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Am J Hum Genet. 2014 Nov 6;95(5):553-64. doi: 10.1016/j.ajhg.2014.10.005. Epub 2014 Oct 30.

PRIMUS: rapid reconstruction of pedigrees from genome-wide estimates of identity by descent.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
2
Channing Division of Network Medicine, Harvard School of Public Health, Boston, MA 02115, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
3
Channing Division of Network Medicine, Harvard School of Public Health, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
4
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. Electronic address: debnick@uw.edu.
5
Epidemiology, Human Genetics, & Environmental Sciences, University of Texas Health Science Center, Houston, TX 77225, USA. Electronic address: jennifer.e.below@uth.tmc.edu.

Abstract

Understanding and correctly utilizing relatedness among samples is essential for genetic analysis; however, managing sample records and pedigrees can often be error prone and incomplete. Data sets ascertained by random sampling often harbor cryptic relatedness that can be leveraged in genetic analyses for maximizing power. We have developed a method that uses genome-wide estimates of pairwise identity by descent to identify families and quickly reconstruct and score all possible pedigrees that fit the genetic data by using up to third-degree relatives, and we have included it in the software package PRIMUS (Pedigree Reconstruction and Identification of the Maximally Unrelated Set). Here, we validate its performance on simulated, clinical, and HapMap pedigrees. Among these samples, we demonstrate that PRIMUS can verify reported pedigree structures and identify cryptic relationships. Finally, we show that PRIMUS reconstructed pedigrees, all of which were previously unknown, for 203 families from a cohort collected in Starr County, TX (1,890 samples).

PMID:
25439724
PMCID:
PMC4225580
DOI:
10.1016/j.ajhg.2014.10.005
[Indexed for MEDLINE]
Free PMC Article

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