Y-mer: a k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data
Determining genetic ancestry of an individual is challenging from poorly preserved or mixed samples that permit only ultra-low coverage sequence at depths less than 0.1 × at target loci. Leveraging recent advances in telomere-to-telomere sequencing of whole genomes with long reads, we develop a new k-mer based method, Y-mer, and show how information from hundreds of thousands of k-mers in distance-based models enables accurate inference of chrY haplogroup from whole-genome sequence at depth less than 0.01x. We test the performance of Y-mer on ancient DNA and prenatal screening data, showing its potential for genetic ancestry inference for cell-free, forensic and ancient DNA research.
Authors
- Kaarel Krjutškov (ORCID: https://orcid.org/0000-0003-1297-1464)
- Maido Remm (ORCID: https://orcid.org/0000-0003-3966-8422)
- Lauris Kaplinski (ORCID: https://orcid.org/0000-0001-6682-7295)
- Andres Salumets (ORCID: https://orcid.org/0000-0002-1251-8160)
- Tarmo Puurand
- Märt Möls (ORCID: https://orcid.org/0000-0002-5845-3534)
- Toomas Kivisild (ORCID: https://orcid.org/0000-0002-6297-7808)
- Kadri Maal
Institutions
- Karolinska University Hospital (SE)
- Karolinska Institutet (SE)
- Competence Centre on Health Technologies (Estonia) (EE)
- University of Tartu (EE)
- KU Leuven (BE)
Publication Details
- Journal
- Genome biology
- Published
- 2025-08-12
- DOI
- https://doi.org/10.1186/s13059-025-03714-3
- Citations
- 1
- Primary Topic
- Forensic and Genetic Research
- Type
- article
- Field-Weighted Citation Impact
- 1.82
Funders
- Eesti Teadusagentuur
- Fonds Wetenschappelijk Onderzoek
- Tartu Ülikool
- HORIZON EUROPE Framework Programme