Faculty, Staff and Student Publications
Language
English
Publication Date
1-1-2026
Journal
Bioinformatics Advances
DOI
10.1093/bioadv/vbag006
PMID
41640622
PMCID
PMC12866910
PubMedCentral® Posted Date
1-12-2026
PubMedCentral® Full Text Version
Post-print
Abstract
Motivation: The availability of large-scale genetic data presents a unique opportunity to study the genetic ancestries of individuals, which requires an efficient and scalable method. The existing global ancestry methods are accurate, but they cannot scale to large genetic datasets. Identity-by-descent (IBD) segments are DNA segments shared by individuals such that they are inherited from a common recent ancestor without recombination. These IBD segments, which reflect co-ancestry, provide an efficient alternative for inferring genetic ancestry.
Results: We introduced a reference-based global ancestry inference method called FRAME (Fast Reference-based Ancestry Makeup Estimation). FRAME utilizes partial local ancestry information estimated through IBD segments. Instead of using sophisticated local ancestry inference methods designed to make the best calls at each site, we employed an efficient IBD method for faster and space-efficient algorithms that are robust to genotyping errors. Additionally, we introduced a new method of panel refinement that can enrich the ancestral homogeneity of individual haplotypes in the reference panel, thus leading to more accurate ancestry composition estimates. We benchmarked the performance of our method with real and simulated data. FRAME consumes ∼10-100 times less memory while maintaining a comparable accuracy.
Published Open-Access
yes
Recommended Citation
Shakya, Pramesh; Naseri, Ardalan; Zhi, Degui; et al., "Frame: Fast Reference-Based Ancestry Makeup Estimation Tool" (2026). Faculty, Staff and Student Publications. 773.
https://digitalcommons.library.tmc.edu/uthshis_docs/773
Comments
Availability and implementation: Source code is available at https://github.com/ucfcbb/FRAME.