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Shared genomic segment analysis. Mapping disease predisposition genes in extended pedigrees using SNP genotype assays
A Thomas1, N J Camp, J M Farnham
1Department of Biomedical Informatics, University of Utah, 391 Chipeta Way, Salt Lake City, UT 84108, USA. alun@genepi.med.utah.edu
Annals of Human Genetics
|December 21, 2007
Summary
High-density genotype assays and extended pedigrees effectively pinpoint predisposition genes by analyzing shared DNA segments. This method, utilizing runs of identical-by-state loci, proves robust for gene discovery in complex diseases like prostate cancer.
Area of Science:
- Genetics
- Bioinformatics
- Medical Genomics
Background:
- High-density genotype assays are crucial for genetic studies.
- Extended pedigrees provide valuable data for gene localization.
- Genomic mismatch scanning and dense single nucleotide polymorphism (SNP) maps are established tools.
Purpose of the Study:
- To evaluate the utility of high-density genotype assays for identifying predisposition genes.
- To leverage extended pedigrees for robust gene localization.
- To refine methods for detecting shared genomic segments among relatives.
Main Methods:
- Reviewing distributions of shared genomic segments (identical by descent) in dense SNP maps.
- Utilizing long runs of loci where cases share alleles identically by state (IBS) for gene localization.
- Evaluating the distribution of IBS runs under a null hypothesis via simulation.
Main Results:
- Dense genotype assays combined with extended pedigrees are effective for gene localization.
- Runs of single locus statistics are powerful, tractable, and robust for finding shared DNA.
- The methods were successfully illustrated using a prostate cancer pedigree linked to chromosome 1p23.
Conclusions:
- High-density genotype assays and extended pedigrees offer a powerful design for gene detection.
- Runs of simple single locus statistics are a reliable method for identifying shared DNA.
- This approach enhances the ability to detect genes contributing to complex diseases.
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