The SureSeq™ Breast Cancer + CNV Panel has been developed to provide comprehensive coverage of 7 key genes implicated in breast and ovarian cancer, including BRCA1 and BRCA2 (Table 1). Detecting SNVs and indels, as well as exon-level to whole gene CNVs, the SureSeq Breast Cancer + CNV Panel provides researchers with a single NGS workflow to study clinically relevant aberrations and alleviates the burden of running multiple assays.
* Exon examples not yet available
Loss-of-function mutations in BRCA1 and BRCA2 have been implicated in an increased risk for breast and ovarian cancer1,2. Screening for germline mutations in these genes allows research into familial risk of developing breast and ovarian cancer. Facilitated by OGT’s expert bait design, the hybridization-based SureSeq Breast Cancer + CNV Panel delivers excellent coverage uniformity, allowing consistent detection of SNVs and indels (Figure 1).
Figure 1a: Illustration of the excellent coverage uniformity across BRCA1 exons 9, 10 and 11. Depth of coverage per base (grey). Gene coding region as defined by RefSeq (blue).
To gain a comprehensive picture of breast and ovarian cancer, researchers often have to employ different methods for investigating SNVs, indels, and CNVs. The SureSeq Breast Cancer + CNV Panel offers reliable CNV detection in all genes covered by the panel, ranging from single-exon events up to deletions and duplications of complete genes. The panel has been fully validated on germline samples, with CNV detection 100% concordant with MLPA data, providing researchers with a single NGS assay for profiling of CNVs in BRCA1, BRCA2 and 5 other key genes implicated in breast and ovarian cancer (Figures 2 - 3).
Figure 2: Detection of germline deletions in BRCA1 and BRCA2. [A] BRCA1 deletion of exon 20 (4.99kb) and [B] BRCA2 deletion of exons 14-17 (4.21kb).
Interpret is OGT’s powerful and easy-to-use NGS analysis solution, facilitating analysis and visualization of a wide range of somatic variants and structural aberrations. Designed to work seamlessly with all SureSeq panels, Interpret perfectly complements the SureSeq Breast Cancer + CNV Panel, delivering fast and accurate detection of all SNVs, indels and CNVs covered by the panel. Following detection, all variants can be easily visualized in the user-friendly variant browser, for an effortless translation of all your sequencing data into meaningful results.
You never have to sequence genes you’re not interested in and can always modify each panel to what’s relevant to your research. If the SureSeq Breast Cancer + CNV Panel doesn’t meet your exact requirements (see table 2 for a detailed breakdown of the numbers), you can choose from our regularly updated, expert-curated library of pre-optimized cancer content to create your ideal custom SureSeq myPanel™ Breast and/or Ovarian Cancer Panel.
We were delighted with the performance of the SureSeq panel. It showed complete concordance with our other techniques, detecting all known mutations with excellent sensitivity down to 1% [MAF (minor allele frequency)], including, in one case, a JAK2 V617F mutation which was not detected by ddPCR due to a second mutation under the primer. The panel also demonstrated mutations in other genes in samples with low level JAK2 V617F and good correlation between allele frequencies and quantitative analysis by ddPCR. We are planning to adopt the panel in the near future.
Dr Anna Skowronska
R&D Scientist, Haemato-Oncology Team, West Midlands Regional Genetics Laboratory, Birmingham Women’s NHS Foundation Trust, UK