ArticlePLoS genetics2015
Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it, 28 citations in OpenAlex.
- Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits.Genome medicine · 2022Pooled it
- The Importance of Copy Number Variant Analysis in Patients with Monogenic Kidney Disease.Kidney international reports · 2024Article
- Copy-number analysis from genome sequencing data of 11,754 rare-disease parent-child trios: A model for identifying autosomal recessive human gene knockouts including a novel gene for autosomal recessive retinopathy.Genetics in medicine open · 2024Article
- A genotype-to-phenotype approach suggests under-reporting of single nucleotide variants in nephrocystin-1 (NPHP1) related disease (UK 100,000 Genomes Project).Scientific reports · 2023Article
- Article
- Cytogenetically visible inversions are formed by multiple molecular mechanisms.Human mutation · 2020Article
- CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels.Genetics in medicine : official journal of the American College of Medical Genetics · 2020Article
- Enzyme-free optical DNA mapping of the human genome using competitive binding.Nucleic acids research · 2019Article
- 2018 Victor A. McKusick Leadership Award: Molecular Mechanisms for Genomic and Chromosomal Rearrangements.American journal of human genetics · 2019Article
- Article
- Article
- Mapping the genomic landscape of inherited retinal disease genes prioritizes genes prone to coding and noncoding copy-number variations.Genetics in medicine : official journal of the American College of Medical Genetics · 2018Article
- Assessment of the incorporation of CNV surveillance into gene panel next-generation sequencing testing for inherited retinal diseases.Journal of medical genetics · 2018Article
- The behavioural phenotype of Potocki-Lupski syndrome: a cross-syndrome comparison.Journal of neurodevelopmental disorders · 2018Article
- The value of new genome references.Experimental cell research · 2017Review
- Alternate-locus aware variant calling in whole genome sequencing.Genome medicine · 2016Article
- Nonrecurrent PMP22-RAI1 contiguous gene deletions arise from replication-based mechanisms and result in Smith-Magenis syndrome with evident peripheral neuropathy.Human genetics · 2016Article
- Major influence of repetitive elements on disease-associated copy number variants (CNVs).Human genomics · 2016Review
- Copy number analysis of the low-copy repeats at the primate NPHP1 locus by array comparative genomic hybridization.Genomics data · 2016Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 1 country.
Funding
Abstract
Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases-about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual's susceptibility to acquiring disease-associated alleles.
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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.