Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Reducing pervasive false positive identical-by-descent segments detected
  by large-scale pedigree analysis   Analysis of genomic segments shared identical-by-descent (IBD) between
individuals is fundamental to many genetic applications, from demographic
inference to estimating the heritability of diseases, but IBD detection
accuracy in non-simulated data is largely unknown. In principle, it can be
evaluated using known pedigrees, as IBD segments are by definition inherited
without recombination down a family tree. We extracted 25,432 genotyped
European individuals containing 2,952 father-mother-child trios from the
23andMe, Inc. dataset. We then used GERMLINE, a widely used IBD detection
method, to detect IBD segments within this cohort. Exploiting known familial
relationships, we identified a false positive rate over 67% for 2-4 centiMorgan
(cM) segments, in sharp contrast with accuracies reported in simulated data at
these sizes. Nearly all false positives arose from the allowance of haplotype
switch errors when detecting IBD, a necessity for retrieving long (> 6 cM)
segments in the presence of imperfect phasing. We introduce HaploScore, a
novel, computationally efficient metric that scores IBD segments proportional
to the number of switch errors they contain. Applying HaploScore filtering to
the IBD data at a precision of 0.8 produced a 13-fold increase in recall when
compared to length-based filtering. We replicate the false IBD findings and
demonstrate the generalizability of HaploScore to alternative data sources
using an independent cohort of 555 European individuals from the 1000 Genomes
project. HaploScore can improve the accuracy of segments reported by any IBD
detection method, provided that estimates of the genotyping error rate and
switch error rate are available.

31
The categories of this paper are: ao-sci
11
The categories of this paper are: hep-lat
24
The categories of this paper are: dg-ga
20
The categories of this paper are: acc-phys
34
The categories of this paper are: chem-ph
15
The categories of this paper are: nucl-ex
1
The categories of this paper are: cs
25
The categories of this paper are: patt-sol
8
The categories of this paper are: hep-ex
37
The categories of this paper are: supr-con
27
The categories of this paper are: comp-gas
19
The categories of this paper are: eess
3
The categories of this paper are: physics
32
The categories of this paper are: atom-ph
5
The categories of this paper are: gr-qc
4
The categories of this paper are: cond-mat