Y-mer: a k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Tarmo Puurand, Märt Möls, Lauris Kaplinski, Kadri Maal, Kaarel Krjutskov, Andres Salumets, Toomas Kivisild, Maido Remm
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引用次数: 0

Abstract

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.
Y-mer:一种基于k-mer的方法,用于从超低测序深度数据中确定人类Y染色体单倍群
对于保存不良或混合样品,仅允许在目标位点深度小于0.1 ×的超低覆盖序列,确定个体的遗传祖先是具有挑战性的。利用端粒到端粒全基因组长reads测序的最新进展,我们开发了一种新的基于k-mer的方法,Y-mer,并展示了基于距离的模型中来自数十万k-mer的信息如何能够在深度小于0.01x的全基因组序列中准确推断chrY单倍群。我们测试了Y-mer在古代DNA和产前筛查数据上的表现,显示了它在无细胞、法医和古代DNA研究中遗传祖先推断的潜力。
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来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
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