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Baardman R, Lemmink HH, Yenamandra VK, Commandeur-Jan SZ, Viel M, Kooi KA, Diercks GFH, Meijer R, van Geel M, Scheffer H, Sinke RJ, Sikkema-Raddatz B, Bolling MC, van den Akker PC. Evolution of genome diagnostics in epidermolysis bullosa: Unveiling the power of next-generation sequencing. J Eur Acad Dermatol Venereol 2024. [PMID: 38465480 DOI: 10.1111/jdv.19938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024]
Abstract
BACKGROUND Genome diagnostics is considered gold standard diagnostics for epidermolysis bullosa (EB), a phenotypically and genetically heterogeneous group of rare disorders characterized by blistering and wounding of mucocutaneous tissues. EB is caused by pathogenic variants in genes encoding proteins of the dermo-epidermal junction. Accurate genetic diagnosis of EB is crucial for prognostication, counselling and precision-medicine. Genome diagnostics for EB started in 1991 with the introduction of Sanger sequencing (SS), analysing one gene at a time. In 2013, SS was superseded by next-generation sequencing (NGS), that allow for high-throughput sequencing of multiple genes in parallel. Several studies have shown a beneficial role for NGS in EB diagnostics, but its true benefit has not been quantified. OBJECTIVES To determine the benefit of NGS in EB by systematically evaluating the performance of different genome diagnostics used over time based on robust data from the Dutch EB Registry. METHODS The diagnostic performances of SS and NGS were systematically evaluated in a retrospective observational study including all index cases with a clinical diagnosis of EB in whom genome diagnostics was performed between 01 January 1994 and 01 January 2022 (n = 308), registered at the Dutch EB Expertise Centre. RESULTS Over time, a genetic diagnosis was made in 289/308 (94%) EB cases. The diagnostic yield increased from 89% (SS) to 95% (NGS). Most importantly, NGS significantly reduced diagnostic turnaround time (39 days vs. 211 days, p < 0.001). The likelihood of detecting variants of uncertain significance and additional findings increased from 5% and 1% (SS) to 22% and 13% (NGS) respectively. CONCLUSIONS Our study quantifies the benefit of NGS-based methods and demonstrate they have had a major impact on EB diagnostics through an increased diagnostic yield and a dramatically decreased turnaround time (39 days). Although our diagnostic yield is high (95%), further improvement of genome diagnostics is urgently needed to provide a genetic diagnosis in all EB patients.
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Affiliation(s)
- R Baardman
- Department of Dermatology, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - H H Lemmink
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - V K Yenamandra
- Academy of Scientific and Innovative Research South Campus, CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - S Z Commandeur-Jan
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M Viel
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - K A Kooi
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - G F H Diercks
- Department of Dermatology, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pathology, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - R Meijer
- Department of Genetics, University Medical Center Nijmegen, University of Nijmegen, Nijmegen, The Netherlands
| | - M van Geel
- Department of Genetics, Maastricht University Medical Center, University of Maastricht, Maastricht, The Netherlands
| | - H Scheffer
- Department of Genetics, University Medical Center Nijmegen, University of Nijmegen, Nijmegen, The Netherlands
| | - R J Sinke
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - B Sikkema-Raddatz
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M C Bolling
- Department of Dermatology, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - P C van den Akker
- Department of Dermatology, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, UMCG Centers of Expertise for Blistering Diseases and Genodermatoses, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Mattocks CJ, Watkins G, Ward D, Janssens T, Bosgoed EAJ, van der Donk K, Ligtenberg MJ, Pot B, Theelen J, Cross NCP, Scheffer H, Matthijs G. Interlaboratory diagnostic validation of conformation-sensitive capillary electrophoresis for mutation scanning. Clin Chem 2010; 56:593-602. [PMID: 20167696 DOI: 10.1373/clinchem.2009.135426] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Indirect alternatives to sequencing as a method for mutation scanning are of interest to diagnostic laboratories because they have the potential for considerable savings in both time and costs. Ideally, such methods should be simple, rapid, and highly sensitive, and they should be validated formally to a very high standard. Currently, most reported methods lack one or more of these characteristics. We describe the optimization and validation of conformation-sensitive capillary electrophoresis (CSCE) for diagnostic mutation scanning. METHODS We initially optimized the performance of CSCE with a systematic panel of plasmid-based controls. We then compared manual analysis by visual inspection with automated analysis by BioNumerics software (Applied Maths) in a blinded interlaboratory validation with 402 BRCA1 (breast cancer 1, early onset) and BRCA2 (breast cancer 1, early onset) variants previously characterized by Sanger sequencing. RESULTS With automated analysis, we demonstrated a sensitivity of >99% (95% CI), which is indistinguishable from the sensitivity for conventional sequencing by capillary electrophoresis. The 95% CI for specificity was 90%-93%; thus, CSCE greatly reduces the number of fragments that need to be sequenced to fully characterize variants. By manual analysis, the 95% CIs for sensitivity and specificity were 98.3%-99.4% and 93.1%-95.5%, respectively. CONCLUSIONS CSCE is amenable to a high degree of automation, and analyses can be multiplexed to increase both capacity and throughput. We conclude that once it is optimized, CSCE combined with analysis with BioNumerics software is a highly sensitive and cost-effective mutation-scanning technique suitable for routine genetic diagnostic analysis of heterozygous nucleotide substitutions, small insertions, and deletions.
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