Data simulation software for whole-genome association and other studies in human genetics

Scott M. Dudek, Alison A. Motsinger, Digna R. Velez, Scott M. Williams, Marylyn Deriggi Ritchie

Research output: Chapter in Book/Report/Conference proceedingConference contribution

52 Citations (Scopus)

Abstract

Genome-wide association studies have become a reality in the study of the genetics of complex disease. This technology provides a wealth of genomic information on patient samples, from which we hope to learn novel biology and detect important genetic and environmental factors for disease processes. Because strategies for analyzing these data have not kept pace with the laboratory methods that generate the data it is unlikely that these advances will immediately lead to an improved understanding of the genetic contribution to common human disease and drug response. Currently, no single analytical method will allow us to extract all information from a whole-genome association study. Thus, many novel methods are being proposed and developed. It will be vital for the success of these new methods, to have the ability to simulate datasets consisting of polymorphisms throughout the genome with realistic linkage disequilibrium patterns. Within these datasets, we can embed genetic models of disease whereby we can evaluate the ability of novel methods to detect these simulated effects. This paper describes a new software package, genomeSIM, for the simulation of large-scale genomic data in population based case-control samples. It allows for single SNP, as well as gene-gene interaction models to be associated with disease risk. We describe the algorithm and demonstrate its utility for future genetic studies of whole-genome association.

Original languageEnglish (US)
Title of host publicationProceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006
Pages499-510
Number of pages12
StatePublished - Dec 1 2006
Event11th Pacific Symposium on Biocomputing 2006, PSB 2006 - Maui, HI, United States
Duration: Jan 3 2006Jan 7 2006

Other

Other11th Pacific Symposium on Biocomputing 2006, PSB 2006
CountryUnited States
CityMaui, HI
Period1/3/061/7/06

Fingerprint

Genome-Wide Association Study
Medical Genetics
Software
Genes
Inborn Genetic Diseases
Genetic Models
Linkage Disequilibrium
Single Nucleotide Polymorphism
Polymorphism
Software packages
Genetics
Genome
Technology
Pharmaceutical Preparations
Population
Datasets

All Science Journal Classification (ASJC) codes

  • Computational Theory and Mathematics
  • Biomedical Engineering
  • Medicine(all)

Cite this

Dudek, S. M., Motsinger, A. A., Velez, D. R., Williams, S. M., & Ritchie, M. D. (2006). Data simulation software for whole-genome association and other studies in human genetics. In Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006 (pp. 499-510)
Dudek, Scott M. ; Motsinger, Alison A. ; Velez, Digna R. ; Williams, Scott M. ; Ritchie, Marylyn Deriggi. / Data simulation software for whole-genome association and other studies in human genetics. Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006. 2006. pp. 499-510
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Dudek, SM, Motsinger, AA, Velez, DR, Williams, SM & Ritchie, MD 2006, Data simulation software for whole-genome association and other studies in human genetics. in Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006. pp. 499-510, 11th Pacific Symposium on Biocomputing 2006, PSB 2006, Maui, HI, United States, 1/3/06.

Data simulation software for whole-genome association and other studies in human genetics. / Dudek, Scott M.; Motsinger, Alison A.; Velez, Digna R.; Williams, Scott M.; Ritchie, Marylyn Deriggi.

Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006. 2006. p. 499-510.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Dudek SM, Motsinger AA, Velez DR, Williams SM, Ritchie MD. Data simulation software for whole-genome association and other studies in human genetics. In Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006. 2006. p. 499-510