ArticlePLoS genetics2014
Relationship estimation from whole-genome sequence data.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
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- Complex kinship testing using the MGIEasy Pa-SNPs genotyping kit.International journal of legal medicine · 2025Article
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- Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Deep Screening for X Chromosome Parent-of-Origin Effects on Neurobehavioral and Neuroanatomical Phenotypes in 47,XXY Klinefelter Syndrome.Biological psychiatry global open science · 2024Article
- Hippocampal aggregation signatures of pathogenic UBQLN2 in amyotrophic lateral sclerosis and frontotemporal dementia.Brain : a journal of neurology · 2024Article
- Developing a Framework for Self-regulatory Governance in Healthcare AI Research: Insights from South Korea.Asian bioethics review · 2024Article
- Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques.bioRxiv : the preprint server for biology · 2024Article
- RaPID-Query for fast identity by descent search and genealogical analysis.Bioinformatics (Oxford, England) · 2023Article
- KIN: a method to infer relatedness from low-coverage ancient DNA.Genome biology · 2023Article
- Parent-offspring inference in inbred populations.Molecular ecology resources · 2022Article
- Applications of massively parallel sequencing in forensic genetics.Genetics and molecular biology · 2022Article
- GRAPE: genomic relatedness detection pipeline.F1000Research · 2022Article
- A machine learning approach for missing persons cases with high genotyping errors.Frontiers in genetics · 2022Article
- The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry.Horticulture research · 2021Article
- Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta).Molecular ecology resources · 2021Article
- Host genetic effects in pneumonia.American journal of human genetics · 2021Article
- Infantile onset Sandhoff disease: clinical manifestation and a novel common mutation in Thai patients.BMC pediatrics · 2021Article
- PATRIOT: A Pipeline for Tracing Identity-by-Descent for Chromosome Segments to Improve Genomic Prediction in Self-Pollinating Crop Species.Frontiers in plant science · 2021Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
The determination of the relationship between a pair of individuals is a fundamental application of genetics. Previously, we and others have demonstrated that identity-by-descent (IBD) information generated from high-density single-nucleotide polymorphism (SNP) data can greatly improve the power and accuracy of genetic relationship detection. Whole-genome sequencing (WGS) marks the final step in increasing genetic marker density by assaying all single-nucleotide variants (SNVs), and thus has the potential to further improve relationship detection by enabling more accurate detection of IBD segments and more precise resolution of IBD segment boundaries. However, WGS introduces new complexities that must be addressed in order to achieve these improvements in relationship detection. To evaluate these complexities, we estimated genetic relationships from WGS data for 1490 known pairwise relationships among 258 individuals in 30 families along with 46 population samples as controls. We identified several genomic regions with excess pairwise IBD in both the pedigree and control datasets using three established IBD methods: GERMLINE, fastIBD, and ISCA. These spurious IBD segments produced a 10-fold increase in the rate of detected false-positive relationships among controls compared to high-density microarray datasets. To address this issue, we developed a new method to identify and mask genomic regions with excess IBD. This method, implemented in ERSA 2.0, fully resolved the inflated cryptic relationship detection rates while improving relationship estimation accuracy. ERSA 2.0 detected all 1(st) through 6(th) degree relationships, and 55% of 9(th) through 11(th) degree relationships in the 30 families. We estimate that WGS data provides a 5% to 15% increase in relationship detection power relative to high-density microarray data for distant relationships. Our results identify regions of the genome that are highly problematic for IBD mapping and introduce new software to accurately detect 1(st) through 9(th) degree relationships from whole-genome sequence data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.