publication . Article . 2016

Genotype distribution-based inference of collective effects in genome-wide association studies: insights to age-related macular degeneration disease mechanism.

Hyung Jun Woo; Chenggang Yu; Kamal Kumar; Bert Gold; Jaques Reifman;
Open Access English
  • Published: 01 Aug 2016 Journal: BMC Genomics, volume 17, issue 1 (eissn: 1471-2164, Copyright policy)
  • Publisher: BioMed Central
Abstract
Background Genome-wide association studies provide important insights to the genetic component of disease risks. However, an existing challenge is how to incorporate collective effects of interactions beyond the level of independent single nucleotide polymorphism (SNP) tests. While methods considering each SNP pair separately have provided insights, a large portion of expected heritability may reside in higher-order interaction effects. Results We describe an inference approach (discrete discriminant analysis; DDA) designed to probe collective interactions while treating both genotypes and phenotypes as random variables. The genotype distributions in case and co...
Subjects
free text keywords: Methodology Article, Genome-wide association, Machine learning, Epistasis, Single-nucleotide polymorphism, Age-related macular degeneration, Biotechnology, Genetics, SNP, Inference, Bioinformatics, Allele frequency, Genetic association, Locus (genetics), Genome-wide association study, Biology
72 references, page 1 of 5

Kim, YA, Wuchty, S, Przytycka, TM. Identifying causal genes and dysregulated pathways in complex diseases. PLoS Comput Biol. 2011; 7: e1001095 [OpenAIRE] [PubMed] [DOI]

Haines, JL, Hauser, MA, Schmidt, S, Scott, WK, Olson, LM, Gallins, P. Complement factor H variant increases the risk of age-related macular degeneration. Science. 2005; 308: 419-21 [OpenAIRE] [PubMed] [DOI]

Edwards, AO, Ritter, R, Abel, KJ, Manning, A, Panhuysen, C, Farrer, LA. Complement factor H polymorphism and age-related macular degeneration. Science. 2005; 308: 421-4 [PubMed] [DOI]

Wang, WY, Barratt, BJ, Clayton, DG, Todd, JA. Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet. 2005; 6: 109-18 [OpenAIRE] [PubMed] [DOI]

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007; 447: 661-78 [OpenAIRE] [PubMed] [DOI]

Gold, B, Kirchhoff, T, Stefanov, S, Lautenberger, J, Viale, A, Garber, J. Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. Proc Natl Acad Sci USA. 2008; 105: 4340-5 [OpenAIRE] [PubMed] [DOI]

Bergeron-Sawitzke, J, Gold, B, Olsh, A, Schlotterbeck, S, Lemon, K, Visvanathan, K. Multilocus analysis of age-related macular degeneration. Eur J Hum Genet. 2009; 17: 1190-9 [OpenAIRE] [PubMed] [DOI]

Manolio, TA. Bringing genome-wide association findings into clinical use. Nat Rev Genet. 2013; 14: 549-58 [OpenAIRE] [PubMed] [DOI]

Welter, D, MacArthur, J, Morales, J, Burdett, T, Hall, P, Junkins, H. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014; 42: D1001-1006 [OpenAIRE] [PubMed] [DOI]

Ripke, S, Neale, BM, Corvin, A, Walters, JT, Farh, KH, Holmans, PA. Biological insights from 108 schizophrenia-associated genetic loci. Nature. 2014; 511: 421-7 [OpenAIRE] [PubMed] [DOI]

Locke, AE, Kahali, B, Berndt, SI, Justice, AE, Pers, TH, Day, FR. Genetic studies of body mass index yield new insights for obesity biology. Nature. 2015; 518: 197-206 [OpenAIRE] [PubMed] [DOI]

Morris, AP, Zeggini, E. An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol. 2010; 34: 188-93 [OpenAIRE] [PubMed] [DOI]

Neale, BM, Rivas, MA, Voight, BF, Altshuler, D, Devlin, B, Orho-Melander, M. Testing for an unusual distribution of rare variants. PLoS Genet. 2011; 7: e1001322 [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: 82-93 [OpenAIRE] [PubMed] [DOI]

Clarke, GM, Anderson, CA, Pettersson, FH, Cardon, LR, Morris, AP, Zondervan, KT. Basic statistical analysis in genetic case-control studies. Nat Protoc. 2011; 6: 121-133 [OpenAIRE] [PubMed] [DOI]

72 references, page 1 of 5
Abstract
Background Genome-wide association studies provide important insights to the genetic component of disease risks. However, an existing challenge is how to incorporate collective effects of interactions beyond the level of independent single nucleotide polymorphism (SNP) tests. While methods considering each SNP pair separately have provided insights, a large portion of expected heritability may reside in higher-order interaction effects. Results We describe an inference approach (discrete discriminant analysis; DDA) designed to probe collective interactions while treating both genotypes and phenotypes as random variables. The genotype distributions in case and co...
Subjects
free text keywords: Methodology Article, Genome-wide association, Machine learning, Epistasis, Single-nucleotide polymorphism, Age-related macular degeneration, Biotechnology, Genetics, SNP, Inference, Bioinformatics, Allele frequency, Genetic association, Locus (genetics), Genome-wide association study, Biology
72 references, page 1 of 5

Kim, YA, Wuchty, S, Przytycka, TM. Identifying causal genes and dysregulated pathways in complex diseases. PLoS Comput Biol. 2011; 7: e1001095 [OpenAIRE] [PubMed] [DOI]

Haines, JL, Hauser, MA, Schmidt, S, Scott, WK, Olson, LM, Gallins, P. Complement factor H variant increases the risk of age-related macular degeneration. Science. 2005; 308: 419-21 [OpenAIRE] [PubMed] [DOI]

Edwards, AO, Ritter, R, Abel, KJ, Manning, A, Panhuysen, C, Farrer, LA. Complement factor H polymorphism and age-related macular degeneration. Science. 2005; 308: 421-4 [PubMed] [DOI]

Wang, WY, Barratt, BJ, Clayton, DG, Todd, JA. Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet. 2005; 6: 109-18 [OpenAIRE] [PubMed] [DOI]

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007; 447: 661-78 [OpenAIRE] [PubMed] [DOI]

Gold, B, Kirchhoff, T, Stefanov, S, Lautenberger, J, Viale, A, Garber, J. Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. Proc Natl Acad Sci USA. 2008; 105: 4340-5 [OpenAIRE] [PubMed] [DOI]

Bergeron-Sawitzke, J, Gold, B, Olsh, A, Schlotterbeck, S, Lemon, K, Visvanathan, K. Multilocus analysis of age-related macular degeneration. Eur J Hum Genet. 2009; 17: 1190-9 [OpenAIRE] [PubMed] [DOI]

Manolio, TA. Bringing genome-wide association findings into clinical use. Nat Rev Genet. 2013; 14: 549-58 [OpenAIRE] [PubMed] [DOI]

Welter, D, MacArthur, J, Morales, J, Burdett, T, Hall, P, Junkins, H. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014; 42: D1001-1006 [OpenAIRE] [PubMed] [DOI]

Ripke, S, Neale, BM, Corvin, A, Walters, JT, Farh, KH, Holmans, PA. Biological insights from 108 schizophrenia-associated genetic loci. Nature. 2014; 511: 421-7 [OpenAIRE] [PubMed] [DOI]

Locke, AE, Kahali, B, Berndt, SI, Justice, AE, Pers, TH, Day, FR. Genetic studies of body mass index yield new insights for obesity biology. Nature. 2015; 518: 197-206 [OpenAIRE] [PubMed] [DOI]

Morris, AP, Zeggini, E. An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol. 2010; 34: 188-93 [OpenAIRE] [PubMed] [DOI]

Neale, BM, Rivas, MA, Voight, BF, Altshuler, D, Devlin, B, Orho-Melander, M. Testing for an unusual distribution of rare variants. PLoS Genet. 2011; 7: e1001322 [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: 82-93 [OpenAIRE] [PubMed] [DOI]

Clarke, GM, Anderson, CA, Pettersson, FH, Cardon, LR, Morris, AP, Zondervan, KT. Basic statistical analysis in genetic case-control studies. Nat Protoc. 2011; 6: 121-133 [OpenAIRE] [PubMed] [DOI]

72 references, page 1 of 5
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publication . Article . 2016

Genotype distribution-based inference of collective effects in genome-wide association studies: insights to age-related macular degeneration disease mechanism.

Hyung Jun Woo; Chenggang Yu; Kamal Kumar; Bert Gold; Jaques Reifman;