Incorporating ENCODE information into association analysis of whole genome sequencing data

BMC Proceedings

Volumn 10, Issue , 2016, Pages

  Kim, Taebeom ^a   Wei, Peng ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BLOOD PRESSURE; CHROMOSOME 15; GENE; GENE LOCUS; GENETIC ASSOCIATION STUDY; GENETIC DATABASE; GENETIC VARIABILITY; SNUPN GENE; WHOLE GENOME SEQUENCING;

EID: 85015981868     PISSN: None     EISSN: 17536561     Source Type: Journal    
DOI: 10.1186/s12919-016-0040-y     Document Type: Article

References (17)

1. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, et al. Finding the missing heritability of complex diseases. Nature. 2009; 461(7265): 747-53.
2. 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.
3. 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.
4. 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.
5. Morrison AC, Voorman A, Johnson AD, Liu X, Yu J, Li A, Muzny D, Yu F, Rice K, Zhu C, et al. Whole-genome sequence-based analysis of high-density lipoprotein cholesterol. Nat Genet. 2013; 45(8): 899-901.
6. 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.
7. 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.
8. 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.
9. 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.
10. Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, et al. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014; 111(17): 6131-8.
11. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012; 337(6099): 1190-5.
12. Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 2012; 22(9): 1790-7.
13. Chen H, Meigs JB, Dupuis J. Sequence kernel association test for quantitative traits in family samples. Genet Epidemiol. 2013; 37(2): 196-204.
14. 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.
15. 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.
16. Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol. 2010; 6(12): E1001025.
17. Tobin MD, Sheehan NA, Scurrah KJ, Burton PR. Adjusting for treatment effects in studies of quantitative traits: Antihypertensive therapy and systolic blood pressure. Stat Med. 2005; 24(19): 2911-35.