ArticleNPJ genomic medicine2022
An evaluation of pipelines for DNA variant detection can guide a reanalysis protocol to increase the diagnostic ratio of genetic diseases.
Article in NPJ genomic medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- A global survey of systems biology-based predictions of gene-rare disease associations to enhance new diagnoses.Scientific reports · 2026Article
- Accurate and cost-effective workflow integrating trio pooled-WES for novel gene discovery in neurodevelopmental disorders.European journal of human genetics : EJHG · 2026Article
- Personalised genomic strategies improve diagnostic yield in inherited retinal dystrophies: a stepwise, patient-centred approach.Eye (London, England) · 2025Article
- Refining rare disease variant discovery in an isolated Andean community through imputation-enhanced IBD and kinship inference from whole exome sequencing data.Human molecular genetics · 2025Article
- Accelerating genetic diagnostics in retinitis pigmentosa: implementation of a semi-automated bespoke cohort analysis workflow for Hong Kong Genome Project.Human genetics · 2025Article
- Long-Read Whole-Genome Sequencing as a Tool for Variant Detection in Inherited Retinal Dystrophies.International journal of molecular sciences · 2025Article
- A genomic strategy for precision medicine in rare diseases: integrating customized algorithms into clinical practice.Journal of translational medicine · 2025Article
- From DNA to Big Data: NGS Technologies and Their Applications.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Genomic Insights into Idiopathic Granulomatous Mastitis through Whole-Exome Sequencing: A Case Report of Eight Patients.International journal of molecular sciences · 2024Article
- Cas9-targeted-based long-read sequencing for genetic screening ofFrontiers in genetics · 2024Article
- Sync for Genes Phase 5: Computable artifacts for sharing dynamically annotated FHIR-formatted genomic variants.Learning health systems · 2023Article
- Beyond the exome: What's next in diagnostic testing for Mendelian conditions.American journal of human genetics · 2023Review
- Article
- Prioritization of New Candidate Genes for Rare Genetic Diseases by a Disease-Aware Evaluation of Heterogeneous Molecular Networks.International journal of molecular sciences · 2023Article
- Five years' experience of the clinical exome sequencing in a Spanish single center.Scientific reports · 2022Article
- Aggregated Genomic Data as Cohort-Specific Allelic Frequencies can Boost Variants and Genes Prioritization in Non-Solved Cases of Inherited Retinal Dystrophies.International journal of molecular sciences · 2022Article
- Presence of rare potential pathogenic variants in subjects under 65 years old with very severe or fatal COVID-19.Scientific reports · 2022Article
Corrections and comments
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Authors and funding
16 authors.
Funding
Abstract
Clinical exome (CE) sequencing has become a first-tier diagnostic test for hereditary diseases; however, its diagnostic rate is around 30-50%. In this study, we aimed to increase the diagnostic yield of CE using a custom reanalysis algorithm. Sequencing data were available for three cohorts using two commercial protocols applied as part of the diagnostic process. Using these cohorts, we compared the performance of general and clinically relevant variant calling and the efficacy of an in-house bioinformatic protocol (FJD-pipeline) in detecting causal variants as compared to commercial protocols. On the whole, the FJD-pipeline detected 99.74% of the causal variants identified by the commercial protocol in previously solved cases. In the unsolved cases, FJD-pipeline detects more INDELs and non-exonic variants, and is able to increase the diagnostic yield in 2.5% and 3.2% in the re-analysis of 78 cancer and 62 cardiovascular cases. These results were considered to design a reanalysis, filtering and prioritization algorithm that was tested by reassessing 68 inconclusive cases of monoallelic autosomal recessive retinal dystrophies increasing the diagnosis by 4.4%. In conclusion, a guided NGS reanalysis of unsolved cases increases the diagnostic yield in genetic disorders, making it a useful diagnostic tool in medical genetics.
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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.