Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Identifying lineage effects when controlling for population structure
  improves power in bacterial association studies   Bacteria pose unique challenges for genome-wide association studies (GWAS)
because of strong structuring into distinct strains and substantial linkage
disequilibrium across the genome. While methods developed for human studies can
correct for strain structure, this risks considerable loss- of-power because
genetic differences between strains often contribute substantial phenotypic
variability. 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 3144 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.

23
The categories of this paper are: solv-int
37
The categories of this paper are: supr-con
19
The categories of this paper are: eess
12
The categories of this paper are: nucl-th
14
The categories of this paper are: math-ph
11
The categories of this paper are: hep-lat
6
The categories of this paper are: astro-ph
33
The categories of this paper are: plasm-ph
36
The categories of this paper are: cmp-lg
8
The categories of this paper are: hep-ex
3
The categories of this paper are: physics
7
The categories of this paper are: hep-th
4
The categories of this paper are: cond-mat
28
The categories of this paper are: alg-geom
32
The categories of this paper are: atom-ph
30
The categories of this paper are: q-alg