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

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

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).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Validation Study

MeSH terms

  • Base Sequence
  • Computer Simulation
  • Exome / genetics
  • Gene Frequency
  • Genetics, Population / methods*
  • Humans
  • Molecular Sequence Data
  • Pedigree*
  • Pulmonary Disease, Chronic Obstructive / genetics*
  • Sequence Analysis, DNA
  • Software*
  • Texas

Supplementary concepts

  • COPD, Severe Early-Onset