publication . Article . 2014

Genotypic discrepancies arising from imputation.

Hinrichs, Anthony L; Culverhouse, Robert C; Suarez, Brian K;
Open Access English
  • Published: 01 Jun 2014 Journal: BMC Proceedings, volume 8, issue Suppl 1, page S17 (issn: 1753-6561, Copyright policy)
  • Publisher: Springer Nature
Abstract
The ideal genetic analysis of family data would include whole genome sequence on all family members. A strategy of combining sequence data from a subset of key individuals with inexpensive, genome-wide association study (GWAS) chip genotypes on all individuals to infer sequence level genotypes throughout the families has been suggested as a highly accurate alternative. This strategy was followed by the Genetic Analysis Workshop 18 data providers. We examined the quality of the imputation to identify potential consequences of this strategy by comparing discrepancies between GWAS genotype calls and imputed calls for the same variants. Overall, the inference and im...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Medicine, Pedigree chart, Inference, Population, education.field_of_study, education, Genetic analysis, Bioinformatics, Missing data, False positive paradox, Genome-wide association study, Imputation (statistics), Medicine, business.industry, business, Proceedings
Funded by
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| Identifying T2D Variants by DNA Sequencing in Multiethnic Samples
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1U01DK085584-01
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Identification and Replication of Type 2 Diabetes Genes in Mexican Americans
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085501-02
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Discovery of Functional Variants in Type 2 Diabetes Genes in Mexican Americans
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085524-05
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| DEVELOPING STRATEGIES FOR JOINT GENE-ENVIRONMENT ANALYSIS
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R21DA033827-01
  • Funding stream: NATIONAL INSTITUTE ON DRUG ABUSE

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