ArticleGenetics in medicine : official journal of the American College of Medical Genetics2016
Novel mutations in genes causing hereditary spastic paraplegia and Charcot-Marie-Tooth neuropathy identified by an optimized protocol for homozygosity mapping based on whole-exome sequencing.
Article in Genetics in medicine : official journal of the American College of Medical Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 28 papers.
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28 citing papers in PubMed, 39 citations in OpenAlex.
- Whole-exome sequencing to analyze population structure, parental inbreeding, and familial linkage.Proceedings of the National Academy of Sciences of the United States of America · 2016Trial
- Biallelic variants in COX18 cause a mitochondrial disorder primarily manifesting as peripheral neuropathy.Brain : a journal of neurology · 2026Article
- Variant Ataxia-Telangiectasia Presenting as Tremor-Dystonia Syndrome in a Bulgarian Religious Minority.Genes · 2025Article
- Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data.Human genomics · 2024Review
- Alternative splicing expands the clinical spectrum of NDUFS6-related mitochondrial disorders.Genetics in medicine : official journal of the American College of Medical Genetics · 2024Article
- Hereditary spastic paraparesis type 46 (SPG46): new GBA2 variants in a large Italian case series and review of the literature.Neurogenetics · 2024Review
- Genome-wide analysis of runs of homozygosity in Pakistani controls with no history of speech or language-related developmental phenotypes.Annals of human biology · 2023Article
- Case report: Hereditary spastic paraplegia with a novel homozygous mutation inFrontiers in neurology · 2023Article
- Characterization of Arabian Peninsula whole exomes: Contributing to the catalogue of human diversity.iScience · 2022Article
- The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases.Human mutation · 2022Article
- High diagnostic rate of trio exome sequencing in consanguineous families with neurogenetic diseases.Brain : a journal of neurology · 2022Article
- Bi-allelic variants in neuronal cell adhesion molecule cause a neurodevelopmental disorder characterized by developmental delay, hypotonia, neuropathy/spasticity.American journal of human genetics · 2022Article
- Spastic paraplegia type 46: novel and recurrent GBA2 gene variants in a compound heterozygous Italian patient with spastic ataxia phenotype.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2021Review
- Genetic Survey of Autosomal Recessive Peripheral Neuropathy Cases Unravels High Genetic Heterogeneity in a Turkish Cohort.Neurology. Genetics · 2021Article
- AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data.Nature communications · 2021Article
- Behr syndrome and hypertrophic cardiomyopathy in a family with a novel UCHL1 deletion.Journal of neurology · 2020Article
- Evaluation of population stratification adjustment using genome-wide or exonic variants.Genetic epidemiology · 2020Article
- Improved Diagnosis of Rare Disease Patients through Systematic Detection of Runs of Homozygosity.The Journal of molecular diagnostics : JMD · 2020Article
- Mutated ATP10B increases Parkinson's disease risk by compromising lysosomal glucosylceramide export.Acta neuropathologica · 2020Article
- Glucocerebrosidase: Functions in and Beyond the Lysosome.Journal of clinical medicine · 2020Review
Corrections and comments
- Erratum issuedParma, Yesim [corrected to Parman, Yesim]
Authors and funding
15 authors at 8 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
purposeHomozygosity mapping is an effective approach for detecting molecular defects in consanguineous families by delineating stretches of genomic DNA that are identical by descent. Constant developments in next-generation sequencing created possibilities to combine whole-exome sequencing (WES) and homozygosity mapping in a single step.
methodsBasic optimization of homozygosity mapping parameters was performed in a group of families with autosomal-recessive (AR) mutations for which both single-nucleotide polymorphism (SNP) array and WES data were available. We varied the criteria for SNP extraction and PLINK thresholds to estimate their effect on the accuracy of homozygosity mapping based on WES.
resultsOur protocol showed high specificity and sensitivity for homozygosity detection and facilitated the identification of novel mutations in GAN, GBA2, and ZFYVE26 in four families affected by hereditary spastic paraplegia or Charcot-Marie-Tooth disease. Filtering and mapping with optimized parameters was integrated into the HOMWES (homozygosity mapping based on WES analysis) tool in the GenomeComb package for genomic data analysis.
conclusionWe present recommendations for detection of homozygous regions based on WES data and a bioinformatics tool for their identification, which can be widely applied for studying AR disorders.Genet Med 18 6, 600-607.
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