Rare variant genotype imputation with thousands of study-specific whole-genome sequences: implications for cost-effective study designs.

ABSTRACT: The utility of genotype imputation in genome-wide association studies is increasing as progressively larger reference panels are improved and expanded through whole-genome sequencing. Developing general guidelines for optimally cost-effective imputation, however, requires evaluation of performance issues that include the relative utility of study-specific compared with general/multipopulation reference panels; genotyping with various array scaffolds; effects of different ethnic backgrounds; and assessment of ranges of allele frequencies. Here we compared the effectiveness of study-specific reference panels to the commonly used 1000 Genomes Project (1000G) reference panels in the isolated Sardinian population and in cohorts of European ancestry including samples from Minnesota (USA). We als

SUBMITTER: Pistis G 

PROVIDER: S-EPMC4463504 | biostudies-literature | 2015 Jul

REPOSITORIES: biostudies-literature