2011) Genome Res , vol.21 , pp. 1498-1505
    • Ajay, S.S.1
  • 3
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley,D.R. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1
  • 5
    • 71149112981 scopus 로고    scopus 로고
    • Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genomewide association studies
    • Browning,B.L. and Yu,Z. (2009) Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genomewide association studies. Am. J. Hum. Genet., 85, 847-861.
    • (2009) Am. J. Hum. Genet. , vol.85 , pp. 847-861
    • Browning, B.L.1    Yu, Z.2
  • 6
    • 79959725029 scopus 로고    scopus 로고
    • Variation in genome-wide mutation rates within and between human families
    • Conrad,D. et al. (2011) Variation in genome-wide mutation rates within and between human families. Nat. Genet., 43, 712-714.
    • (2011) Nat. Genet. , vol.43 , pp. 712-714
    • Conrad, D.1
  • 7
    • 79960405019 scopus 로고    scopus 로고
    • The variant call format and vcftools
    • Danecek,P. et al. (2011) The variant call format and vcftools. Bioinformatics, 27, 2156-2158.
    • (2011) Bioinformatics , vol.27 , pp. 2156-2158
    • Danecek, P.1
  • 8
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • Depristo,M.A. et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet., 43, 491-498.
    • (2011) Nat. Genet. , vol.43 , pp. 491-498
    • Depristo, M.A.1
  • 9
    • 74949138753 scopus 로고    scopus 로고
    • Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays
    • Drmanac,R. et al. (2010) Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science, 327, 78-81.
    • (2010) Science , vol.327 , pp. 78-81
    • Drmanac, R.1
  • 10
    • 0003516147 scopus 로고    scopus 로고
    • Cambridge University Press, Cambridge, UK
    • Durbin,R. et al. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge, UK.
    • (1998) Biological Sequence Analysis
    • Durbin, R.1
  • 11
    • 0029130796 scopus 로고
    • Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population
    • Excoffier,L. and Slatkin,M. (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol., 12, 921-927.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 921-927
    • Excoffier, L.1    Slatkin, M.2
  • 12
    • 74249110768 scopus 로고    scopus 로고
    • Human triallelic sites: evidence for a new mutational mechanism?
    • Hodgkinson,A. and Eyre-Walker,A. (2010) Human triallelic sites: evidence for a new mutational mechanism? Genetics, 184, 233-241.
    • (2010) Genetics , vol.184 , pp. 233-241
    • Hodgkinson, A.1    Eyre-Walker, A.2
  • 13
    • 67651222400 scopus 로고    scopus 로고
    • A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    • Howie,B.N. et al. (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet., 5, e1000529.
    • (2009) PLoS Genet , vol.5
    • Howie, B.N.1
  • 14
    • 77954198372 scopus 로고    scopus 로고
    • Design of association studies with pooled or un-pooled nextgeneration sequencing data
    • Kim,S.Y. et al. (2010) Design of association studies with pooled or un-pooled nextgeneration sequencing data. Genet. Epidemiol., 34, 479-491.
    • (2010) Genet. Epidemiol. , vol.34 , pp. 479-491
    • Kim, S.Y.1
  • 15
    • 79958078775 scopus 로고    scopus 로고
    • Estimation of allele frequency and association mapping using next-generation sequencing data
    • Kim,S.Y. et al. (2011) Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics, 12, 231.
    • (2011) BMC Bioinformatics , vol.12 , pp. 231
    • Kim, S.Y.1
  • 16
    • 79957950801 scopus 로고    scopus 로고
    • SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
    • Le,S.Q. and Durbin,R. (2010) SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res., 21, 952-960.
    • (2010) Genome Res , vol.21 , pp. 952-960
    • Le, S.Q.1    Durbin, R.2
  • 17
    • 55549101623 scopus 로고    scopus 로고
    • DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome
    • Ley,T. J. et al. (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature, 456, 66-72.
    • (2008) Nature , vol.456 , pp. 66-72
    • Ley, T.J.1
  • 18
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with burrowswheeler transform
    • Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with burrowswheeler transform. Bioinformatics, 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 19
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with burrows-wheeler transform
    • Li,H. and Durbin,R. (2010) Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics, 26, 589-595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 20
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li,H. et al. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1
  • 21
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and samtools
    • Li,H. et al. (2009a) The sequence alignment/map format and samtools. Bioinformatics, 25, 2078-2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 22
    • 79954553212 scopus 로고    scopus 로고
    • Improving SNP discovery by base alignment quality
    • Li,H. (2011) Improving SNP discovery by base alignment quality. Bioinformatics, 27, 1157-1158.
    • (2011) Bioinformatics , vol.27 , pp. 1157-1158
    • Li, H.1
  • 23
  • 24
    • 78649508578 scopus 로고    scopus 로고
    • MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
    • Li,Y. et al. (2010a) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet. Epidemiol., 34, 816-834.
    • (2010) Genet. Epidemiol. , vol.34 , pp. 816-834
    • Li, Y.1
  • 25
    • 78049323331 scopus 로고    scopus 로고
    • Resequencing of 200 human exomes identifies an excess of lowfrequency non-synonymous coding variants
    • Li,Y. et al. (2010b) Resequencing of 200 human exomes identifies an excess of lowfrequency non-synonymous coding variants. Nat. Genet., 42, 969-972.
    • (2010) Nat. Genet. , vol.42 , pp. 969-972
    • Li, Y.1
  • 26
    • 79957951017 scopus 로고    scopus 로고
    • Low-coverage sequencing: Implications for design of complex trait association studies
    • Li,Y. et al. (2011) Low-coverage sequencing: Implications for design of complex trait association studies. Genome Res., 21, 940-951.
    • (2011) Genome Res , vol.21 , pp. 940-951
    • Li, Y.1
  • 27
    • 70149093912 scopus 로고    scopus 로고
    • Recurring mutations found by sequencing an acute myeloid leukemia genome
    • Mardis,E.R. et al. (2009) Recurring mutations found by sequencing an acute myeloid leukemia genome. N. Engl. J. Med., 361, 1058-1066.
    • (2009) N. Engl. J. Med. , vol.361 , pp. 1058-1066
    • Mardis, E.R.1
  • 28
    • 78149246036 scopus 로고    scopus 로고
    • SeqEM: an adaptive genotype-calling approach for nextgeneration sequencing studies
    • Martin,E.R. et al. (2010) SeqEM: an adaptive genotype-calling approach for nextgeneration sequencing studies. Bioinformatics, 26, 2803-2810.
    • (2010) Bioinformatics , vol.26 , pp. 2803-2810
    • Martin, E.R.1
  • 29
    • 80052226692 scopus 로고    scopus 로고
    • Sequence-specific error profile of illumina sequencers
    • Nakamura,K. et al. (2011) Sequence-specific error profile of illumina sequencers. Nucleic Acids Res., 39, e90.
    • (2011) Nucleic Acids Res , vol.39
    • Nakamura, K.1
  • 30
    • 79956314887 scopus 로고    scopus 로고
    • Genotype and SNP calling from next-generation sequencing data
    • Nielsen,R. et al. (2011) Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet., 12, 443-451.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 443-451
    • Nielsen, R.1
  • 31
    • 54949108148 scopus 로고    scopus 로고
    • Enredo and pecan: genome-wide mammalian consistency-based multiple alignment with paralogs
    • Paten,B. et al. (2008) Enredo and pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res., 18, 1814-1828.
    • (2008) Genome Res , vol.18 , pp. 1814-1828
    • Paten, B.1
  • 32
    • 74449093973 scopus 로고    scopus 로고
    • A comprehensive catalogue of somatic mutations from a human cancer genome
    • Pleasance,E.D. et al. (2010a) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, 463, 191-196.
    • (2010) Nature , vol.463 , pp. 191-196
    • Pleasance, E.D.1
  • 33
    • 74449085934 scopus 로고    scopus 로고
    • Asmall-cell lung cancer genome with complex signatures of tobacco exposure
    • Pleasance,E.D. et al. (2010b)Asmall-cell lung cancer genome with complex signatures of tobacco exposure. Nature, 463, 184-190.
    • (2010) Nature , vol.463 , pp. 184-190
    • Pleasance, E.D.1
  • 34
    • 77951799158 scopus 로고    scopus 로고
    • Analysis of genetic inheritance in a family quartet by wholegenome sequencing
    • Roach,J.C. et al. (2010) Analysis of genetic inheritance in a family quartet by wholegenome sequencing. Science, 328, 636-639.
    • (2010) Science , vol.328 , pp. 636-639
    • Roach, J.C.1
  • 35
    • 77957252585 scopus 로고    scopus 로고
    • Application of second-generation sequencing to cancer genomics
    • Robison,K. (2010) Application of second-generation sequencing to cancer genomics. Brief. Bioinformatics, 11, 524-534.
    • (2010) Brief. Bioinformatics , vol.11 , pp. 524-534
    • Robison, K.1
  • 36
    • 0036155283 scopus 로고    scopus 로고
    • Score tests for association between traits and haplotypes when linkage phase is ambiguous
    • Schaid,D.J. et al. (2002) Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am. J. Hum. Genet., 70, 425-434.
    • (2002) Am. J. Hum. Genet. , vol.70 , pp. 425-434
    • Schaid, D.J.1
  • 37
    • 70349969478 scopus 로고    scopus 로고
    • Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
    • Shah,S.P. et al. (2009) Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 461, 809-813.
    • (2009) Nature , vol.461 , pp. 809-813
    • Shah, S.P.1
  • 38
    • 77954319020 scopus 로고    scopus 로고
    • Sequencing of 50 human exomes reveals adaptation to high altitude
    • Yi,X. et al. (2010) Sequencing of 50 human exomes reveals adaptation to high altitude. Science, 329, 75-78.
    • (2010) Science , vol.329 , pp. 75-78
    • Yi, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.