publication . Article . 2010

A novel approach for haplotype-based association analysis using family data

Chen, Yixuan; Li, Xin; Li, Jing;
Open Access English
  • Published: 01 Jan 2010 Journal: BMC Bioinformatics, volume 11, issue Suppl 1, page S45 (issn: 1471-2105, Copyright policy)
  • Publisher: Springer Nature
Abstract
Background Haplotype-based approaches have been extensively studied for case-control association mapping in recent years. It has been shown that haplotype methods can provide more consistent results comparing to single-locus based approaches, especially in cases where causal variants are not typed. Improved power has been observed by clustering similar or rare haplotypes into groups to reduce the degrees of freedom of association tests. For family-based association studies, one commonly used strategy is Transmission Disequilibrium Tests (TDT), which examine the imbalanced transmission of alleles/haplotypes to affected and normal children. Many extensions have be...
Subjects
free text keywords: Biochemistry, Molecular Biology, Computer Science Applications, Research, Applied Mathematics, Structural Biology, Bioinformatics, Haplotype estimation, Genetic association, Pedigree chart, Disequilibrium, medicine.symptom, medicine, Linkage disequilibrium, Genetics, Transmission disequilibrium test, Haplotype, Association mapping, Biology
Funded by
NIH| Multi-point and multi-locus analysis of genomic association data
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01LM008991-05
  • Funding stream: NATIONAL LIBRARY OF MEDICINE
,
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
,
NIH| HUMAN GENETIC ANALYSIS RESOURCE
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3P41RR003655-11S1
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
,
NIH| FAMILIAL AND BIRTH COHORT EFFECTS ON THE AGING SENSES
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AG021917-07
  • Funding stream: NATIONAL INSTITUTE ON AGING
27 references, page 1 of 2

A haplotype map of the human genome. Nature. 2005; 437 (7063): 1299-320 [OpenAIRE] [PubMed] [DOI]

McPeek, MS, Strahs, A. Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping. Am J Hum Genet. 1999; 65 (3): 858-75 [OpenAIRE] [PubMed] [DOI]

Toivonen, HT, Onkamo, P, Vasko, K, Ollikainen, V, Sevon, P, Mannila, H, Herr, M, Kere, J. Data mining applied to linkage disequilibrium mapping. Am J Hum Genet. 2000; 67: 133-45 [OpenAIRE] [PubMed] [DOI]

Liu, JS, Sabatti, C, Teng, J, Keats, BJ, Risch, N. Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Res. 2001; 11 (10): 1716-24 [OpenAIRE] [PubMed] [DOI]

Tzeng, JY, Devlin, B, Wasserman, L, Roeder, K. On the identification of disease mutations by the analysis of haplotype similarity and goodness of fit. Am J Hum Genet. 2003; 72 (4): 891-902 [OpenAIRE] [PubMed] [DOI]

Molitor, J, Marjoram, P, Thomas, D. Fine-scale mapping of disease genes with multiple mutations via spatial clustering techniques. Am J Hum Genet. 2003; 73 (6): 1368-84 [OpenAIRE] [PubMed] [DOI]

Durrant, C, Zondervan, KT, Cardon, LR, Hunt, S, Deloukas, P, Morris, AP. Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes. Am J Hum Genet. 2004; 75: 35-43 [OpenAIRE] [PubMed] [DOI]

Li, J, Jiang, T. Haplotype-based linkage disequilibrium mapping via direct data mining. Bioinformatics. 2005; 21 (24): 4384-93 [OpenAIRE] [PubMed] [DOI]

Li, J, Zhou, Y, Elston, RC. Haplotype-based quantitative trait mapping using a clustering algorithm. BMC Bioinformatics. 2006; 7: 258 [OpenAIRE] [PubMed] [DOI]

Igo, JRP, Li, J, Goddard, KA. Association Mapping by Generalized Linear Regression with Density-based Haplotype Clustering. Genetic Epidemiology. 2008; 32: 1-11 [OpenAIRE] [PubMed] [DOI]

Pritchard, JK, Stephens, M, Rosenberg, NA, Donnelly, P. Association mapping in structured populations. Am J Hum Genet. 2000; 67: 170-81 [OpenAIRE] [PubMed] [DOI]

Li, X, Li, J. Comparison of haplotyping methods using families and unrelated individuals on simulated rheumatoid arthritis data. BMC Proc. 2007; 1 (Suppl 1): S55 [OpenAIRE] [PubMed] [DOI]

Deng, HW, Li, J, Recker, RR. Effect of polygenes on Xiong's transmission disequilibrium test of a QTL in nuclear families with multiple children. Genet Epidemiol. 2001; 21 (3): 243-65 [OpenAIRE] [PubMed] [DOI]

Deng, HW, Li, J. The effects of selected sampling on the transmission disequilibrium test of a quantitative trait locus. Genet Res. 2002; 79 (2): 161-74 [PubMed] [DOI]

Seltman, H, Roeder, K, Devlin, B. Transmission/disequilibrium test meets measured haplotype analysis: family-based association analysis guided by evolution of haplotypes. Am J Hum Genet. 2001; 68 (5): 1250-63 [OpenAIRE] [PubMed] [DOI]

27 references, page 1 of 2
Abstract
Background Haplotype-based approaches have been extensively studied for case-control association mapping in recent years. It has been shown that haplotype methods can provide more consistent results comparing to single-locus based approaches, especially in cases where causal variants are not typed. Improved power has been observed by clustering similar or rare haplotypes into groups to reduce the degrees of freedom of association tests. For family-based association studies, one commonly used strategy is Transmission Disequilibrium Tests (TDT), which examine the imbalanced transmission of alleles/haplotypes to affected and normal children. Many extensions have be...
Subjects
free text keywords: Biochemistry, Molecular Biology, Computer Science Applications, Research, Applied Mathematics, Structural Biology, Bioinformatics, Haplotype estimation, Genetic association, Pedigree chart, Disequilibrium, medicine.symptom, medicine, Linkage disequilibrium, Genetics, Transmission disequilibrium test, Haplotype, Association mapping, Biology
Funded by
NIH| Multi-point and multi-locus analysis of genomic association data
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01LM008991-05
  • Funding stream: NATIONAL LIBRARY OF MEDICINE
,
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
,
NIH| HUMAN GENETIC ANALYSIS RESOURCE
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3P41RR003655-11S1
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
,
NIH| FAMILIAL AND BIRTH COHORT EFFECTS ON THE AGING SENSES
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01AG021917-07
  • Funding stream: NATIONAL INSTITUTE ON AGING
27 references, page 1 of 2

A haplotype map of the human genome. Nature. 2005; 437 (7063): 1299-320 [OpenAIRE] [PubMed] [DOI]

McPeek, MS, Strahs, A. Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping. Am J Hum Genet. 1999; 65 (3): 858-75 [OpenAIRE] [PubMed] [DOI]

Toivonen, HT, Onkamo, P, Vasko, K, Ollikainen, V, Sevon, P, Mannila, H, Herr, M, Kere, J. Data mining applied to linkage disequilibrium mapping. Am J Hum Genet. 2000; 67: 133-45 [OpenAIRE] [PubMed] [DOI]

Liu, JS, Sabatti, C, Teng, J, Keats, BJ, Risch, N. Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Res. 2001; 11 (10): 1716-24 [OpenAIRE] [PubMed] [DOI]

Tzeng, JY, Devlin, B, Wasserman, L, Roeder, K. On the identification of disease mutations by the analysis of haplotype similarity and goodness of fit. Am J Hum Genet. 2003; 72 (4): 891-902 [OpenAIRE] [PubMed] [DOI]

Molitor, J, Marjoram, P, Thomas, D. Fine-scale mapping of disease genes with multiple mutations via spatial clustering techniques. Am J Hum Genet. 2003; 73 (6): 1368-84 [OpenAIRE] [PubMed] [DOI]

Durrant, C, Zondervan, KT, Cardon, LR, Hunt, S, Deloukas, P, Morris, AP. Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes. Am J Hum Genet. 2004; 75: 35-43 [OpenAIRE] [PubMed] [DOI]

Li, J, Jiang, T. Haplotype-based linkage disequilibrium mapping via direct data mining. Bioinformatics. 2005; 21 (24): 4384-93 [OpenAIRE] [PubMed] [DOI]

Li, J, Zhou, Y, Elston, RC. Haplotype-based quantitative trait mapping using a clustering algorithm. BMC Bioinformatics. 2006; 7: 258 [OpenAIRE] [PubMed] [DOI]

Igo, JRP, Li, J, Goddard, KA. Association Mapping by Generalized Linear Regression with Density-based Haplotype Clustering. Genetic Epidemiology. 2008; 32: 1-11 [OpenAIRE] [PubMed] [DOI]

Pritchard, JK, Stephens, M, Rosenberg, NA, Donnelly, P. Association mapping in structured populations. Am J Hum Genet. 2000; 67: 170-81 [OpenAIRE] [PubMed] [DOI]

Li, X, Li, J. Comparison of haplotyping methods using families and unrelated individuals on simulated rheumatoid arthritis data. BMC Proc. 2007; 1 (Suppl 1): S55 [OpenAIRE] [PubMed] [DOI]

Deng, HW, Li, J, Recker, RR. Effect of polygenes on Xiong's transmission disequilibrium test of a QTL in nuclear families with multiple children. Genet Epidemiol. 2001; 21 (3): 243-65 [OpenAIRE] [PubMed] [DOI]

Deng, HW, Li, J. The effects of selected sampling on the transmission disequilibrium test of a quantitative trait locus. Genet Res. 2002; 79 (2): 161-74 [PubMed] [DOI]

Seltman, H, Roeder, K, Devlin, B. Transmission/disequilibrium test meets measured haplotype analysis: family-based association analysis guided by evolution of haplotypes. Am J Hum Genet. 2001; 68 (5): 1250-63 [OpenAIRE] [PubMed] [DOI]

27 references, page 1 of 2
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