ArticleGenome research2020
Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 15 citations in OpenAlex.
- Association between gut microbiota and Hirschsprung disease: a bidirectional two-sample Mendelian randomization study.Frontiers in microbiology · 2024Article
- Urine miRNA signature as potential non-invasive diagnostic biomarker for Hirschsprung's disease.Frontiers in molecular neuroscience · 2024Article
- The prognostic value of RASGEF1A RNA expression and DNA methylation in cytogenetically normal acute myeloid leukemia.Cancer biomarkers : section A of Disease markers · 2023Article
- Artificial intelligence-based approaches for the detection and prioritization of genomic mutations in congenital surgical diseases.Frontiers in pediatrics · 2023Review
- Whole genome sequencing reveals epistasis effects within RET for Hirschsprung disease.Scientific reports · 2022Article
- Human Pluripotent Stem Cell-Based Models for Hirschsprung Disease: From 2-D Cell to 3-D Organoid Model.Cells · 2022Review
- Adult patients with allied disorders of Hirschsprung's disease in emergency department: An 11-year retrospective study.World journal of gastrointestinal surgery · 2022Article
- A multi-enhancerGenome research · 2021Article
- Roles of Enteric Neural Stem Cell Niche and Enteric Nervous System Development in Hirschsprung Disease.International journal of molecular sciences · 2021Review
- The Emerging Genetic Landscape of Hirschsprung Disease and Its Potential Clinical Applications.Frontiers in pediatrics · 2021Review
Corrections and comments
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Authors and funding
12 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is widely recognized that noncoding genetic variants play important roles in many human diseases, but there are multiple challenges that hinder the identification of functional disease-associated noncoding variants. The number of noncoding variants can be many times that of coding variants; many of them are not functional but in linkage disequilibrium with the functional ones; different variants can have epistatic effects; different variants can affect the same genes or pathways in different individuals; and some variants are related to each other not by affecting the same gene but by affecting the binding of the same upstream regulator. To overcome these difficulties, we propose a novel analysis framework that considers convergent impacts of different genetic variants on protein binding, which provides multiscale information about disease-associated perturbations of regulatory elements, genes, and pathways. Applying it to our whole-genome sequencing data of 918 short-segment Hirschsprung disease patients and matched controls, we identify various novel genes not detected by standard single-variant and region-based tests, functionally centering on neural crest migration and development. Our framework also identifies upstream regulators whose binding is influenced by the noncoding variants. Using human neural crest cells, we confirm cell stage-specific regulatory roles of three top novel regulatory elements on our list, respectively in the
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