Publication-only abstracts (abstract number preceded by an "e"), published in conjunction with the 2018 ASCO Annual Meeting but not presented at the Meeting, can be found online only.
Using GeneReader NGS system to identify mutations in BRCA 1/2 genes in matched FFPE and blood samples.
2018 ASCO Annual Meeting
J Clin Oncol 36, 2018 (suppl; abstr e17536)
Author(s): Vishal Kapoor, Nathan Dennison, Adam Burke, Alexander Burton, Richard Dyson, Lea Thoegerson, Dietrich Lueerssen, Bodil Oester, Andrew Robb, Leif Schauser, Kyriakos Ttavas, Juergen Lauber, Simon Hughes; QIAGEN Manchester, Manchester, United Kingdom; QIAGEN Aarhus, Aarhus, Denmark; QIAGEN, Manchester, United Kingdom; Qiagen Manchester Ltd., Manchester, United Kingdom
Background: Supported by strong clinical evidence, testing for germline mutations in BRCA1 and BRCA2 in suspected familial breast cancer cases has gradually become common practice, especially in countries like the US. However, while less widely known and much harder to detect, somatic aberrations in these genes also play a critical role in cancer evolution, outcome and management. Methods: In order to enable full investigation of mutations in BRCA 1/2 genes, we have developed the GeneRead QIAact BRCA Advanced UMI Panel that is compatible with a range of clinical samples. To provide a fully integrated solution enabling any laboratory to adopt the test, we used the GeneReader NGS System, combining wet bench sample processing, target sequence enrichment, and optimized bioinformatics for BRCA 1/2 gene analysis. The performance of this assay has been demonstrated by running a set of matched FFPE and Blood samples harbouring BRCA 1/2 mutations. Results: The assay, which was designed to cover the entire coding regions of both genes +/- 20bp flanking intronic sequences, in combination with a specifically designed bioinformatics pipeline can detect both single nucleotide variants (SNVs) as well as Insertion/Deletions (InDels) in challenging real-world patient samples from both breast and ovarian tumour types. For sequencing, samples were pooled and run in a 8-plex (FFPE) or 12-plex (Blood) configuration per flowcell, which yielded sequencing results with an average coverage of ≥300x unique molecular index (UMI) across all target regions. For FFPE and blood samples > 95% and > 99% of the target regions showed sufficient uniform amplification and sequencing coverage, to detect mutant alleles at a minimum 5% and 50% allele frequency, respectively. Mutational status was correctly confirmed in all matched samples, resulting in 100% concordance with an alternative testing technology. Conclusions: These results support the use of the GeneReader NGS System to detect BRCA 1/2 mutations relevant to both germline and somatic cancers. This fully integrated workflow together with an optimized BRCA pipeline enables an easy implementation of the test by any molecular cancer research laboratory.