Benchmarking whole exome sequencing in the German network for personalized medicine.
Eur J Cancer
; 211: 114306, 2024 Nov.
Article
em En
| MEDLINE
| ID: mdl-39293347
ABSTRACT
INTRODUCTION:
Whole Exome Sequencing (WES) has emerged as an efficient tool in clinical cancer diagnostics to broaden the scope from panel-based diagnostics to screening of all genes and enabling robust determination of complex biomarkers in a single analysis.METHODS:
To assess concordance, six formalin-fixed paraffin-embedded (FFPE) tissue specimens and four commercial reference standards were analyzed by WES as matched tumor-normal DNA at 21 NGS centers in Germany, each employing local wet-lab and bioinformatics. Somatic and germline variants, copy-number alterations (CNAs), and complex biomarkers were investigated. Somatic variant calling was performed in 494 diagnostically relevant cancer genes. The raw data were collected and re-analyzed with a central bioinformatic pipeline to separate wet- and dry-lab variability.RESULTS:
The mean positive percentage agreement (PPA) of somatic variant calling was 76 % while the positive predictive value (PPV) was 89 % in relation to a consensus list of variants found by at least five centers. Variant filtering was identified as the main cause for divergent variant calls. Adjusting filter criteria and re-analysis increased the PPA to 88 % for all and 97 % for the clinically relevant variants. CNA calls were concordant for 82 % of genomic regions. Homologous recombination deficiency (HRD), tumor mutational burden (TMB), and microsatellite instability (MSI) status were concordant for 94 %, 93 %, and 93 % of calls, respectively. Variability of CNAs and complex biomarkers did not decrease considerably after harmonization of the bioinformatic processing and was hence attributed mainly to wet-lab differences.CONCLUSION:
Continuous optimization of bioinformatic workflows and participating in round robin tests are recommended.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Benchmarking
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Medicina de Precisão
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Variações do Número de Cópias de DNA
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Sequenciamento do Exoma
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Neoplasias
Limite:
Humans
País/Região como assunto:
Europa
Idioma:
En
Revista:
Eur J Cancer
Ano de publicação:
2024
Tipo de documento:
Article
País de publicação:
Reino Unido