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A phylogenetic codon substitution model for antibody lineages

Abstract:

Phylogenetic methods have shown promise in understanding the development ofbroadly neutralizing antibody lineages (bNAbs). However, the mutational process that generates these lineages – somatic hypermutation (SHM) – is biased by hotspot motifs, which violates important assumptions in most phylogenetic substitution models. Here, we develop a modified GY94-type substitution model that partially accounts for this context-dependency while preserving independence of sites during calculation. This...

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Publication status:
Published
Peer review status:
Peer reviewed
Version:
Publisher's version

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Publisher copy:
10.1534/genetics.116.196303

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Department:
Linacre College
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Department:
Oxford, MSD, Doctoral Training Centre - MSD
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Department:
Oxford, MSD, NDM, Human Genetics Wt Centre
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Funding agency for:
Hoehn, KB
Publisher:
Genetics Society of America Publisher's website
Journal:
Genetics Journal website
Volume:
206
Issue:
1
Pages:
417-427
Publication date:
2017-05-05
Acceptance date:
2017-03-10
DOI:
EISSN:
1943-2631
ISSN:
0016-6731
Pubs id:
pubs:685577
URN:
uri:36f6c533-ea16-422d-8b9c-4a77ec298f97
UUID:
uuid:36f6c533-ea16-422d-8b9c-4a77ec298f97
Local pid:
pubs:685577

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