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Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae

Abstract:

Whole-genome sequencing has facilitated genome-wide analyses of association, prediction and heritability in many organisms. However, such analyses in bacteria are still in their infancy, being limited by difficulties including genome plasticity and strong population structure. Here we propose a suite of methods including linear mixed models, elastic net and LD-score regression, adapted to bacterial traits using innovations such as frequency-based allele coding, both insertion/deletion and nuc...

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Publication status:
Published
Peer review status:
Peer reviewed

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Authors


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Role:
Author
ORCID:
0000-0001-8899-3323
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Role:
Author
ORCID:
0000-0003-4397-2224
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Institution:
University of Oxford
Division:
MSD
Department:
NDM
Sub department:
Tropical Medicine
Role:
Author
ORCID:
0000-0002-1013-7815
Publisher:
Oxford University Press
Journal:
NAR Genomics and Bioinformatics More from this journal
Volume:
4
Issue:
1
Article number:
lqac011
Publication date:
2022-02-22
Acceptance date:
2022-02-01
DOI:
EISSN:
2631-9268
Language:
English
Keywords:
Pubs id:
1241552
Local pid:
pubs:1241552
Deposit date:
2022-02-28

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