SureSeq myPanel™ NGS Custom Breast Cancer Panel

SureSeq myPanel offers:

• Hybridisation-based enrichment delivering unparalleled coverage uniformity — detect low frequency breast cancer variants consistently with confidence and minimise the requirement for supplementary fill-in with Sanger sequencing
• Pre-optimised panels that meet your technical requirements and work with your samples — no more lengthy in-house optimisation, decreasing assay development time
• Bespoke panel content — sequence only what’s relevant for your cancer research, increase throughput and save on sequencing reagents
• Panel content designed with experts and from current literature to target all relevant regions including intronic and splice sites — get the most comprehensive insight into disease-driving mutations

Getting started with SureSeq myPanel NGS Custom Breast Cancer Panel could not be simpler...

Simply mix and match the genes or individual exons you require and get the most out of your sequencing runs.

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SureSeq: For research use only; not for use in diagnostic procedures.

Breast cancer is the second most common cancer in women after skin cancer. Approximately one out of eight women will be diagnosed in their lifetime with some form of breast cancer. Next generation sequencing (NGS) has enabled the simultaneous study of mutations in high-penetrance breast cancer predisposition genes. These include BRCA1, BRCA2 and other high-risk breast cancer susceptibility genes such as TP53 (Li-Fraumeni syndrome), PTEN (Cowden’s syndrome) and PIK3CA, as well as more moderate-risk genes such as PALB2, BRIP1, RAD51C and RAD51D.

Choose your ideal breast cancer NGS panel from our range of fully tested and optimised NGS panel content. Simply mix and match the genes or individual exons you require and get the most out of your sequencing runs. Use in conjunction with the SureSeq FFPE DNA Repair Mix* for improved NGS library yields, %OTR and mean target coverage from challenging FFPE derived samples.

Superior Coverage Uniformity

Mutations in BRCA1 and BRCA2 genes lead to an increased susceptibility to breast, ovarian, and other cancers.  Figure1a, illustrates the superior uniformity of coverage of key exons of BRCA1, and Figure 1b, BRCA2 from an FFPE sample with SureSeq compared to an amplicon-based panel.

Figure 1a. BRCA1 exons 8, 9, 10 and 11 coverage, Figure 1b. BRCA2 exons 11, 12 and 13. (A) SureSeq, (B) Amplicon panel. Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

Key Genomic Regions Covered

The PI3K pathway is the most frequently enhanced oncogenic pathway in breast cancer. Among mechanisms of PI3K enhancement, PIK3CA mutations are most frequently (∼30%) observed, with the majority of PIK3CA somatic mutations located in two “hot spots”: E542K or E545K in exon 9, and H1047R or H1047L in exon 20¹, figures 2a and 2b.

Figure 2a and 2b: Illustration of the excellent uniformity of coverage of PIK3CA exons 9 (2a) and 20 (2b). Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

GC-rich regions: handled with ease

Sequencing of another frequently mutated breast cancer gene, TP53, where point mutations are predominantly located in exons 5-8², is often hampered by the GC-rich content, which can lead to technical challenges in assay design and analysis. OGT’s innovative bait design overcomes this issue, offering a high level of uniform coverage for these difficult genes to sequence in FFPE samples, Figure 3.

Figure 3: TP53 exons 3 – 9, exceptional uniformity of coverage in spite of the high GC content of the region. Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

Getting started with your next SureSeq myPanel Custom Cancer Panel could not be simpler...

Select from any of the following myPanel breast cancer whole gene or exonic content below

Panels you may be interested in:

Panel I:

Panel II:

Panel III:

Panel IV:

Talk to us about your custom breast cancer NGS requirements and let our expertise work in helping you to advance your cancer research…

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References

1. Mukohara, Breast Cancer (Dove Med Press). 2015; 7: 111–123.
2. Langerød et al, Clin Cancer Res; 20(13); 3569–80

*The SureSeq™ FFPE DNA Repair Mix can only be purchased in conjunction with SureSeq NGS panels, not as a standalone product.

For more information about the SureSeq Breast Cancer NGS Panel or any cancer analysis products contact us at products@ogt.com.

SureSeq: For research use only; not for use in diagnostic procedures.