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SureSeq myPanel™ NGS Custom Breast Cancer Panel

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Applications:

Choose your perfect breast cancer NGS panel from our range of fully tested and optimised panel content. Simply mix and match the genes or individual exons you require and get the most out of your sequencing runs.

Find out more

For more information about any OGT product or service, please contact us.

Email: contact@ogt.com
Phone: +44 (0)1865 856800 (US: 914 467 5285)

Details

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.

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

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.

Let's talk about panel content >

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

Figure 1b

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.

Figures 2a & 2bFigure 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

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...

SureSeq myPanel

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

APC BRCA2 CHEK2 GATA3 PIK3CA RB1
ATM
 BRIP1
 EGFR
 MSH6
 PTEN
 SF3B1
BARD1
 CDH1
 ERBB2
 NBN
 RAD51C
 STK11
BRCA1
 CDK12
 ESR1
 PALB2
 RAD51D
 TP53


Panels you may be interested in:

Panel I:

Number Gene Number of exons
1 BRCA1 All
2 BRCA2 All
3 TP53 All


Panel II:

Number Gene Number of exons
1 BRCA1 All
2 BRCA2 All
3 CDH1 All
4 PALB2 All
5 PTEN All
6 TP53 All


Panel III:

Number Gene Number of exons
1 ATM All
2 BRCA1 All
3 BRCA2 All
4 CDH1 All
5 CHEK2
 All
6 PALB2 All
7 PTEN All
8 TP53 All


Panel IV:

Number Gene Number of exons
1 ATM
 All
2 BARD1
 All
3 BRCA1
 All
4 BRCA2
 All
5 BRIP1
 All
6 CDK12
 All
7 CHEK2
 All
8 PALB2
 All
9 RAD51C All
10 RAD51D All
11 TP53 All


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

Let's talk about panel content >

Ordering Information

ProductContentsCat. No.Price
SureSeq myPanel NGS Custom Breast Cancer Panel Enrichment baits; SureSeq Interpret Software Various Get a quote
SureSeq FFPE DNA Repair Mix Enzyme, mix and buffers sufficient for 16 FFPE DNA samples 500079* Get a quote
SureSeq NGS Library Preparation Complete Solution (16) Bundle of 1x SureSeq library preparation kit (16), containing adaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit – Collection A, 1x SureSeq Hyb & Wash Kit (16), 1x Dynabeads M270 Streptavidin (2ml) and 1x AMPure XP beads (10ml). Sufficient for 16 samples 500084  Get a quote
SureSeq NGS Library Preparation Complete Solution (48) Bundle of 3x SureSeq NGS Library Preparation Kit (16), containing adaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit – Collection B, 3x SureSeq NGS Hyb & Wash Kit (16), 3x Dynabeads M270 Streptavidin (2ml) and 3x AMPure XP beads (10ml). Sufficient for 48 samples 500085  Get a quote
SureSeq NGS Library Preparation and Hyb & Wash Kit (16) Bundle of 1x SureSeq NGS Library Preparation Kit (16), containing adaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit – Collection A and 1x SureSeq Hyb & Wash Kit (16). Sufficient for 16 samples 500082  Get a quote
SureSeq NGS Library Preparation and Hyb & Wash Kit (48) Bundle of 3x SureSeq NGS Library Preparation Kit (16), containing adaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit – Collection B and 3x SureSeq Hyb & Wash kit (16). Sufficient for 48 samples 500083  Get a quote
SureSeq NGS Library Preparation Kit (16) Bundle of 1 x library preparation kit (16), containing adaptors, PCR primers and enzymes sufficient for 16 samples and 1 x SureSeq NGS Index Kit – Collection A 500070  Get a quote
SureSeq NGS Library Preparation Kit (48)  Bundle of 3 x library preparation kit (16), containing adaptors, PCR primers and enzymes sufficient for 48 samples and 1 x SureSeq NGS Index Kit – Collection B 500073  Get a quote
SureSeq NGS Hyb & Wash Kit (16) Hybridisation buffer, Wash buffer, Cot and blocking oligos. Sufficient for 16 samples 500075  Get a quote
SureSeq NGS Hyb & Wash Kit (48) Bundle of 3x SureSeq NGS Hyb & Wash Kit (16), containing Hybridisation buffer, Wash buffer, Cot and blocking oligos. Sufficient for 48 samples 500086  Get a quote
SureSeq NGS Index Kit - Collection A (16) 16 different indexes, each sufficient for 4 samples [included with SureSeq NGS Library Preparation Kit (16)] 500071 Get a quote
SureSeq NGS Index Kit - Collection B (48) 48 different indexes, each sufficient for 4 samples [included with SureSeq NGS Library Preparation Kit (48)] 500072 Get a quote
Dynabeads™ M270 Streptavidin, 2ml Sample capture beads, sufficient for 20 samples 500080** Get a quote
AMPure® XP beads, 10ml Sample purification beads, sufficient for 16 samples 500081**  Get a quote

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

** Only for use with SureSeq NGS panels

References

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

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.

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