publication . Other literature type . Article . 2009

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

Browning, Brian L.; Browning, Sharon R.;
  • Published: 01 Feb 2009
  • Publisher: Elsevier BV
Abstract
We present methods for imputing data for ungenotyped markers and for inferring haplotype phase in large data sets of unrelated individuals and parent-offspring trios. Our methods make use of known haplotype phase when it is available, and our methods are computationally efficient so that the full information in large reference panels with thousands of individuals is utilized. We demonstrate that substantial gains in imputation accuracy accrue with increasingly large reference panel sizes, particularly when imputing low-frequency variants, and that unphased reference panels can provide highly accurate genotype imputation. We place our methodology in a unified fra...
Subjects
free text keywords: Genetics(clinical), Genetics, Article, Data set, Genotype, Markov chain, Imputation (statistics), Imputation (genetics), Inference, Allele frequency, Haplotype, Biology
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