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

BMC Proceedings

Proceedings

Charles YK Cheung¹  Matthew P Conomos¹  Timothy Thornton¹  Steven M Lewis²  Christopher G Glazner²  Serge Sverdlov²  Elizabeth Marchani Blue³  Ellen M Wijsman⁴ 

[1] Department of Biostatistics, University of Washington, 98195, Seattle, WA, USA;Department of Statistics, University of Washington, 98195, Seattle, WA, USA;Division of Medical Genetics, Department of Medicine, University of Washington, 98195, Seattle, WA, USA;Division of Medical Genetics, Department of Medicine, University of Washington, 98195, Seattle, WA, USA;Department of Biostatistics, University of Washington, 98195, Seattle, WA, USA;

关键词: Minor Allele Frequency;    Reference Panel;    Impute Genotype;    Imputation Marker;    Pairwise Kinship Coefficient;   

DOI  :  10.1186/1753-6561-8-S1-S19

来源: Springer

【 摘 要 】

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 testing for association. Replacing missing data with imputed alleles improved association signals as well. Analyses were performed with knowledge of the underlying model.

【 授权许可】

CC BY   
© Blue et al.; licensee BioMed Central Ltd. 2014