Kinship Decouple and Phenotype Selection (KDPS): a tool for phenotype-aware decoupling of related subjects

Abstract Relatedness within genomic cohorts is a potential source of bias for many genetic analyses. Existing tools to break relatedness are phenotype-naïve; they indiscriminately remove subjects to break relationship, risking the loss of valuable data, especially in studies targeting uncommon and r...

Celý popis

Uloženo v:
Podrobná bibliografie
Vydáno v:Briefings in bioinformatics Ročník 26; číslo 5
Hlavní autoři: Gu, Wanjun, Xi, Jiachen, Cao, Steven, Salem, Rany M
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 01.09.2025
Oxford Publishing Limited (England)
Témata:
Algorithms
Biobanks
Datasets
Decoupling
Epidemiology
Genetic analysis
Genetics
Genomics - methods
Genotype & phenotype
Humans
Pedigree
Phenotype
Phenotypes
Retention
Software
sample selection
subject relatedness
greedy algorithm
kinship decoupling
phenotype prioritization
genetic epidemiology
ISSN:1467-5463, 1477-4054, 1477-4054
On-line přístup:Získat plný text
Tagy: Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
Popis
Shrnutí:Abstract Relatedness within genomic cohorts is a potential source of bias for many genetic analyses. Existing tools to break relatedness are phenotype-naïve; they indiscriminately remove subjects to break relationship, risking the loss of valuable data, especially in studies targeting uncommon and rare phenotypes. To address this limitation, we developed the Kinship Decouple and Phenotype Selection (KDPS) tool, with a novel algorithm designed to enhance the precision of subject selection in genetic and epidemiological research by incorporating phenotype prioritization. KDPS separates related individuals by considering relatedness (kinship or identity by descent) scores and allows prioritizing subjects based on phenotypes of interest. This approach enables the retention of valuable subjects for analysis, even in the face of necessary exclusions due to relatedness. Furthermore, KDPS accommodates a wide range of phenotypes, including quantitative and categorical, and allows for customization to either prioritize specific phenotypes or maximization of sample size. In simulations based on the UK Biobank dataset and real-world datasets, KDPS demonstrated significant improvements in retention of subjects with prioritized phenotypes and computational efficiency compared to previously published software. The ability of this method to process biobank-scale studies within practical timeframes marks the ability of this method to process biobank-scale studies within practical timeframes and marks a considerable advancement over existing techniques. KDPS offers tailored solutions for complex analytical challenges and broad applicability in genetics and epidemiology research. To our knowledge, KDPS is the first tool to perform phenotype-aware decoupling, paving the way for more powerful genetic and epidemiological analyses.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbaf561