SureSeq myPanel™ NGS Custom Prostate Cancer Panel
Choose your ideal prostate cancer NGS panel from our range of fully optimised NGS 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
Prostate cancer is now the second leading cause of cancer in men, with recent genome-wide studies helping to clarify the genetic basis of this common but complex disease1. Many of these studies have reinforced the importance of homologous end repair genes including: ATM, BRCA1, BRCA2 and PALB2, in the mechanism of prostate cancer development. Mutations in these genes result in cells having to repair lesions through other non-conservative mutagenic mechanisms.
SureSeq myPanel offers:
- Hybridisation-based enrichment delivering unparalleled coverage uniformity — detect low frequency prostate 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 prostate cancer NGS panel from our range of fully 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.
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Superior Coverage Uniformity
A number of genetic factors have been found that increase prostate cancer risk, including heritable mutations in the genes BRCA1 and BRCA2. BRCA1 is a key player in cellular control systems, having been linked to DNA damage response and repair, transcriptional regulation and chromatin modelling2, while BRCA2 function is linked to DNA recombination and repair processes, being of particular importance in the regulation of RAD51 activity.
Figure 1a, illustrates the superior uniformity of coverage of key exons of BRCA1, and Figure 1b, BRCA2 from an FFPE sample.
Figure 1a
Figure 1b
Figure 1a. BRCA1 exon 9 and 10 coverage. Figure 1b. BRCA2 exon 11 coverage. Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).
PALB2 is a BRCA2 binding protein and the BRCA2-PALB2 interaction is essential for BRCA2-mediated DNA repair. Recently it has been shown that correct PALB2 function is necessary for the homologous recombination repair via interaction with BRCA1, revealing that PALB2 is actually a linker between BRCA1 and BRCA23. The ATM gene, located on chromosome 11q 22–23, includes 66 exons with a 9168 base pair coding sequence, and encodes a PI3K-related protein kinase (PIKK) that helps maintain genomic integrity. The PI3K-AKT-mTOR oncogenic pathway is frequently enhanced in prostate cancer playing a vital role in development and maintenance4.
Figures 2 and 3 illustrate the excellent uniformity of coverage of key exons of PALB2 and ATM, respectively.
Figure 2a
Figure 2b
Figure 3a
Figure 3b
Figures 3a and 3b. Illustration of the excellent uniformity of coverage of PALB2 exons 5 (2a) and 13 (2b) and ATM exons 45 (3a) and 62 (3b). 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 Prostate Cancer whole gene or exonic content below:
| ATM | BRCA1 | BRCA2 | PALB2 |
|---|
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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Ordering Information
| Product | Contents | Cat. No. | Price |
|---|---|---|---|
| SureSeq myPanel NGS Custom Prostate Cancer Panels | 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
- Thoma, C, (2015) The complex relationships of malignant cells in lethal metastatic castration-resistant disease, Nature Reviews Urology 12, 237
- Castro, E. et al, (2012) The role of BRCA1 and BRCA2 in prostate cancer. Asian Journal of Andrology, 14 (3):409-414.
- Pakkanen, S. et al, (2009) PALB2 variants in hereditary and unselected Finnish Prostate cancer cases. Journal of Negative Results in BioMedicine, 8 (1).
- Angèle, S. et al, (2004). ATM polymorphisms as risk factors for prostate cancer development. British Journal of Cancer, 91(4): 783–787.
Disclaimer
SureSeq: For research use only; not for use in diagnostic procedures.
Resources
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
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
Catalogue
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.
Lab Programme
Gene list
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 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.