RT Journal Article
SR Electronic
T1 Efficient genome-wide sequencing and low coverage pedigree analysis from non-invasively collected samples
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 029520
DO 10.1101/029520
A1 Noah Snyder-Mackler
A1 William H. Majoros
A1 Michael L. Yuan
A1 Amanda O. Shaver
A1 Jacob B. Gordon
A1 Gisela H. Kopp
A1 Stephen A. Schlebusch
A1 Jeffrey D. Wall
A1 Susan C. Alberts
A1 Sayan Mukherjee
A1 Xiang Zhou
A1 Jenny Tung
YR 2015
UL http://biorxiv.org/content/early/2015/10/21/029520.abstract
AB Research on the genetics of natural populations was revolutionized in the 1990’s by methods for genotyping non-invasively 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 non-invasively 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 non-invasive samples are available. The lab protocol and software (“WHODAD”) are freely available at www.tung-lab.org/protocols and www.xzlab.org/software, respectively.