ArticleJournal of clinical medicine2021
The Mutational Concordance of Fixed Formalin Paraffin Embedded and Fresh Frozen Gastro-Oesophageal Tumours Using Whole Exome Sequencing.
Article in Journal of clinical medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 10 citations in OpenAlex.
- Article
- Leveraging mRNA technology for antigen based immuno-oncology therapies.Journal for immunotherapy of cancer · 2025Review
- DNA Quantity and Quality Comparisons between Cryopreserved and FFPE Tumors from Matched Pan-Cancer Samples.Current oncology (Toronto, Ont.) · 2024Article
- Genomic heterogeneity at baseline is associated with T790M resistance mutations in EGFR-mutated lung cancer treated with the first-/second-generation tyrosine kinase inhibitors.The journal of pathology. Clinical research · 2024Article
- Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data.NAR genomics and bioinformatics · 2021Article
- Multimodality Treatment in Metastatic Gastric Cancer: Working Together to Tailor the Continuum of Care.Journal of clinical medicine · 2021Article
- Testing EGFR with Idylla on Cytological Specimens of Lung Cancer: A Review.International journal of molecular sciences · 2021Review
Corrections and comments
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Authors and funding
21 authors at 2 institutions in 1 country.
Funding
Abstract
1.
backgroundThe application of massively parallel sequencing has led to the identification of aberrant druggable pathways and somatic mutations within therapeutically relevant genes in gastro-oesophageal cancer. Given the widespread use of formalin-fixed paraffin-embedded (FFPE) samples in the study of this disease, it would be beneficial, especially for the purposes of biomarker evaluation, to assess the concordance between comprehensive exome-wide sequencing data from archival FFPE samples originating from a prospective clinical study and those derived from fresh-frozen material. 2.
methodsWe analysed whole-exome sequencing data to define the mutational concordance of 16 matched fresh-frozen and FFPE gastro-oesophageal tumours (
resultsAlthough there was increased degradation of DNA in FFPE samples compared with frozen samples, sequencing data from only two FFPE samples failed to reach an adequate mapping quality threshold. Using a filtering threshold of mutant read counts of at least ten and a minimum of 5% variant allele frequency (VAF) we found that there was a high median mutational concordance of 97% (range 80.1-98.68%) between fresh-frozen and FFPE gastro-oesophageal tumour-derived exomes. However, the majority of FFPE tumours had higher mutant-allele heterogeneity (MATH) scores when compared with corresponding frozen tumours (
conclusionsThese data suggest that comprehensive genomic data can be generated from exome sequencing of selected DNA samples extracted from archival FFPE gastro-oesophageal tumour tissues within the context of prospective clinical trials.
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