publication . Article . 2016

Incorporating ENCODE information into association analysis of whole genome sequencing data

Taebeom Kim; Peng Wei;
Open Access English
  • Published: 01 Oct 2016 Journal: BMC Proceedings, volume 10, issue Suppl 7, pages 257-261 (eissn: 1753-6561, Copyright policy)
  • Publisher: BioMed Central
With the rapidly decreasing cost of the next-generation sequencing technology, a large number of whole genome sequences have been generated, enabling researchers to survey rare variants in the protein-coding and regulatory regions of the genome. However, it remains a daunting task to identify functional variants associated with complex diseases from whole genome sequencing (WGS) data because of the millions of candidate variants and yet moderate sample size. We propose to incorporate the Encyclopedia of DNA Elements (ENCODE) information in the association analysis of WGS data to boost the statistical power. We use the RegulomeDB and PolyPhen2 scores as external ...
free text keywords: Proceedings, Whole genome sequencing, ENCODE, Locus (genetics), Genetics, Genetic association, Gene, Genome, Nonsynonymous substitution, Bioinformatics, Exome sequencing, Biology
Funded by
NIH| Genetic Susceptibility and Risk Model for Pancreatic Cancer
  • Funder: National Institutes of Health (NIH)
  • Project Code: 4R01CA169122-04
NIH| Genetic Analysis of Common Diseases: An Evaluation
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
NIH| Association analysis of rare variants with sequencing data
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HL116720-05
NIH| Genome-wide gene-by-smoking interaction analysis of pulmonary function
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R21HL126032-01
17 references, page 1 of 2

Manolio, TA, Collins, FS, Cox, NJ, Goldstein, DB, Hindorff, LA, Hunter, DJ, McCarthy, MI, Ramos, EM, Cardon, LR, Chakravarti, A. Finding the missing heritability of complex diseases. Nature. 2009; 461 (7265): 747-53 [OpenAIRE] [PubMed] [DOI]

Lee, S, Abecasis, GR, Boehnke, M, Lin, X. Rare-variant association analysis: study designs and statistical tests. Am J Hum Genet. 2014; 95 (1): 5-23 [OpenAIRE] [PubMed] [DOI]

Wu, MC, Lee, S, Cai, T, Li, Y, Boehnke, M, Lin, X. Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet. 2011; 89 (1): 82-93 [OpenAIRE] [PubMed] [DOI]

Pan, W, Kim, J, Zhang, Y, Shen, X, Wei, P. A powerful and adaptive association test for rare variants. Genetics. 2014; 197 (4): 1081-95 [OpenAIRE] [PubMed] [DOI]

Morrison, AC, Voorman, A, Johnson, AD, Liu, X, Yu, J, Li, A, Muzny, D, Yu, F, Rice, K, Zhu, C. Whole-genome sequence-based analysis of high-density lipoprotein cholesterol. Nat Genet. 2013; 45 (8): 899-901 [OpenAIRE] [PubMed] [DOI]

Adzhubei, IA, Schmidt, S, Peshkin, L, Ramensky, VE, Gerasimova, A, Bork, P, Kondrashov, AS, Sunyaev, SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010; 7 (4): 248-9 [OpenAIRE] [PubMed] [DOI]

Hu, H, Huff, CD, Moore, B, Flygare, S, Reese, MG, Yandell, M. VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix. Genet Epidemiol. 2013; 37 (6): 622-34 [OpenAIRE] [PubMed] [DOI]

Price, AL, Kryukov, GV, de Bakker, PI, Purcell, SM, Staples, J, Wei, LJ, Sunyaev, SR. Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet. 2010; 86 (6): 832-8 [OpenAIRE] [PubMed] [DOI]

Wei, P, Liu, X, Fu, YX. Incorporating predicted functions of nonsynonymous variants into gene-based analysis of exome sequencing data: a comparative study. BMC Proc. 2011; 5 (Suppl 9): S20 [DOI]

Kellis, M, Wold, B, Snyder, MP, Bernstein, BE, Kundaje, A, Marinov, GK, Ward, LD, Birney, E, Crawford, GE, Dekker, J. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014; 111 (17): 6131-8 [OpenAIRE] [PubMed] [DOI]

Maurano, MT, Humbert, R, Rynes, E, Thurman, RE, Haugen, E, Wang, H, Reynolds, AP, Sandstrom, R, Qu, H, Brody, J. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012; 337 (6099): 1190-5 [OpenAIRE] [PubMed] [DOI]

Boyle, AP, Hong, EL, Hariharan, M, Cheng, Y, Schaub, MA, Kasowski, M, Karczewski, KJ, Park, J, Hitz, BC, Weng, S. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 2012; 22 (9): 1790-7 [OpenAIRE] [PubMed] [DOI]

Chen, H, Meigs, JB, Dupuis, J. Sequence kernel association test for quantitative traits in family samples. Genet Epidemiol. 2013; 37 (2): 196-204 [OpenAIRE] [PubMed] [DOI]

Dong, C, Wei, P, Jian, X, Gibbs, R, Boerwinkle, E, Wang, K, Liu, X. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet. 2015; 24 (8): 2125-37 [OpenAIRE] [PubMed] [DOI]

Kircher, M, Witten, DM, Jain, P, O’Roak, BJ, Cooper, GM, Shendure, J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014; 46 (3): 310-5 [OpenAIRE] [PubMed] [DOI]

17 references, page 1 of 2
Powered by OpenAIRE Research Graph
Any information missing or wrong?Report an Issue