publication . Article . 2014

A method to incorporate prior information into score test for genetic association studies

Agus Salim;
Open Access English
  • Published: 22 Jan 2014 Journal: BMC Bioinformatics, volume 15, issue 1, page 24 (issn: 1471-2105, Copyright policy)
  • Publisher: Springer Nature
Abstract
Background The interest of the scientific community in investigating the impact of rare variants on complex traits has stimulated the development of novel statistical methodologies for association studies. The fact that many of the recently proposed methods for association studies suffer from low power to identify a genetic association motivates the incorporation of prior knowledge into statistical tests. Results In this article we propose a methodology to incorporate prior information into the region-based score test. Within our framework prior information is used to partition variants within a region into several groups, following which asymptotically independ...
Subjects
free text keywords: Biochemistry, Molecular Biology, Computer Science Applications, Methodology Article, Prior information, Association analysis, Score test, Rare variants, Applied Mathematics, Structural Biology
Funded by
NIH| QUANTITATIVE TRAIT LOCUS MAPPING IN HUMAN PEDIGREES
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01MH059490-02
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
,
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
42 references, page 1 of 3

Maher, B. Personal genomes: the case of the missing heritability. Nature. 2008; 456: 18-21 [PubMed]

Park, J-H, Wacholder, S, Gail, MH, Peters, U, Jacobs, KB, Chanock, SJ, Chatterjee, N. Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat Genet. 2010; 42 (7): 570-575 [OpenAIRE] [PubMed] [DOI]

Schork, NJ, Murray, SS, Frazer, KA, Topol, EJ. Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev. 2009; 19 (3): 212-219 [OpenAIRE] [PubMed] [DOI]

Ahituv, N, Kavaslar, N, Schackwitz, W, Ustaszewska, A, Martin, J, Hébert, S, Doelle, H, Ersoy, B, Kryukov, G, Schmidt, S. Medical sequencing at the extremes of human body mass. Am J Hum Genet. 2007; 80 (4): 779-791 [OpenAIRE] [PubMed] [DOI]

Azzopardi, D, Dallosso, AR, Eliason, K, Hendrickson, BC, Jones, N, Rawstorne, E, Colley, J, Moskvina, V, Frye, C, Sampson, JR. Multiple rare nonsynonymous variants in the adenomatous polyposis coli gene predispose to colorectal adenomas. Cancer Res. 2008; 68 (2): 358-363 [OpenAIRE] [PubMed] [DOI]

Bowes, J, Lawrence, R, Eyre, S, Panoutsopoulou, K, Orozco, G, Elliott, K, Ke, X, Morris, A, Thomson, W, Worthington, J. Rare variation at the TNFAIP3 locus and susceptibility to rheumatoid arthritis. Hum Genet. 2010; 128 (6): 627-633 [OpenAIRE] [PubMed] [DOI]

Cohen, JC, Pertsemlidis, A, Fahmi, S, Esmail, S, Vega, GL, Grundy, SM, Hobbs, HH. Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels. Proc Natl Acad Sci U S A. 2006; 103 (6): 1810-1815 [OpenAIRE] [PubMed] [DOI]

Haller, G, Torgerson, DG, Ober, C, Thompson, EE. Sequencing the IL4 locus in African Americans implicates rare noncoding variants in asthma susceptibility. J Allergy Clin Immunol. 2009; 124 (6): 1204-1209 [OpenAIRE] [PubMed] [DOI]

Li, B, Leal, M. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008; 83: 311-321 [OpenAIRE] [PubMed] [DOI]

Madsen, B, Browning, S. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet. 2009; 5: e1000384 [OpenAIRE] [PubMed] [DOI]

Bansal, V, Libiger, O, Torkamani, A, Shork, JN. Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet. 2011; 11: 773-785 [OpenAIRE] [PubMed]

Han, F, Pan, W. A data-adaptive sum test for disease association with multiple common or rare variants. Hum Hered. 2010; 70 (1): 42-54 [OpenAIRE] [PubMed] [DOI]

Li, Y, Byrnes, AE, Li, M. To identify associations with rare variants, just WHaIT: weighted haplotype and imputation-based tests. Am J Hum Genet. 2010; 87 (5): 728-735 [OpenAIRE] [PubMed] [DOI]

Neale, BM, Rivas, MA, Voight, BF, Altshuler, D, Devlin, B, Orho-Melander, M, Kathiresan, S, Purcell, SM, Roeder, K, Daly, MJ. Testing for an unusual distribution of rare variants. PLoS Genet. 2011; 7 (3): e1001322 [OpenAIRE] [PubMed] [DOI]

Quintana, MA, Berstein, JL, Thomas, DC, Conti, DV. Incorporating model uncertainty in detecting rare variants: the Bayesian risk index. Genet Epidemiol. 2011; 35 (7): 638-649 [OpenAIRE] [PubMed] [DOI]

42 references, page 1 of 3
Abstract
Background The interest of the scientific community in investigating the impact of rare variants on complex traits has stimulated the development of novel statistical methodologies for association studies. The fact that many of the recently proposed methods for association studies suffer from low power to identify a genetic association motivates the incorporation of prior knowledge into statistical tests. Results In this article we propose a methodology to incorporate prior information into the region-based score test. Within our framework prior information is used to partition variants within a region into several groups, following which asymptotically independ...
Subjects
free text keywords: Biochemistry, Molecular Biology, Computer Science Applications, Methodology Article, Prior information, Association analysis, Score test, Rare variants, Applied Mathematics, Structural Biology
Funded by
NIH| QUANTITATIVE TRAIT LOCUS MAPPING IN HUMAN PEDIGREES
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01MH059490-02
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
,
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
42 references, page 1 of 3

Maher, B. Personal genomes: the case of the missing heritability. Nature. 2008; 456: 18-21 [PubMed]

Park, J-H, Wacholder, S, Gail, MH, Peters, U, Jacobs, KB, Chanock, SJ, Chatterjee, N. Estimation of effect size distribution from genome-wide association studies and implications for future discoveries. Nat Genet. 2010; 42 (7): 570-575 [OpenAIRE] [PubMed] [DOI]

Schork, NJ, Murray, SS, Frazer, KA, Topol, EJ. Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev. 2009; 19 (3): 212-219 [OpenAIRE] [PubMed] [DOI]

Ahituv, N, Kavaslar, N, Schackwitz, W, Ustaszewska, A, Martin, J, Hébert, S, Doelle, H, Ersoy, B, Kryukov, G, Schmidt, S. Medical sequencing at the extremes of human body mass. Am J Hum Genet. 2007; 80 (4): 779-791 [OpenAIRE] [PubMed] [DOI]

Azzopardi, D, Dallosso, AR, Eliason, K, Hendrickson, BC, Jones, N, Rawstorne, E, Colley, J, Moskvina, V, Frye, C, Sampson, JR. Multiple rare nonsynonymous variants in the adenomatous polyposis coli gene predispose to colorectal adenomas. Cancer Res. 2008; 68 (2): 358-363 [OpenAIRE] [PubMed] [DOI]

Bowes, J, Lawrence, R, Eyre, S, Panoutsopoulou, K, Orozco, G, Elliott, K, Ke, X, Morris, A, Thomson, W, Worthington, J. Rare variation at the TNFAIP3 locus and susceptibility to rheumatoid arthritis. Hum Genet. 2010; 128 (6): 627-633 [OpenAIRE] [PubMed] [DOI]

Cohen, JC, Pertsemlidis, A, Fahmi, S, Esmail, S, Vega, GL, Grundy, SM, Hobbs, HH. Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels. Proc Natl Acad Sci U S A. 2006; 103 (6): 1810-1815 [OpenAIRE] [PubMed] [DOI]

Haller, G, Torgerson, DG, Ober, C, Thompson, EE. Sequencing the IL4 locus in African Americans implicates rare noncoding variants in asthma susceptibility. J Allergy Clin Immunol. 2009; 124 (6): 1204-1209 [OpenAIRE] [PubMed] [DOI]

Li, B, Leal, M. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008; 83: 311-321 [OpenAIRE] [PubMed] [DOI]

Madsen, B, Browning, S. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet. 2009; 5: e1000384 [OpenAIRE] [PubMed] [DOI]

Bansal, V, Libiger, O, Torkamani, A, Shork, JN. Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet. 2011; 11: 773-785 [OpenAIRE] [PubMed]

Han, F, Pan, W. A data-adaptive sum test for disease association with multiple common or rare variants. Hum Hered. 2010; 70 (1): 42-54 [OpenAIRE] [PubMed] [DOI]

Li, Y, Byrnes, AE, Li, M. To identify associations with rare variants, just WHaIT: weighted haplotype and imputation-based tests. Am J Hum Genet. 2010; 87 (5): 728-735 [OpenAIRE] [PubMed] [DOI]

Neale, BM, Rivas, MA, Voight, BF, Altshuler, D, Devlin, B, Orho-Melander, M, Kathiresan, S, Purcell, SM, Roeder, K, Daly, MJ. Testing for an unusual distribution of rare variants. PLoS Genet. 2011; 7 (3): e1001322 [OpenAIRE] [PubMed] [DOI]

Quintana, MA, Berstein, JL, Thomas, DC, Conti, DV. Incorporating model uncertainty in detecting rare variants: the Bayesian risk index. Genet Epidemiol. 2011; 35 (7): 638-649 [OpenAIRE] [PubMed] [DOI]

42 references, page 1 of 3
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