SureSeq myPanel™ NGS Custom Melanoma Cancer Panel
Choose your perfect Melanoma 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
Cutaneous melanoma (CM) is the most dangerous form of skin tumour and causes 90% of skin cancer mortality1. With recurrent somatic mutations in BRAF, NRAS, KIT and NF1 among the most common genetic aberrations underlying pathogenesis of melanoma, next generation sequencing (NGS) has been an invaluable tool in helping to characterise the overall genomic landscape of melanomas.
SureSeq myPanel offers:
- Hybridisation-based enrichment delivering unparalleled coverage uniformity- detect low frequency melanoma variants consistently with confidence
- 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 melanoma 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.
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Superior Coverage Uniformity
The most frequently activated pathway in melanoma is the mitogen-activated protein kinase (MAPK) pathway, often activated through mutations in the V600 codon of BRAF (in 35–50% of melanomas) and the Q61 codon of NRAS (10–25%)2, with mutations being mutually exclusive.
Mutations of KIT are found in particular subsets of melanoma, where the mutations activate signal-transduction pathways (MAPK and PI3K) that ultimately lead to cell proliferation. Approximately 70% of KIT mutations identified in melanoma are found in exon 11, most commonly L576P (Figure 1a and 1b).
Neurofibromatosis type 1 (NF1) is a relatively common tumour predisposition syndrome related to germline aberrations of NF1, a tumour suppressor gene. Recent studies have additionally shown NF1 to play a critical role in somatic events in a wide range of tumours, including melanoma. The tumour suppressor function of neurofibromin is largely attributed to a small central region which comprises 360 amino acids encoded by exons 20-27a3. OGT’s expert bait design offers excellent uniformity for all of these key genes associated with melanoma (Figure 1).
Figure 1. Illustration of the exceptional uniformity of coverage of BRAF exon 15 (1a), NRAS exon 2 (1b) with a SureSeq melanoma panel. Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).
Figure 2. Even coverage of NF1 exon 21 (2a) and KIT exons 10 and 11 (2b) with a SureSeq melanoma panel. Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).
Select from any of the following myPanel melanoma whole gene or exonic content below:
| BRAF | KIT | NF1** | NRAS |
Getting started with your next SureSeq myPanel Custom Cancer Panel could not be simpler...
Talk to us about your custom melanoma NGS panel requirements and let our expertise work in helping advance your cancer research.
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Ordering Information
| Product | Contents | Cat. No. | Price |
|---|---|---|---|
| SureSeq myPanel NGS Custom Melanoma 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 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 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.
**Due to the presence of pseudogenes in NF1, it is recommended that an orthogonal technique is used to verify any mutations detected.
*** Only for use with SureSeq NGS panels
References
1. Garbe et al, European Journal of Cancer 63 (2016) 201-217
2. Tsao et al, Genes & Dev. 2012. 26: 1131-1155
3. Yap et al, Oncotarget, 2014, Vol. 5, No. 15
SureSeq: For research use only; not for use in diagnostic procedures.
Resources
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.
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
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.
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
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.