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Imputation Without Doing Imputation: A New Method for the Detection of Non-Genotyped Causal Variants

Lookup NU author(s): Dr Richard Howey, Professor Heather Cordell



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Genome-wide association studies allow detection of non-genotyped disease-causing variants through testing of nearby genotyped SNPs. This approach may fail when there are no genotyped SNPs in strong LD with the causal variant. Several genotyped SNPs in weak LD with the causal variant may, however, considered together, provide equivalent information. This observation motivates popular but computationally intensive approaches based on imputation or haplotyping. Here we present a new method and accompanying software designed for this scenario. Our approach proceeds by selecting, for each genotyped "anchor" SNP, a nearby genotyped "partner" SNP, chosen via a specific algorithm we have developed. These two SNPs are used as predictors in linear or logistic regression analysis to generate a final significance test. In simulations, our method captures much of the signal captured by imputation, while taking a fraction of the time and disc space, and generating a smaller number of false-positives. We apply our method to a case/control study of severe malaria genotyped using the Affymetrix 500K array. Previous analysis showed that fine-scale sequencing of a Gambian reference panel in the region of the known causal locus, followed by imputation, increased the signal of association to genome-wide significance levels. Our method also increases the signal of association from P approximate to 2x10-6 to P approximate to 6x10-11. Our method thus, in some cases, eliminates the need for more complex methods such as sequencing and imputation, and provides a useful additional test that may be used to identify genetic regions of interest.

Publication metadata

Author(s): Howey R, Cordell HJ

Publication type: Article

Publication status: Published

Journal: Genetic Epidemiology

Year: 2014

Volume: 38

Issue: 3

Pages: 173-190

Print publication date: 01/04/2014

Online publication date: 17/02/2014

Acceptance date: 31/12/2013

Date deposited: 21/05/2014

ISSN (print): 0741-0395

ISSN (electronic): 1098-2272

Publisher: John Wiley & Sons


DOI: 10.1002/gepi.21792


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Funder referenceFunder name
087436Wellcome Trust
566Bill & Melinda Gates Foundation through the Foundation of the National Institutes of Health as part of the Grand Challenges in Global Health Initiative
WT077383/Z/05/ZWellcome Trust