| Added by | pcoopman |
|---|---|
| Last modified by | standudu |
| Group name | EquipePC |
| Item Type | Journal Article |
| Title | Benchmarking of Amplicon-Based Next-Generation Sequencing Panels Combined with Bioinformatics Solutions for Germline BRCA1 and BRCA2 Alteration Detection |
| Creator | Vendrell et al. |
| Author | Julie A. Vendrell |
| Author | Paul Vilquin |
| Author | Marion Larrieux |
| Author | Charles Van Goethem |
| Author | Jérôme Solassol |
| Abstract | The recent deployment of next-generation sequencing approaches in routine laboratory analysis has considerably modified the landscape of BRCA1 and BRCA2 germline alteration detection in patients with a high risk of developing breast and/or ovarian cancer. Several commercial multiplex amplicon-based panels and bioinformatics solutions are currently available. In this study, we evaluated the combinations of several BRCA testing assays and bioinformatics solutions for the identification of single-nucleotide variants, insertion/deletion variants, and copy number variations (CNVs). Four assays (BRCA Tumor, BRCA HC, Ion AmpliSeq BRCA, and Access Array BRCA) and two commercial bioinformatics solutions (SeqNext software version 4.3.1 and Sophia DDM version 5.0.13) were tested on a set of 28 previously genotyped samples. All solutions exhibited accurate detection of single-nucleotide variants and insertion/deletion variants, except for Ion AmpliSeq BRCA, which exhibited a decrease in coverage. Of interest, for CNV analysis, the best accuracy was observed with the Sophia DDM platform regardless of the BRCA kit used. Finally, the performance of the most relevant combination (BRCA Tumor and Sophia DDM) was blindly validated on an independent set of 152 samples. Altogether, our results emphasize the need to accurately compare and control both molecular next-generation sequencing approaches and bioinformatics pipelines to limit the number of discrepant alterations and to provide a powerful tool for reliable detection of genetic alterations in BRCA1 and BRCA2, notably CNVs. |
| Publication | The Journal of molecular diagnostics: JMD |
| Volume | 20 |
| Issue | 6 |
| Pages | 754-764 |
| Date | 11 2018 |
| Journal Abbr | J Mol Diagn |
| Language | eng |
| DOI | 10.1016/j.jmoldx.2018.06.003 |
| ISSN | 1943-7811 |
| Library Catalog | PubMed |
| Extra | 00000 PMID: 30055349 |
| Tags | Benchmarking, BRCA1 Protein, BRCA2 Protein, clinic, Computational Biology, DNA Copy Number Variations, DNA Mutational Analysis, Germ Cells, High-Throughput Nucleotide Sequencing, Humans, Mutation, Reproducibility of Results |
| Date Added | 2019/10/22 - 16:03:27 |
| Date Modified | 2020/10/04 - 14:02:00 |
| Notes and Attachments | PubMed entry (Attachment) |
Institut de Recherche en Cancérologie de
