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

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2016
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Snyder-Mackler, Noah
Majoros, William H.
Yuan, Michael L.
Shaver, Amanda O.
Gordon, Jacob B.
Schlebusch, Stephen A.
Wall, Jeffrey D.
Alberts, Susan C.
Mukherjee, Sayan
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Genetics. 2016, 203(2), pp. 699-714. ISSN 0016-6731. eISSN 1943-2631. Available under: doi: 10.1534/genetics.116.187492
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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.

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ISO 690SNYDER-MACKLER, Noah, William H. MAJOROS, Michael L. YUAN, Amanda O. SHAVER, Jacob B. GORDON, Gisela H. KOPP, Stephen A. SCHLEBUSCH, Jeffrey D. WALL, Susan C. ALBERTS, Sayan MUKHERJEE, Xiang ZHOU, Jenny TUNG, 2016. Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples. In: Genetics. 2016, 203(2), pp. 699-714. ISSN 0016-6731. eISSN 1943-2631. Available under: doi: 10.1534/genetics.116.187492
BibTex
@article{SnyderMackler2016-06-06Effic-35973,
  year={2016},
  doi={10.1534/genetics.116.187492},
  title={Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples},
  number={2},
  volume={203},
  issn={0016-6731},
  journal={Genetics},
  pages={699--714},
  author={Snyder-Mackler, Noah and Majoros, William H. and Yuan, Michael L. and Shaver, Amanda O. and Gordon, Jacob B. and Kopp, Gisela H. and Schlebusch, Stephen A. and Wall, Jeffrey D. and Alberts, Susan C. and Mukherjee, Sayan and Zhou, Xiang and Tung, Jenny}
}
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