ArticleGenetics in medicine : official journal of the American College of Medical Genetics2016
Capture-based high-coverage NGS: a powerful tool to uncover a wide spectrum of mutation types.
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. 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.
- Diagnosis of hepatic glycogen storage disease patients with overlapping clinical symptoms by massively parallel sequencing: a systematic review of literature.Orphanet journal of rare diseases · 2020Pooled it
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- Towards Personalized Precision Oncology: A Feasibility Study of NGS-Based Variant Analysis of FFPE CRC Samples in a Chilean Public Health System Laboratory.Current issues in molecular biology · 2025Article
- Genetic Profiling of Acute and Chronic Leukemia via Next-Generation Sequencing: Current Insights and Future Perspectives.Hematology reports · 2025Review
- A Cross-Sectional Study of Variant Interpretation and Reporting of NGS Data Using Tertiary Analysis Software: NavifyOncology and therapy · 2025Article
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- Variant Type X91Journal of clinical immunology · 2022Article
- Novel variants in the NARS2 gene as a cause of infantile-onset severe epilepsy leading to fatal refractory status epilepticus: case study and literature review.Neurogenetics · 2021Review
- Multi-Gene Testing Overview with a Clinical Perspective in Metastatic Triple-Negative Breast Cancer.International journal of molecular sciences · 2021Review
- Clinical and genetic spectrum of glycogen storage disease in Iranian population using targeted gene sequencing.Scientific reports · 2021Article
- Efficacy of tocilizumab therapy in a patient with severe pancytopenia associated with a STAT3 gain-of-function mutation.BMC immunology · 2021Article
- A Pilot Study for the Feasibility of Exome-Sequencing in Circulating Tumor Cells Versus Single Metastatic Biopsies in Breast Cancer.International journal of molecular sciences · 2020Article
- Molecular diagnosis of muscular diseases in outpatient clinics: A Canadian perspective.Neurology. Genetics · 2020Article
- Report of a Chinese Cohort with Leukocyte Adhesion Deficiency-I and Four Novel Mutations.Journal of clinical immunology · 2019Article
- DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data.BMC bioinformatics · 2018Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
purposeNext-generation sequencing (NGS) has been widely applied to clinical diagnosis. Target-gene capture followed by deep sequencing provides unbiased enrichment of the target sequences, which not only accurately detects single-nucleotide variations (SNVs) and small insertion/deletions (indels) but also provides the opportunity for the identification of exonic copy-number variants (CNVs) and large genomic rearrangements.
methodCapture NGS has the ability to easily detect SNVs and small indels. However, genomic changes involving exonic deletions/duplications and chromosomal rearrangements require more careful analysis of captured NGS data. Misaligned raw sequence reads may be more than just bad data. Some mutations that are difficult to detect are filtered by the preset analytical parameters. "Loose" filtering and alignment conditions were used for thorough analysis of the misaligned NGS reads. Additionally, using an in-house algorithm, NGS coverage depth was thoroughly analyzed to detect CNVs.
resultsUsing real examples, this report underscores the importance of the accessibility to raw sequence data and manual review of suspicious sequence regions to avoid false-negative results in the clinical application of NGS. Assessment of the NGS raw data generated by the use of loose filtering parameters identified several sequence aberrations, including large indels and genomic rearrangements. Furthermore, NGS coverage depth analysis identified homozygous and heterozygous deletions involving single or multiple exons.
conclusionOur results demonstrate the power of deep NGS in the simultaneous detection of point mutations and intragenic exonic deletion in one comprehensive step.Genet Med 18 5, 513-521.
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