Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations
Open accessAbstract
Background: Detecting mutations in disease genes by full gene sequence analysis is common in clinical diagnostic laboratories. Sanger dideoxy terminator sequencing allows for rapid development and implementation of sequencing assays in the clinical laboratory, but it has limited throughput, and due to cost constraints, only allows analysis of one or at most a few genes in a patient. Next-generation sequencing (NGS), on the other hand, has evolved rapidly, although to date it has mainly been used for large-scale genome sequencing projects and is beginning to be used in the clinical diagnostic testing. One advantage of NGS is that many genes can be analyzed easily at the same time, allowing for mutation detection when there are many possible causative genes for a specific phenotype. In addition, regions of a gene typically not tested for mutations, like deep intronic and promoter mutations, can also be detected. Results: Here we use 20 previously characterized Sanger-sequenced positive controls in disease-causing genes to demonstrate the utility of NGS in a clinical setting using standard PCR based amplification to assess the analytical sensitivity and specificity of the technology for detecting all previously characterized changes (mutations and benign SNPs). The positive controls chosen for validation range from simple substitution mutations to complex deletion and insertion mutations occurring in autosomal dominant and recessive disorders. The NGS data was 100% concordant with the Sanger sequencing data identifying all 119 previously identified changes in the 20 samples. Conclusions: We have demonstrated that NGS technology is ready to be deployed in clinical laboratories. However, NGS and associated technologies are evolving, and clinical laboratories will need to invest significantly in staff and infrastructure to build the necessary foundation for success.
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Sequencing is not affected by the same technical problem as SNP chips and thus provides a much more accurate method for genotyping rare variants.
“Sequencing is not affected by the same technical problem as SNP chips and thus provides a much more accurate method for genotyping rare variants.30”
From Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation (2021) · cites this paper as [30]
The Abstract’s Results section reports that next-generation sequencing identified all 119 previously characterized changes in 20 samples, supporting its ability to detect genetic variants. The paper does not compare sequencing with SNP chips, identify a technical problem affecting chips, or establish greater accuracy for genotyping rare variants. Page numbers are not available in our copy. (LLM, conf=0.80)
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- Authors
- Chin, E. L., da Silva, C., & Hegde, M.
- Affiliations
- Emory University (US)
- Corresponding author
- Hegde, Madhuri
- ORCID
- Hegde, Madhuri
- Venue
- BMC Genetics
- Published
- 2013-02-19
- Volume
- 14
- Issue
- 1
- Pages
- 6-6
- ISSN
- 1471-2156 (ISSN-L)
- PMC
- PMC3599218
- OpenAlex
- W2006384917
- Cited by
- 92
- References
- 27
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 5 · 2023: 5 · 2022: 3 · 2021: 6 · 2020: 12 · 2019: 4 · 2018: 6 · 2017: 11 · 2016: 6 · 2015: 6 · 2014: 20 · 2013: 4
- FWCI
- 7.95
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of Neurological Disorders and Stroke (RC1NS069541)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Pediatrics, Perinatology and Child Health › Prenatal Screening and Diagnostics
- Keywords
- next-generation sequencing, mutation detection, analytical sensitivity, analytical specificity, Sanger sequencing comparison, deep intronic mutation, promoter mutations, autosomal dominant disorder, autosomal recessive disorder, positive control
- MeSH terms
- DNA Mutational Analysis, Humans, Mutation, Sensitivity and Specificity, Polymerase Chain Reaction, Sequence Analysis, DNA, Clinical Laboratory Techniques, Polymorphism, Single Nucleotide, Molecular Diagnostic Techniques
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