SureSeq myPanel™ NGS Custom Breast Cancer Panel
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.
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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. 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
| 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
| Product | Contents | Cat. 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 |
| 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 OGT's NGS panels
References
- Mukohara, Breast Cancer (Dove Med Press). 2015; 7: 111–123.
- 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.
Disclaimer
SureSeq: For research use only; not for use in diagnostic procedures.
Resources
Catalogue
Product profile
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SureSeq myPanel™ NGS Custom AML Panels
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SureSeq myPanel™ NGS Custom Breast Cancer panel
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SureSeq myPanel™ NGS Custom Cancer Panels
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SureSeq myPanel™ NGS Custom Colorectal Cancer Panel
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SureSeq myPanel™ NGS Custom Melanoma Cancer Panel
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SureSeq™ FFPE DNA Repair Mix
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SureSeq™ NGS Library Preparation Kit
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SureSeq™ Ovarian Cancer Panel
White paper
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The role of NGS in stratified cancer medicine
In this white paper, two Clinical Scientists, Dr Matthew Smith and Dr George Burghel, share their views on the use of NGS in cancer genomics and its integration into the laboratory.
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Understanding myeloid disorders with next-generation sequencing
How OGT’s SureSeq™ Myeloid Panel helps researchers identify and decipher the complex genetic origins of myeloproliferative disorders
Gene list
Lab Programme
Application note
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Evaluation of enzymatic DNA digestion as an alternative to mechanical DNA fragmentation (sonication) for targeted NGS using the SureSeq™ Myeloid Panel
DNA fragmentation is a crucial first step in the preparation of libraries for NGS. In this application note, Oxford Gene Technology has evaluated an alternative method of fragmentation using the NEBNext® dsDNA Fragmentase®.
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Improving experimental reproducibility through automated hybridisation-based NGS library preparation
In this application note, an Agilent Bravo A Automated Liquid Handling Platform was configured to run the SureSeq NGS library preparation protocol. The results demonstrate marked improvement not only in hands-on-time, but also a number of quality metrics
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Selecting the best NGS enrichment assay for your needs
With NGS now in routine use for a broad range of research and clinical applications, this application note details the value of making the correct choice for the initial sequence enrichment step.
Handbook
Poster
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Optimised, 1-day hybridisation-based NGS protocol yields 1% variant detection in MPN samples, as quickly and cost-effectively as multiplex PCR
Presented at AMP 2016, this poster outlines how the SureSeq™ Core MPN Panel can accurately detect alleles down to 1% variant allele fraction (VAF) in JAK2 (V617F) at a read depth of >1000x, facilitating reliable detection.
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The accurate detection by next-generation sequencing (NGS) of difficult to sequence genes (CALR, CEBPA, FLT3) associated with myeloid disorders using a hybridisation-based enrichment approach
Presented at CGC 2017, this poster highlights the excellent uniformity of coverage obtained from the hybridisation-based enrichment using the SureSeq myPanel NGS Custom AML Panel.
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The Analysis of FFPE Samples by Next-Generation Sequencing (NGS) of Key Genes for Research into Breast and Ovarian Cancer
Presented at AMP Europe 2018, this poster illustrates the confident detection of germline and somatic variants in key cancer-related genes including BRCA1 and TP53.
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The analysis of myeloproliferative neoplasm samples using a rapid (30 minute) hybridisation-based enrichment protocol for next-generation sequencing (NGS)
Presented at the CGC 2017 annual summer meeting in Denver, USA, this poster illustrates the excellent quality data generated by the OGT 1-day hybridisation-based SureSeq LPK protocol in combination with the SureSeq Core MPN Panel.
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The application of a hybridisation-based next-generation sequencing (NGS) enrichment panel for the analysis of key genes involved in ovarian and breast tumours using DNA from FFPE samples
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The application of a hybridisation-based NGS enrichment panel for the analysis of somatic variants in tumour samples and reference standards
Presented at AGT 2017, this poster outlines the application of a hybridisation-based NGS enrichment panel for the analysis of solid tumour somatic variants, demonstrating 100% concordance in variant detection in both genomic and formalin-compromised DNA.
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The application of a one-day hybridisation-based enrichment protocol for NGS incorporating a rapid (30 minute) hybridisation step
Presented at AGT 2017, this poster outlines how OGT has optimised a one-day hybridisation-based enrichment protocol for NGS incorporating a rapid 30 hybridisation step.
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The use of a hybridisation-based NGS enrichment panel for the confident identification of a broad range of low frequency variants from as little as 50ng of challenging clinical research FFPE samples
Presented at AMP 2016, this poster outlines how the SureSeq FFPE DNA Repair Mix significantly improves NGS library yields, with an increase of mean target coverage (increased by >2.2 fold), resulting in more meaningful data.
Flyer
Brochure
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An integrated approach to profiling haematological disorders
For accurate detection of all types of genetic aberrations, various technologies are used. View OGT's integrated portfolio of products that allow the accurate analysis of haematological disorders.
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An integrated approach to tumour profiling
Various technologies are available to study the mutations that cause cancer, but none is capable of accurate detection of all types of genetic aberrations. View OGT's integrated portfolio of products that allow the accurate analysis of solid tumours.