ArticleHuman genome variation2016
Challenges in detecting genomic copy number aberrations using next-generation sequencing data and the eXome Hidden Markov Model: a clinical exome-first diagnostic approach.
Article in Human genome variation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- High Concordance of Copy Number Variants Detected by Chromosomal Microarray and Exome Sequencing in Clinical Diagnostics.Clinical genetics · 2026Article
- Significance of Clinical and Genetic Signatures of Familial Hypercholesterolemia Among Patients With Severe Hypercholesterolemia.JACC. Advances · 2025Article
- Triple Assessments of Atherosclerosis in Patients With Heterozygous Familial Hypercholesterolemia.JACC. Asia · 2025Article
- Improved Efficiency of the Clinical Diagnostic Criteria for Familial Hypercholesterolemia in Children: A Comparison of the Japan Atherosclerosis Society Guidelines of 2017 and 2022.Journal of atherosclerosis and thrombosis · 2024Article
- Validation of the 2022 Clinical Diagnostic Criteria of Familial Hypercholesterolemia in Japan.Journal of atherosclerosis and thrombosis · 2024Article
- Impact of the severe familial hypercholesterolemia status on atherosclerotic risks.Scientific reports · 2023Article
- Coronary Artery and Carotid Artery Plaques in Patients With Heterozygous Familial Hypercholesterolemia.JACC. Advances · 2023Article
- Coronary artery calcium among patients with heterozygous familial hypercholesterolaemia.European heart journal open · 2023Article
- Article
- Intervention of next-generation sequencing in diagnosis of Alzheimer's disease: challenges and future prospects.Dementia & neuropsychologia · 2023Review
- Synergistic effect of lipoprotein (a) and C-reactive protein on prognosis of familial hypercholesterolemia.American journal of preventive cardiology · 2022Article
- Early diagnosis and treatments in childhood are associated with better prognosis in patients with familial hypercholesterolemia.American journal of preventive cardiology · 2022Article
- Algorithmic improvements for discovery of germline copy number variants in next-generation sequencing data.BMC bioinformatics · 2022Article
- Effects of Different Types of Pathogenic Variants on Phenotypes of Familial Hypercholesterolemia.Frontiers in genetics · 2022Article
- The Evolving Role of Next-Generation Sequencing in Screening and Diagnosis of Hemoglobinopathies.Frontiers in physiology · 2021Review
- Evaluation of Next Generation Sequencing for Detecting HER2 Copy Number in Breast and Gastric Cancers.Pathology oncology research : POR · 2020Article
- Exome Sequencing for Prenatal Detection of Genetic Abnormalities in Fetal Ultrasound Anomalies: An Economic Evaluation.Fetal diagnosis and therapy · 2020Article
- Article
- Copy Number Variations in Adult-onset Neuropsychiatric Diseases.Current genomics · 2018Review
- Next Generation Sequencing Methods for Diagnosis of Epilepsy Syndromes.Frontiers in genetics · 2018Review
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) is widely used for the detection of disease-causing nucleotide variants. The challenges associated with detecting copy number variants (CNVs) using NGS analysis have been reported previously. Disease-related exome panels such as Illumina TruSight One are more cost-effective than whole-exome sequencing (WES) because of their selective target regions (~21% of the WES). In this study, CNVs were analyzed using data extracted through a disease-related exome panel analysis and the eXome Hidden Markov Model (XHMM). Samples from 61 patients with undiagnosed developmental delays and 52 healthy parents were included in this study. In the preliminary study to validate the constructed XHMM system (microarray-first approach), 34 patients who had previously been analyzed by chromosomal microarray testing were used. Among the five CNVs larger than 200 kb that were considered as non-pathogenic CNVs and were used as positive controls, four CNVs was successfully detected. The system was subsequently used to analyze different samples from 27 patients (NGS-first approach); 2 of these patients were successfully diagnosed as having pathogenic CNVs (an unbalanced translocation der(5)t(5;14) and a 16p11.2 duplication). These diagnoses were re-confirmed by chromosomal microarray testing and/or fluorescence in situ hybridization. The NGS-first approach generated no false-negative or false-positive results for pathogenic CNVs, indicating its high sensitivity and specificity in detecting pathogenic CNVs. The results of this study show the possible clinical utility of pathogenic CNV screening using disease-related exome panel analysis and XHMM.
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