ArticleEuropean journal of human genetics : EJHG2015
Collapsed haplotype pattern method for linkage analysis of next-generation sequence data.
Article in European journal of human genetics : EJHG, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Identification of autosomal recessive nonsyndromic hearing impairment genes through the study of consanguineous and non-consanguineous families: past, present, and future.Human genetics · 2022Review
- Myopia in African Americans Is Significantly Linked to Chromosome 7p15.2-14.2.Investigative ophthalmology & visual science · 2021Article
- Genetic Variation and Recurrent Haplotypes on Chromosome 6q23-25 Risk Locus in Familial Lung Cancer.Cancer research · 2021Article
- PedMiner: a tool for linkage analysis-based identification of disease-associated variants using family based whole-exome sequencing data.Briefings in bioinformatics · 2021Review
- A Rare Variant Nonparametric Linkage Method for Nuclear and Extended Pedigrees with Application to Late-Onset Alzheimer Disease via WGS Data.American journal of human genetics · 2019Article
- Exome genotyping and linkage analysis identifies two novel linked regions and replicates two others for myopia in Ashkenazi Jewish families.BMC medical genetics · 2019Article
- Application of genome analysis strategies in the clinical testing for pediatric diseases.Pediatric investigation · 2018Article
- Myopia in Chinese families shows linkage to 10q26.13.Molecular vision · 2018Observational
- Whole-Exome Sequencing Identifies the 6q12-q16 Linkage Region and a Candidate Gene, TTK, for Pulmonary Nontuberculous Mycobacterial Disease.American journal of respiratory and critical care medicine · 2017Article
- Caucasian Families Exhibit Significant Linkage of Myopia to Chromosome 11p.Investigative ophthalmology & visual science · 2017Article
- PERCH: A Unified Framework for Disease Gene Prioritization.Human mutation · 2017Article
- Can whole-exome sequencing data be used for linkage analysis?European journal of human genetics : EJHG · 2016Article
- Parametric Linkage Analysis Identifies Five Novel Genome-Wide Significant Loci for Familial Lung Cancer.Human heredity · 2016Article
- Construction of relatedness matrices using genotyping-by-sequencing data.BMC genomics · 2015Article
- Generation of sequence-based data for pedigree-segregating Mendelian or Complex traits.Bioinformatics (Oxford, England) · 2015Article
- Genetic linkage analysis in the age of whole-genome sequencing.Nature reviews. Genetics · 2015Review
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Authors and funding
5 authors.
Funding
Abstract
Recent advances in next-generation sequencing (NGS) make it possible to directly sequence genomes and exomes of individuals with Mendelian diseases and screen sequence data for causal variants. With the reduction in cost of NGS, DNA samples from entire families can be sequenced and linkage analysis can be performed directly using NGS data. Inspired by 'burden' tests, which are used for complex trait rare variant association studies, we developed the collapsed haplotype pattern (CHP) method for linkage analysis. Using data from several deafness genes we demonstrate that the CHP method is substantially more powerful than analyzing individual variants. Unlike applying NGS data filtering approaches, the CHP method provides statistical evidence of a gene's involvement in disease etiology and is also less likely to exclude causal variants in the presence of phenocopies and/or reduced penetrance. The CHP method was implemented in the SEQLinkage software package, which can perform linkage analysis on NGS data or can generate data compatible with many linkage analysis programs, reviving them for use in NGS era.
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