AncestryGeni: A novel genetic ancestry classification pipeline for small and noisy sequence data Journal Article

   

Authors:	Elhaik, E.; Behnamian, S.; Howe, M.; Tang, H.; Yan, H.; Tian, S.; Shivaram, S.; Zepeda Mendoza, C.; MacLachlan, K.; Usmani, S.; Pirooznia, M.; Morgan, G.; Blaney, P.; Maura, F.; Baughn, L. B.
Article Title:	AncestryGeni: A novel genetic ancestry classification pipeline for small and noisy sequence data
Abstract:	Motivation Efforts to address health disparities are often limited by the lack of robust computational tools for inferring genetic ancestry by calculating an individual's genetic similarity to continental groups. We have already shown that a preferred alternative to self-described race is using ancestry-informative markers (AIMs) that can be classified into ancestral components and used to estimate their similarity to those of known populations to identify continental groups. However, real-world genomic data can present challenges, including limited availability of germline DNA, a small number of AIMs for each sample, and the use of different variant calling software, limiting the application of existing solutions. Results Here, we describe a novel supervised machine-learning tool AncestryGeni, which infers genetic ancestry for samples with even a hundred markers and is applicable to any genomic data, including whole exome sequencing (WES) and RNA sequencing (RNA-Seq) data. Applying AncestryGeni to a real-world genomic dataset obtained from the Multiple Myeloma Research Foundation (MMRF) CoMMpass study, we show that it is more accurate than the commonly used FastNGSadmix when using nonstandard genomic material. We also demonstrate that when using AncestryGeni, the tumor-derived sequence obtained from WES and RNA-Seq can be a robust data source to accurately estimate an individual's genetic similarity to a continental group. © 2025 The Author(s).
Journal Title:	Bioinformatics
Volume:	41
Issue:	7
ISSN:	1367-4803
Publisher:	Oxford University Press
Date Published:	2025-07-01
Start Page:	btaf391
Language:	English
DOI:	10.1093/bioinformatics/btaf391
PROVIDER:	scopus
PMCID:	PMC12289551
PUBMED:	40627371
DOI/URL:	https://www.scopus.com/inward/record.uri?eid=2-s2.0-105011509390&doi=10.1093%2fbioinformatics%2fbtaf391&partnerID=40&md5=47d6b4a65b9c4cb746e213437196a0e3
Notes:	Article -- Source: Scopus

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