Identifying distant relatives using benchtop-scale sequencing

August E Woerner; Nicole M Novroski; Sammed Mandape; Jonathan L King; Benjamin Crysup; Michael D Coble

doi:10.1016/j.fsigen.2023.103005

Identifying distant relatives using benchtop-scale sequencing

Forensic Sci Int Genet. 2024 Mar:69:103005. doi: 10.1016/j.fsigen.2023.103005. Epub 2023 Dec 27.

Authors

August E Woerner¹, Nicole M Novroski², Sammed Mandape³, Jonathan L King³, Benjamin Crysup⁴, Michael D Coble⁴

Affiliations

¹ Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA. Electronic address: august.woerner@unthsc.edu.
² Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Anthropology, University of Toronto, Mississauga, ON, Canada.
³ Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.
⁴ Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA.

PMID: 38171224
DOI: 10.1016/j.fsigen.2023.103005

Abstract

The genetic component of forensic genetic genealogy (FGG) is an estimate of kinship, often conducted at genome scales between a great number of individuals. The promise of FGG is substantial: in concert with genealogical records and other nongenetic information, it can indirectly identify a person of interest. A downside of FGG is cost, as it is currently expensive and requires chemistries uncommon to forensic genetic laboratories (microarrays and high throughput sequencing). The more common benchtop sequencers can be coupled with a targeted PCR assay to conduct FGG, though such approaches have limited resolution for kinship. This study evaluates low-pass sequencing, an alternative strategy that is accessible to benchtop sequencers and can produce resolutions comparable to high-pass sequencing. Samples from a three-generation pedigree were augmented to include up to 7th degree relatives (using whole genome pedigree simulations) and the ability to recover the true kinship coefficient was assessed using algorithms qualitatively similar to those found in GEDmatch. We show that up to 7th degree relatives can be reliably inferred from 1 × whole genome sequencing obtainable from desktop sequencers.

Keywords: Genetic genealogy; Genotype imputation; Kinship; Low pass sequencing; Massively parallel sequencing.

Publication types

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

MeSH terms

Algorithms*
DNA Fingerprinting
Genotype
High-Throughput Nucleotide Sequencing*
Humans
Pedigree
Polymorphism, Single Nucleotide