publication . Article . 2014

Identity-by-descent graphs offer a flexible framework for imputation and both linkage and association analyses

Blue, Elizabeth; Cheung, Charles YK; Glazner, Christopher G; Conomos, Matthew P; Lewis, Steven M; Sverdlov, Serge; Thornton, Timothy; Wijsman, Ellen M;
Open Access
  • Published: 01 Jun 2014 Journal: BMC Proceedings, volume 8 (eissn: 1753-6561, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
Abstract
We demonstrate the flexibility of identity-by-descent (IBD) graphs for genotype imputation and testing relationships between genotype and phenotype. We analyzed chromosome 3 and the first replicate of simulated diastolic blood pressure. IBD graphs were obtained from complete pedigrees and full multipoint marker analysis, facilitating subsequent linkage and other analyses. For rare alleles, pedigree-based imputation using these IBD graphs had a higher call rate than did population-based imputation. Combining the two approaches improved call rates for common alleles. We found it advantageous to incorporate known, rather than estimated, pedigree relationships when ...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Medicine, Bioinformatics, Genotype-phenotype distinction, Medicine, business.industry, business, Minor allele frequency, Replicate, Imputation (statistics), Pedigree chart, Identity by descent, Missing data, Population, education.field_of_study, education, Proceedings
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