[1] | Eichler EE, Flint J, Gibson G, Kong A, Leal SM, et al. (2010) Missing heritability and strategies for finding the underlying causes of complex disease. Nature reviews Genetics 11: 446–450.
|
[2] | Gibson G (2010) Hints of hidden heritability in GWAS. Nature genetics 42: 558–560.
|
[3] | Maher B (2008) Personal genomes: The case of the missing heritability. Nature 456: 18–21.
|
[4] | Makowsky R, Pajewski NM, Klimentidis YC, Vazquez AI, Duarte CW, et al. (2011) Beyond missing heritability: prediction of complex traits. PLoS genetics 7: e1002051.
|
[5] | Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747–753.
|
[6] | Clayton DG (2009) Prediction and interaction in complex disease genetics: experience in type 1 diabetes. PLoS genetics 5: e1000540.
|
[7] | de los Campos G, Gianola D, Allison DB (2010) Predicting genetic predisposition in humans: the promise of whole-genome markers. Nature reviews Genetics 11: 880–886.
|
[8] | Jakobsdottir J, Gorin MB, Conley YP, Ferrell RE, Weeks DE (2009) Interpretation of genetic association studies: markers with replicated highly significant odds ratios may be poor classifiers. PLoS genetics 5: e1000337.
|
[9] | Janssens AC, van Duijn CM (2008) Genome-based prediction of common diseases: advances and prospects. Human molecular genetics 17: R166–173.
|
[10] | McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, et al. (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nature reviews Genetics 9: 356–369.
|
[11] | Witte JS (2010) Genome-wide association studies and beyond. Annual review of public health 31: 9–20 24 p following 20.
|
[12] | Park JH, Wacholder S, Gail MH, Peters U, Jacobs KB, et al. (2010) Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat Genet 42: 570–575.
|
[13] | Bodmer W, Bonilla C (2008) Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 40: 695–701.
|
[14] | Pritchard JK (2001) Are rare variants responsible for susceptibility to complex diseases? American journal of human genetics 69: 124–137.
|
[15] | Cohen JC, Kiss RS, Pertsemlidis A, Marcel YL, McPherson R, et al. (2004) Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 305: 869–872.
|
[16] | Frayling IM, Beck NE, Ilyas M, Dove-Edwin I, Goodman P, et al. (1998) The APC variants I1307K and E1317Q are associated with colorectal tumors, but not always with a family history. Proceedings of the National Academy of Sciences of the United States of America 95: 10722–10727.
|
[17] | Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24: 133–141.
|
[18] | Morris AP, Zeggini E (2010) An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34: 188–193.
|
[19] | Li B, Leal SM (2008) Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83: 311–321.
|
[20] | Madsen BE, Browning SR (2009) A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5: e1000384.
|
[21] | Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, et al. (2010) Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 86: 832–838.
|
[22] | Ionita-Laza I, Buxbaum JD, Laird NM, Lange C (2011) A new testing strategy to identify rare variants with either risk or protective effect on disease. PLoS Genet 7: e1001289.
|
[23] | Wu MC, Lee S, Cai T, Li Y, Boehnke M, et al. (2011) Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 89: 82–93.
|
[24] | Han F, Pan W (2010) A data-adaptive sum test for disease association with multiple common or rare variants. Human heredity 70: 42–54.
|
[25] | Morris AP, Zeggini E (2010) An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genetic epidemiology 34: 188–193.
|
[26] | Neale BM, Rivas MA, Voight BF, Altshuler D, Devlin B, et al. (2011) Testing for an unusual distribution of rare variants. PLoS genetics 7: e1001322.
|
[27] | Chernoff H, Lo SH, Zheng T (2009) Discovering influential variables: a method of partitions. Annals of Applied Statistics 3: 1335–1369.
|
[28] | Qiao B, Huang CH, Cong L, Xie J, Lo SH, et al.. (2009) Genome Wide Gene Based Analysis of Rheumatoid Arthritis Associated Interaction with PTPN22 and HLADRB1. BMC Proceedings (Suppl 7): S132.
|
[29] | Huang CH, Cong L, Xie J, QIao B, Lo SH, et al.. (2009) Rheumatoid Arthritis-Associated Gene-Gene Interaction Network for Rheumatoid Arthritis Candidate Genes. BMC Proc (Suppl 7): S75.
|
[30] | Ding Y, Cong L, Ionita-Laza I, Lo SH, Zheng T (2007) Constructing gene association networks for rheumatoid arthritis using the backward genotype-trait association (BGTA) algorithm. BMC Proceedings 1 Suppl 1S13.
|
[31] | Lo SH, Chernoff H, Cong L, Ding Y, Zheng T (2008) Discovering interactions among BRCA1 and other candidate genes associated with sporadic breast cancer. Proc Natl Acad Sci U S A 105: 12387–12392.
|
[32] | Zheng T, Wang S, Cong L, Ding Y, Ionita-Laza I, et al. (2007) Joint study of genetic regulators for expression traits related to breast cancer. BMC Proceedings 1 Suppl 1S10.
|
[33] | Marchini J, Donnelly P, Cardon LR (2005) Genome-wide strategies for detecting multiple loci that influence complex diseases. Nature genetics 37: 413–417.
|
[34] | Hu T, Sinnott-Armstrong NA, Kiralis JW, Andrew AS, Karagas MR, et al. (2011) Characterizing genetic interactions in human disease association studies using statistical epistasis networks. BMC bioinformatics 12: 364.
|
[35] | Cordell HJ (2009) Detecting gene-gene interactions that underlie human diseases. Nature reviews Genetics 10: 392–404.
|
[36] | Hamza TH, Chen H, Hill-Burns EM, Rhodes SL, Montimurro J, et al. (2011) Genome-wide gene-environment study identifies glutamate receptor gene GRIN2A as a Parkinson's disease modifier gene via interaction with coffee. PLoS genetics 7: e1002237.
|
[37] | Andreasen CH, Mogensen MS, Borch-Johnsen K, Sandbaek A, Lauritzen T, et al. (2008) Non-replication of genome-wide based associations between common variants in INSIG2 and PFKP and obesity in studies of 18,014 Danes. PloS one 3: e2872.
|
[38] | Wang H, Lo SH, Zheng T, Hu I (2012) Interaction-based feature selection and classification for high-dimensional biological data. Bioinformatics 28: 2834–2842.
|
[39] | Thomas D (2010) Gene–environment-wide association studies: emerging approaches. Nature reviews Genetics 11: 259–272.
|
[40] | Thomas D (2010) Methods for investigating gene-environment interactions in candidate pathway and genome-wide association studies. Annual review of public health 31: 21–36.
|
[41] | Almasy L, Dyer TD, Peralta JM, Kent JW Jr, Charlesworth JC, et al. (2011) Genetic Analysis Workshop 17 mini-exome simulation. BMC Proceedings 5 Suppl 9S2.
|