Biology subjects

Sapin, E.

Publications and source records attributed to Sapin, E..

2 recordsLinked to original sources

bioRxiv2026

A Novel Method for Across-Chromosome Phasing without Relative Data

MotivationAcross-chromosome phasing identifies which haplotypes of different chromosomes come from the same parent. This differs from within-chromosome phasing, which uses linkage disequilibrium patterns to determine which alleles were co-inherited within each chromosome but does not match haplotypes across different chromosomes. While across-chromosome phasing can be conducted using genotypes from parents or close relatives, current methods perform poorly for samples of unrelated individuals. Here, we introduce a novel approach for across-chromosome phasing that employs a window-based SNP-similarity metric, eliminating the need for data from close relatives or detection of identical-by-descent haplotypes. ResultsUsing UK Biobank offspring with both parents genotyped as a gold standard, we evaluated the performance of our method by phasing the offspring without using parental data. In genomic data with no within-chromosomal phase errors, our algorithm achieved a mean across-chromosome phasing accuracy of 95%, with 53% of individuals phased perfectly. When data was pre-phased computationally using a standard within-chromosomal phasing algorithm, mean accuracy for across-chromosome phasing dropped to 83.1%. Thus, our method is limited primarily by the accuracy of within-chromosome phasing, and can approach near perfect across-chromosome phasing accuracy as within-chromosome phasing accuracy improves. Contactemmanuel.sapin@colorado.edu and matthew.c.keller@colorado.edu

genomics↗

bioRxiv2026

Near perfect identification of half sibling versus niece/nephew avuncular pairs without pedigree information or genotyped relatives

Motivation: Large-scale genomic biobanks contain thousands of second-degree relatives with missing pedigree metadata. Accurately distinguishing half-sibling (HS) from niece/nephew-avuncular (N/A) pairs--both sharing approximately 25% of the genome--remains a significant challenge. Current SNP-based methods rely on Identical-By-Descent (IBD) segment counts and age differences, but substantial distributional overlap leads to high misclassification rates. There is a critical need for a scalable, genotype-only method that can resolve these "half-degree" ambiguities without requiring observed pedigrees or extensive relative information. Results: We present a novel computational framework that achieves near-complete separation of HS and N/A pairs using only genotype data. Our approach utilizes across-chromosome phasing to derive haplotype-level sharing features that summarize how IBD is distributed across parental homologues. By modeling these features with a Gaussian mixture model (GMM), we demonstrate near-perfect classification accuracy (> 98%) in biobank-scale data. Furthermore, we show that these high-confidence relationship labels can serve as long-range phasing anchors, providing structural constraints that improve the accuracy of across-chromosome homologue assignment. This method provides a robust, scalable solution for pedigree reconstruction and the control of cryptic relatedness in large-scale genomic studies.

bioinformatics↗