Performance of non-formalin fixed paraffin embedded samples in hybrid capture and amplicon next-generation sequencing panels.

BACKGROUND: Genomic profiling using next-generation sequencing (NGS) is fundamental for driving prognostic and therapy in cancer. Formalin-fixed paraffin embedded (FFPE) tissue is the widely used material, whereas non-FFPE may represent an alternative. However, studies comparing the NGS performance of non-FFPE materials to FFPE are still lacking in the literature. The objective of this study was to characterize in non-FFPE preparations the nucleic acid yield and NGS performance on both a capture-based and an amplicon-based NGS platform. NGS quality metrics obtained from non-FFPE preparations were compared to FFPE. METHODS: We analyzed the cellularity and nucleic acid yield in 111 tumors from non-FFPE preparations. In addition, comprehensive hybrid capture panel sequencing metrics obtained from DNA and RNA libraries were compared between independent non-FFPE and FFPE samples. A paired comparison between non-FFPE and FFPE samples was performed to analyze concordance in mutant allele detection using an amplicon panel. RESULTS: The mean target coverage from DNA libraries was 2× higher in non-FFPE samples than in FFPE. The detection of exogenous DNA was 2.5× higher in non-FFPE than in FFPE. Conversely, a lower performance was observed in non-FFPE RNA libraries in comparison to FFPE DNA libraries with no impact in minimum standard cutoffs. The variant allele detection in non-FFPE was found to be comparable to that of FFPE tumor samples in matched samples. CONCLUSIONS: Non-FFPE was demonstrated to be a suitable material for DNA and RNA library preparations using a comprehensive NGS panel. This is the first study reporting library quality metrics according to the TSO500 analysis pipeline.

Novel Mutations in Pilomatrixoma, CTNNB1 p.s45F, and FGFR2 p.s252L: A Report of Three Cases Diagnosed by Fine-Needle Aspiration Biopsy, with Review of the Literature.

Pilomatrixoma (calcifying epithelioma of Malherbe) is an uncommon benign skin appendageal tumor that differentiates toward hair matrix cells. It is misdiagnosed in up to 75% of cases by nondermatologists. Although the histopathological findings are well recognized and characteristic, diagnosis by fine-needle aspiration biopsy may be quite challenging. Several reports have emphasized the challenges in cytodiagnosis of pilomatrixoma, leading to a false-positive diagnosis. The lesions may show avidity for fludeoxyglucose on positron emission tomography/computed tomography scan, raising concern of a possible malignant neoplasm. CTNNB1 mutations have been reported in a high percentage of pilomatrixomas. Expression of ß-catenin, the protein encoded by CTNNB1, is also frequently observed. To determine if routine cytological specimens can be successfully used to perform additional investigation and support or confirm the diagnosis in three cases of pilomatrixoma, we performed molecular analysis and immunohistochemistry to search for CTNNB1 mutation and ß-catenin, respectively. ß-Catenin positivity by immunohistochemistry was observed in basaloid cells in all three cases. Exon 3 mutations in CTNNB1 were detected in all cases. In addition, we detected a fibroblast growth factor receptor 2 (FGFR2) mutation in one of the cases. We reviewed the literature and present the clinical and morphological characteristics that must be considered along with other findings to accurately achieve the correct diagnosis, in correlation with the results of the ancillary technique. In conclusion, routine cytological specimens can be successfully used to perform additional investigations and support cytodiagnosis in difficult cases.