Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples.

Abstract:

:Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software ("WHODAD") are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively.

journal_name

Genetics

journal_title

Genetics

authors

Snyder-Mackler N,Majoros WH,Yuan ML,Shaver AO,Gordon JB,Kopp GH,Schlebusch SA,Wall JD,Alberts SC,Mukherjee S,Zhou X,Tung J

doi

10.1534/genetics.116.187492

subject

Has Abstract

pub_date

2016-06-01 00:00:00

pages

699-714

issue

2

eissn

0016-6731

issn

1943-2631

pii

genetics.116.187492

journal_volume

203

pub_type

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