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Identifying lineage effects when controlling for population structure improves power in bacterial association studies.

Earle, Sarah G and Wu, Chieh-Hsi and Charlesworth, Jane and Stoesser, Nicole and Gordon, N Claire and Walker, Timothy M and Spencer, Chris C A and Iqbal, Zamin and Clifton, David A and Hopkins, Katie L and Woodford, Neil and Smith, E Grace and Ismail, Nazir and Llewelyn, Martin J and Peto, Tim E and Crook, Derrick W and McVean, Gil and Walker, A Sarah and Wilson, Daniel J (2016) Identifying lineage effects when controlling for population structure improves power in bacterial association studies. Nature microbiology, 1. p. 16041. ISSN 2058-5276.

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Official URL: http://www.nature.com/articles/nmicrobiol201641

Abstract

Bacteria pose unique challenges for genome-wide association studies because of strong structuring into distinct strains and substantial linkage disequilibrium across the genome(1,2). Although methods developed for human studies can correct for strain structure(3,4), this risks considerable loss-of-power because genetic differences between strains often contribute substantial phenotypic variability(5). Here, we propose a new method that captures lineage-level associations even when locus-specific associations cannot be fine-mapped. We demonstrate its ability to detect genes and genetic variants underlying resistance to 17 antimicrobials in 3,144 isolates from four taxonomically diverse clonal and recombining bacteria: Mycobacterium tuberculosis, Staphylococcus aureus, Escherichia coli and Klebsiella pneumoniae. Strong selection, recombination and penetrance confer high power to recover known antimicrobial resistance mechanisms and reveal a candidate association between the outer membrane porin nmpC and cefazolin resistance in E. coli. Hence, our method pinpoints locus-specific effects where possible and boosts power by detecting lineage-level differences when fine-mapping is intractable.

Item Type: Article
Subjects: WC Communicabable diseases
Divisions: Clinical Support > Infectious Diseases
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Depositing User: Mr Philip O'Reilly
Date Deposited: 30 Mar 2017 15:33
Last Modified: 30 Mar 2017 15:33
URI: http://www.repository.heartofengland.nhs.uk/id/eprint/1331

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