Benchmarking relatedness inference methods with genome-wide data from thousands of relatives

Monica D. Ramstetter, Thomas D. Dyer, Donna M. Lehman, Joanne E. Curran, Ravindranath Duggirala, John Blangero, Jason G. Mezey, Amy L. Williams

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

Inferring relatedness from genomic data is an essential component of genetic association studies, population genetics, forensics, and genealogy. While numerous methods exist for inferring relatedness, thorough evaluation of these approaches in real data has been lacking. Here, we report an assessment of 12 state-of-the-art pairwise relatedness inference methods using a data set with 2485 individuals contained in several large pedigrees that span up to six generations. We find that all methods have high accuracy (92–99%) when detecting first- and second-degree relationships, but their accuracy dwindles to <43% for seventh-degree relationships. However, most identical by descent (IBD) segment-based methods inferred seventh-degree relatives correct to within one relatedness degree for.76% of relative pairs. Overall, the most accurate methods are Estimation of Recent Shared Ancestry (ERSA) and approaches that compute total IBD sharing using the output from GERMLINE and Refined IBD to infer relatedness. Combining information from the most accurate methods provides little accuracy improvement, indicating that novel approaches, such as new methods that leverage relatedness signals from multiple samples, are needed to achieve a sizeable jump in performance.

Original languageEnglish (US)
Pages (from-to)75-82
Number of pages8
JournalGenetics
Volume207
Issue number1
DOIs
StatePublished - 2017

Keywords

  • Admixture
  • Identical by descent
  • Relatedness estimation

ASJC Scopus subject areas

  • Genetics

Fingerprint Dive into the research topics of 'Benchmarking relatedness inference methods with genome-wide data from thousands of relatives'. Together they form a unique fingerprint.

Cite this