correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes

Emil Nyerki; Tibor Kalmár; Oszkár Schütz; Rui M Lima; Endre Neparáczki; Tibor Török; Zoltán Maróti

doi:10.1186/s13059-023-02882-4

correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes

Genome Biol. 2023 Feb 28;24(1):38. doi: 10.1186/s13059-023-02882-4.

Authors

Emil Nyerki^#^{1

2}, Tibor Kalmár^#¹, Oszkár Schütz³, Rui M Lima⁴, Endre Neparáczki^{2

3}, Tibor Török^{2

3}, Zoltán Maróti^{5

6}

Affiliations

¹ Department of Pediatrics, University of Szeged Albert Szent-Györgyi Medical Center Faculty of Medicine, Szeged, Hungary.
² Department of Archaeogenetics, Institute of Hungarian Research, Budapest, Hungary.
³ Department of Genetics, University of Szeged, Szeged, Hungary.
⁴ Institute of Plant Biology, Biological Research Centre, Szeged, Hungary.
⁵ Department of Pediatrics, University of Szeged Albert Szent-Györgyi Medical Center Faculty of Medicine, Szeged, Hungary. maroti.zoltan@med.u-szeged.hu.
⁶ Department of Archaeogenetics, Institute of Hungarian Research, Budapest, Hungary. maroti.zoltan@med.u-szeged.hu.

^# Contributed equally.

Abstract

Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×-11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data.

Keywords: Ancient DNA; Forensic; Genomics; Kinship; Low coverage.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Forensic Medicine*
Genome, Human*
Humans
Whole Genome Sequencing