ArticleNature biotechnology2014
A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.
Article in Nature biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- PIEZO1 variants that reduce open channel probability are associated with familial osteoarthritis.The Journal of biological chemistry · 2026Article
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- BICEP: Bayesian inference for rare genomic variant causality evaluation in pedigrees.Briefings in bioinformatics · 2024Article
- Variant ranking pipeline for complex familial disorders.Scientific reports · 2024Article
- RAB1A haploinsufficiency phenocopies the 2p14-p15 microdeletion and is associated with impaired neuronal differentiation.American journal of human genetics · 2023Article
- DIS3 Variants are Associated With Primary Ovarian Insufficiency: Importance of Transcription/Translation in Oogenesis.The Journal of clinical endocrinology and metabolism · 2023Observational
- Neurite outgrowth deficits caused by rare PLXNB1 mutation in pediatric bipolar disorder.Molecular psychiatry · 2023Article
- Common genetic risk factors in ASD and ADHD co-occurring families.Human genetics · 2023Article
- NOD/RIPK2 signalling pathway contributes to osteoarthritis susceptibility.Annals of the rheumatic diseases · 2022Article
- A dominant negative ADIPOQ mutation in a diabetic family with renal disease, hypoadiponectinemia, and hyperceramidemia.NPJ genomic medicine · 2022Article
- Polygenic risk impacts PDGFRA mutation penetrance in non-syndromic cleft lip and palate.Human molecular genetics · 2022Article
- A Novel Gene CDC27 Causes SLE and Is Associated With the Disease Activity.Frontiers in immunology · 2022Article
- The history and geographic distribution of a KCNQ1 atrial fibrillation risk allele.Nature communications · 2021Article
- Whole-exome sequencing identifies genes associated with Tourette's disorder in multiplex families.Molecular psychiatry · 2021Article
- A framework for high-resolution phenotyping of candidate male infertility mutants: from human to mouse.Human genetics · 2021Review
- FANCM c5791C>T stopgain mutation (rs144567652) is a familial colorectal cancer risk factor.Molecular genetics & genomic medicine · 2020Article
- Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias.HGG advances · 2020Article
- Functional gene networks reveal distinct mechanisms segregating in migraine families.Brain : a journal of neurology · 2020Article
- Higher burden of rare frameshift indels in genes related to synaptic transmission separate familial hemiplegic migraine from common types of migraine.Journal of medical genetics · 2020Article
- Missing heritability in Parkinson's disease: the emerging role of non-coding genetic variation.Journal of neural transmission (Vienna, Austria : 1996) · 2020Review
11 more citing papers are in PubMed but not listed here.
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25 authors.
Funding
Abstract
High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present pedigree-VAAST (pVAAST), a disease-gene identification tool designed for high-throughput sequence data in pedigrees. pVAAST uses a sequence-based model to perform variant and gene-based linkage analysis. Linkage information is then combined with functional prediction and rare variant case-control association information in a unified statistical framework. pVAAST outperformed linkage and rare-variant association tests in simulations and identified disease-causing genes from whole-genome sequence data in three human pedigrees with dominant, recessive and de novo inheritance patterns. The approach is robust to incomplete penetrance and locus heterogeneity and is applicable to a wide variety of genetic traits. pVAAST maintains high power across studies of monogenic, high-penetrance phenotypes in a single pedigree to highly polygenic, common phenotypes involving hundreds of pedigrees.
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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.