메뉴 건너뛰기




Volumn 28, Issue 13, 2012, Pages 1745-1751

Seqchip: A powerful method to integrate sequence and genotype data for the detection of rare variant associations

Author keywords

[No Author keywords available]

Indexed keywords

ADENOMA; ARTICLE; CASE CONTROL STUDY; COLORECTAL TUMOR; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENETICS; GENOTYPE; HUMAN; METHODOLOGY; PHENOTYPE;

EID: 84863995321     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts263     Document Type: Article
Times cited : (5)

References (39)
  • 1
    • 34147154100 scopus 로고    scopus 로고
    • Medical sequencing at the extremes of human body mass
    • Ahituv, N. et al. (2007) Medical sequencing at the extremes of human body mass. Am. J. Hum. Genet., 80, 779-791.
    • (2007) Am. J. Hum. Genet. , vol.80 , pp. 779-791
    • Ahituv, N.1
  • 2
    • 80054728031 scopus 로고    scopus 로고
    • Comparison of statistical tests for disease association with rare variants
    • Basu, S. and Pan, W. (2011) Comparison of statistical tests for disease association with rare variants. Genet. Epidemiol., 35, 606-619.
    • (2011) Genet. Epidemiol. , vol.35 , pp. 606-619
    • Basu, S.1    Pan, W.2
  • 3
    • 78349264203 scopus 로고    scopus 로고
    • A covering method for detecting genetic associations between rare variants and common phenotypes
    • Bhatia, G. et al. (2010) A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput. Biol., 6, e1000954.
    • (2010) PLoS Comput. Biol. , vol.6
    • Bhatia, G.1
  • 4
    • 44349132708 scopus 로고    scopus 로고
    • Common and rare variants in multifactorial susceptibility to common diseases
    • Bodmer, W. and Bonilla, C. (2008) Common and rare variants in multifactorial susceptibility to common diseases. Nat. Genet., 40, 695-701.
    • (2008) Nat. Genet. , vol.40 , pp. 695-701
    • Bodmer, W.1    Bonilla, C.2
  • 5
    • 3843056691 scopus 로고    scopus 로고
    • Multiple rare alleles contribute to low plasma levels of HDL cholesterol
    • Cohen, J.C. et al. (2004) Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science, 305, 869-872.
    • (2004) Science , vol.305 , pp. 869-872
    • Cohen, J.C.1
  • 6
    • 32444441330 scopus 로고    scopus 로고
    • Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels
    • Cohen, J.C. et al. (2006) Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels. Proc. Natl Acad. Sci. USA, 103, 1810-1815.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 1810-1815
    • Cohen, J.C.1
  • 7
    • 79960408008 scopus 로고    scopus 로고
    • Enriching targeted sequencing experiments for rare disease alleles
    • Edwards, T.L. et al. (2010) Enriching targeted sequencing experiments for rare disease alleles. Bioinformatics, 27, 2112-2118.
    • (2010) Bioinformatics , vol.27 , pp. 2112-2118
    • Edwards, T.L.1
  • 8
    • 8644235804 scopus 로고    scopus 로고
    • Multiple rare variants in different genes account for multifactorial inherited susceptibility to colorectal adenomas
    • Fearnhead, N.S. et al. (2004) Multiple rare variants in different genes account for multifactorial inherited susceptibility to colorectal adenomas. Proc. Natl Acad. Sci. USA, 101, 15992-15997.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 15992-15997
    • Fearnhead, N.S.1
  • 9
    • 13144305057 scopus 로고    scopus 로고
    • The APC variants I1307K and E1317Q are associated with colorectal tumors, but not always with a family history
    • Frayling, I.M. et al. (1998) The APC variants I1307K and E1317Q are associated with colorectal tumors, but not always with a family history. Proc. Natl Acad. Sci. USA, 95, 10722-10727.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 10722-10727
    • Frayling, I.M.1
  • 10
    • 58149175796 scopus 로고    scopus 로고
    • Practical issues in imputation-based association mapping
    • Guan, Y. and Stephens, M. (2008) Practical issues in imputation-based association mapping. PLoS Genet., 4, e1000279.
    • (2008) PLoS Genet , vol.4
    • Guan, Y.1    Stephens, M.2
  • 11
    • 77951028197 scopus 로고    scopus 로고
    • Adata-adaptive sum test for disease association with multiple common or rare variants
    • Han, F. and Pan, W. (2010)Adata-adaptive sum test for disease association with multiple common or rare variants. Hum. Hered., 70, 42-54.
    • (2010) Hum. Hered. , vol.70 , pp. 42-54
    • Han, F.1    Pan, W.2
  • 12
    • 79952253512 scopus 로고    scopus 로고
    • A new testing strategy to identify rare variants with either risk or protective effect on disease
    • Ionita-Laza, I. et al. (2011) A new testing strategy to identify rare variants with either risk or protective effect on disease. PLoS Genet., 7, e1001289.
    • (2011) PLoS Genet , vol.7
    • Ionita-Laza, I.1
  • 13
    • 42649084334 scopus 로고    scopus 로고
    • Rare independent mutations in renal salt handling genes contribute to blood pressure variation
    • Ji, W. et al. (2008) Rare independent mutations in renal salt handling genes contribute to blood pressure variation. Nat. Genet., 40, 592-599.
    • (2008) Nat. Genet. , vol.40 , pp. 592-599
    • Ji, W.1
  • 14
    • 0033931066 scopus 로고    scopus 로고
    • The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal cancer patients in Korea
    • Kim, H.C. et al. (2000) The E-cadherin gene (CDH1) variants T340A and L599V in gastric and colorectal cancer patients in Korea. Gut, 47, 262-267.
    • (2000) Gut , vol.47 , pp. 262-267
    • Kim, H.C.1
  • 15
    • 34147116715 scopus 로고    scopus 로고
    • Most rare missense alleles are deleterious in humans: implications for complex disease and association studies
    • Kryukov, G.V. et al. (2007) Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am. J. Hum. Genet., 80, 727-739.
    • (2007) Am. J. Hum. Genet. , vol.80 , pp. 727-739
    • Kryukov, G.V.1
  • 16
    • 62649084535 scopus 로고    scopus 로고
    • Power of deep, all-exon resequencing for discovery of human trait genes
    • Kryukov, G.V. et al. (2009) Power of deep, all-exon resequencing for discovery of human trait genes. Proc. Natl Acad. Sci. USA, 106, 3871-3876.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 3871-3876
    • Kryukov, G.V.1
  • 17
    • 84859171835 scopus 로고    scopus 로고
    • The empirical power of rare variant association methods: results from sanger sequencing in 1,998 individuals
    • Ladouceur, M. et al. (2012) The empirical power of rare variant association methods: results from sanger sequencing in 1, 998 individuals. PLoS Genet., 8, e1002496.
    • (2012) PLoS Genet , vol.8
    • Ladouceur, M.1
  • 18
    • 0034703393 scopus 로고    scopus 로고
    • Germline APC variants in patients with multiple colorectal adenomas, with evidence for the particular importance of E1317Q
    • Lamlum, H. et al. (2000) Germline APC variants in patients with multiple colorectal adenomas, with evidence for the particular importance of E1317Q. Hum. Mol. Genet., 9, 2215-2221.
    • (2000) Hum. Mol. Genet. , vol.9 , pp. 2215-2221
    • Lamlum, H.1
  • 19
    • 67149117126 scopus 로고    scopus 로고
    • Discovery of rare variants via sequencing: implications for the design of complex trait association studies
    • Li, B. and Leal, S.M. (2009) Discovery of rare variants via sequencing: implications for the design of complex trait association studies. PLoS Genet., 5, e1000481.
    • (2009) PLoS Genet , vol.5
    • Li, B.1    Leal, S.M.2
  • 20
    • 78649508578 scopus 로고    scopus 로고
    • MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
    • Li, Y. et al. (2010) 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
  • 21
    • 66249126496 scopus 로고    scopus 로고
    • Proper analysis of secondary phenotype data in casecontrol association studies
    • Lin, D.Y. and Zeng, D. (2009) Proper analysis of secondary phenotype data in casecontrol association studies. Genet. Epidemiol., 33, 256-265.
    • (2009) Genet. Epidemiol. , vol.33 , pp. 256-265
    • Lin, D.Y.1    Zeng, D.2
  • 22
    • 0037387832 scopus 로고    scopus 로고
    • Germline mutations in the TGF-beta and Wnt signalling pathways are a rare cause of the "multiple" adenoma phenotype
    • Lipton, L. et al. (2003) Germline mutations in the TGF-beta and Wnt signalling pathways are a rare cause of the "multiple" adenoma phenotype. J. Med. Genet., 40, e35.
    • (2003) J. Med. Genet. , vol.40
    • Lipton, L.1
  • 23
    • 78449245227 scopus 로고    scopus 로고
    • A novel adaptive method for the analysis of nextgeneration sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions
    • Liu, D.J. and Leal, S.M. (2010a) A novel adaptive method for the analysis of nextgeneration sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions. PLoS Genet., 6, e1001156.
    • (2010) PLoS Genet , vol.6
    • Liu, D.J.1    Leal, S.M.2
  • 24
    • 78649775312 scopus 로고    scopus 로고
    • Replication strategies for rare variant complex trait association studies via next-generation sequencing
    • Liu, D.J. and Leal, S.M. (2010b) Replication strategies for rare variant complex trait association studies via next-generation sequencing. Am. J. Hum. Genet., 87, 790-801.
    • (2010) Am. J. Hum. Genet. , vol.87 , pp. 790-801
    • Liu, D.J.1    Leal, S.M.2
  • 25
    • 84858337563 scopus 로고    scopus 로고
    • Aflexible likelihood framework for detecting associations with secondary phenotypes in genetic studies using selected samples: application to sequence data
    • Liu, D.J. and Leal, S.M. (2011)Aflexible likelihood framework for detecting associations with secondary phenotypes in genetic studies using selected samples: application to sequence data. Eur. J. Hum. Genet., 20, 449-456.
    • (2011) Eur. J. Hum. Genet. , vol.20 , pp. 449-456
    • Liu, D.J.1    Leal, S.M.2
  • 26
    • 78650854718 scopus 로고    scopus 로고
    • Three ways of combining genotyping and resequencing in case-control association studies
    • Longmate, J.A. et al. (2010) Three ways of combining genotyping and resequencing in case-control association studies. PLoS ONE, 5, e14318.
    • (2010) PLoS ONE , vol.5
    • Longmate, J.A.1
  • 27
    • 61449168010 scopus 로고    scopus 로고
    • Agroupwise association test for rare mutations using a weighted sum statistic
    • Madsen, B.E. and Browning, S.R. (2009)Agroupwise association test for rare mutations using a weighted sum statistic. PLoS Genet., 5, e1000384.
    • (2009) PLoS Genet , vol.5
    • Madsen, B.E.1    Browning, S.R.2
  • 28
    • 76649136928 scopus 로고    scopus 로고
    • An evaluation of statistical approaches to rare variant analysis in genetic association studies
    • Morris, A.P. and Zeggini, E. (2010)An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet. Epidemiol., 34, 188-193.
    • (2010) Genet. Epidemiol. , vol.34 , pp. 188-193
    • Morris, A.P.1    Zeggini, E.2
  • 29
    • 4143145303 scopus 로고    scopus 로고
    • Meta-analysis of genetic association studies
    • Munafo, M.R. and Flint, J. (2004) Meta-analysis of genetic association studies. Trends Genet., 20, 439-444.
    • (2004) Trends Genet , vol.20 , pp. 439-444
    • Munafo, M.R.1    Flint, J.2
  • 30
    • 79953752624 scopus 로고    scopus 로고
    • Testing for an unusual distribution of rare variants
    • Neale, B.M. et al. (2011) Testing for an unusual distribution of rare variants. PLoS Genet., 7, e1001322.
    • (2011) PLoS Genet , vol.7
    • Neale, B.M.1
  • 31
    • 77953121877 scopus 로고    scopus 로고
    • Pooled association tests for rare variants in exon-resequencing studies
    • Price, A.L. et al. (2010) Pooled association tests for rare variants in exon-resequencing studies. Am. J. Hum. Genet., 86, 832-838.
    • (2010) Am. J. Hum. Genet. , vol.86 , pp. 832-838
    • Price, A.L.1
  • 32
    • 82255162545 scopus 로고    scopus 로고
    • A rare penetrant mutation in CFH confers high risk of age-related macular degeneration
    • Raychaudhuri, S. et al. (2011) A rare penetrant mutation in CFH confers high risk of age-related macular degeneration. Nat. Genet., 43, 1232-1236.
    • (2011) Nat. Genet. , vol.43 , pp. 1232-1236
    • Raychaudhuri, S.1
  • 33
    • 80054975975 scopus 로고    scopus 로고
    • Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease
    • Rivas, M.A. et al. (2011) Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat. Genet., 43, 1066-1073.
    • (2011) Nat. Genet. , vol.43 , pp. 1066-1073
    • Rivas, M.A.1
  • 34
    • 34047177395 scopus 로고    scopus 로고
    • Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL
    • Romeo, S. et al. (2007) Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat. Genet., 39, 513-516.
    • (2007) Nat. Genet. , vol.39 , pp. 513-516
    • Romeo, S.1
  • 35
    • 61749090233 scopus 로고    scopus 로고
    • Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans
    • Romeo, S. et al. (2009) Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans. J. Clin. Invest., 119, 70-79.
    • (2009) J. Clin. Invest. , vol.119 , pp. 70-79
    • Romeo, S.1
  • 36
    • 79960943621 scopus 로고    scopus 로고
    • Fine mapping of five loci associated with low-density lipoprotein cholesterol detects variants that double the explained heritability
    • Sanna, S. et al. (2011) Fine mapping of five loci associated with low-density lipoprotein cholesterol detects variants that double the explained heritability. PLoS Genet., 7, e1002198.
    • (2011) PLoS Genet , vol.7
    • Sanna, S.1
  • 37
    • 80051499915 scopus 로고    scopus 로고
    • Rare-variant association testing for sequencing data with the sequence kernel association test
    • Wu, M.C. et al. (2011) Rare-variant association testing for sequencing data with the sequence kernel association test. Am. J. Hum. Genet., 89, 82-93.
    • (2011) Am. J. Hum. Genet. , vol.89 , pp. 82-93
    • Wu, M.C.1
  • 38
    • 78249243049 scopus 로고    scopus 로고
    • Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes
    • Zawistowski, M. et al. (2010) Extending rare-variant testing strategies: analysis of noncoding sequence and imputed genotypes. Am. J. Hum. Genet., 87, 604-617.
    • (2010) Am. J. Hum. Genet. , vol.87 , pp. 604-617
    • Zawistowski, M.1
  • 39
    • 78751490178 scopus 로고    scopus 로고
    • Acomparison of approaches to account for uncertainty in analysis of imputed genotypes
    • Zheng, J. et al. (2011)Acomparison of approaches to account for uncertainty in analysis of imputed genotypes. Genet. Epidemiol., 35, 102-110.
    • (2011) Genet. Epidemiol. , vol.35 , pp. 102-110
    • Zheng, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.