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Product summary

  • Technology NGS
  • Application Solid tumour
  • Areas of interest Breast cancer
  • Gene Targets 1 - 24+
  • Aberration Types SNV, indel, CNV
  • Product Code Various
  • Regulatory Status For research use only; not for diagnostic procedures.

Documentation

Ancillary products

Overview

Introduction

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 (on target rate) and mean target coverage from challenging FFPE derived samples.

Getting started with your SureSeq myPanel NGS Custom Panel could not be simpler, find out more in this video…

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SureSeq myPanel process

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

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

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Features
  • Hybridisation-based enrichment delivering unparalleled coverage uniformity - detect low frequency breast cancer variants consistently with confidence
  • Bespoke panels with pre-optimised content - Create your ideal panel and sequence only what’s relevant for your research
  • Panel content designed with experts and from current literature - Get the most comprehensive insight into disease-driving mutations
  • Complimentary Interpret NGS data analysis software - Easy-to-use analysis solution for accurate detection of all variants

Gene targets

Select a gene to view exon coverage examples:

* Exon examples not yet available

APC Exon 5 (hg19 chr5:112116487-112116600). Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

APC Exon 5

APC Exon 8 (hg19 chr5:112154663-112155041). Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

APC Exon 8

APC Exon 14 (hg19 chr5:112173250-112181936). Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

APC Exon 14

Want to customise these gene targets?

We have a regularly updated, expert-curated library of pre-optimised cancer panel content for you to select from. Simply mix and match the gene, exonic or intronic content you need to create a breast cancer NGS cancer panel that meets your exact requirements.

Customise this panel

Capabilities

Superior coverage uniformity

Mutations in BRCA1 and BRCA2 genes lead to an increased susceptibility to breast, ovarian, and other cancers. Figure 1, illustrates the superior uniformity of coverage of key exons of BRCA1, and Figure 2, BRCA2 from an FFPE sample with SureSeq compared to an amplicon-based panel.

Figure 1: BRCA1 exons 8, 9, 10 and 11 coverage. [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).

Figure 1: BRCA1 exons 8, 9, 10 and 11 coverage. [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).

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Figure 2: BRCA2 exons 11, 12 and 13 coverage. [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).

Figure 2: BRCA2 exons 11, 12 and 13 coverage. [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).

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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 2 “hot spots”: E542K or E545K in exon 9, and H1047R or H1047L in exon 201, Figure 3.

Figure 3: Illustration of the excellent uniformity of coverage of PIK3CA [A] exon 9 and [B] exon 20. Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

Figure 3: Illustration of the excellent uniformity of coverage of PIK3CA [A] exon 9 and [B] exon 20. Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

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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 4.

Figure 4: 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).

Figure 4: 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).

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SureSeq myPanel NGS Custom Breast Cancer Panel workflow

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Content selection

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  • SureSeq myPanel NGS Custom Breast Cancer panel
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Library preparation

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Sequencing

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Data analysis

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What our customers say

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.

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Dr Anna Skowronska

R&D Scientist, Haemato-Oncology Team, West Midlands Regional Genetics Laboratory, Birmingham Women’s NHS Foundation Trust, UK

References

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

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