A novel molecular diagnostics platform for somatic and germline precision oncology

Abstract

BackgroundNext‐generation sequencing (NGS) opens new options in clinical oncology, from therapy selection to genetic counseling. However, realization of this potential not only requires succeeding in the bioinformatics and interpretation of the results, but also in their integration into the clinical practice. We have developed a novel NGS diagnostic platform aimed at detecting (1) somatic genomic alterations associated with the response to approved targeted cancer therapies and (2) germline mutations predisposing to hereditary malignancies.MethodsNext‐generation sequencing libraries enriched in the exons of 215 cancer genes (97 for therapy selection and 148 for predisposition, with 30 informative for both applications), as well as selected introns from 17 genes involved in drug‐related rearrangements, were prepared from 39 tumors (paraffin‐embedded tissues/cytologies), 36 germline samples (blood) and 10 cell lines using hybrid capture. Analysis of NGS results was performed with specifically developed bioinformatics pipelines.ResultsThe platform detects single‐nucleotide variants (SNVs) and insertions/deletions (indels) with sensitivity and specificity >99.5% (allelic frequency ≥0.1), as well as copy‐number variants (CNVs) and rearrangements. Somatic testing identified tailored approved targeted drugs in 35/39 tumors (89.74%), showing a diagnostic yield comparable to that of leading commercial platforms. A somatic EGFR p.E746_S752delinsA mutation in a mediastinal metastasis from a breast cancer prompted its anatomopathologic reassessment, its definite reclassification as a lung cancer and its treatment with gefitinib (partial response sustained for 15 months). Testing of 36 germline samples identified two pathogenic mutations (in CDKN2A and BRCA2). We propose a strategy for interpretation and reporting of results adaptable to the aim of the request, the availability of tumor and/or normal samples and the scope of the informed consent.ConclusionWith an adequate methodology, it is possible to translate to the clinical practice the latest advances in precision oncology, integrating under the same platform the identification of somatic and germline genomic alterations.

Validity of an NGS‑based multiple gene panel in identifying actionable mutations for patients with NSCLC in a Chinese hospital

“…Among the 23 NSCLC samples, 69.57% (16/23) of the patients carried the mutations with available matched targeted therapeutic options (Table III). This proportion is consistent with the previous study (23). In this study, EGFR mutations which occurred in exon 18–21 were the most common mutations carried by 14 patients.…”

Prevalence of germline mutations in the TP53 gene in patients with early-onset breast cancer in the Mexican population

“…Five pathogenic TP53 variants were identified according to the variant classification criteria described by Cabanillas et al, 2017 [36]. The overall prevalence of these variants was 6.4% (5/78), a percentage that rises to 9.4% if we consider only patients who were diagnosed before the age of 36 (5/53).…”

“…Pipeline data analysis was performed as described by Cabanillas et al, 2017 [36]. Briefly, FASTQ files were evaluated using quality checks from Fast QC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).…”

New Chondrosarcoma Cell Lines with Preserved Stem Cell Properties to Study the Genomic Drift During In Vitro/In Vivo Growth

“…Enriched libraries were sequenced (2 × 101 bp) in an Illumina HiSeq4000 sequencer. WES results were processed using the bioinformatics software HD Genome One (DREAMgenics, Oviedo, Spain), certified with IVD/CE-marking (see Supplementary Materials for a comprehensive description of the exome analysis, [33,34,35,36,37,38,39,40,41,42,43,44,45,46,47]). The datasets generated during the study are available in the European Nucleotide Archive repository [48].…”