SureSeq myPanel™ NGS Custom Colorectal Cancer Panel
Choose your perfect colorectal 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
Colorectal cancer (CRC) is the third most common cancer in men (746,000 cases,10.0% of the total) and the second in women (614,000 cases, 9.2% of the total) worldwide1. Next generation sequencing (NGS) has enabled the simultaneous study of mutations in high-penetrance colorectal cancer genes. These include KRAS, APC and TP53 as well as more moderate-risk genes such as ERBB2, PTEN and BRAF.2
SureSeq myPanel offers:
- Hybridisation-based enrichment delivering unparalleled coverage uniformity- detect low frequency colorectal 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 colorectal 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 to 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
KRAS mutations are found in approximately 35-45% of colorectal cancers with around 80% occurring in codon 12 and 15% in codon 13 of exon 2; other commonly reported mutations are found in exons 3 and 43. The tumor suppressor gene APC plays an important role in CRC development. Absence of the APC protein leads to accumulation of betacatenin in the cytoplasm, which may contribute to tumour progression. 60% of all somatic mutations in APC occur within the mutation cluster region between codons 1286 and 1513 on exon 154. Figures 1a, b, c and 2 illustrate the superior uniformity of coverage of these key genomic regions.
Figure 1 a, b, c. KRAS exons 2, 3 and 4 coverage.
Figure 2. APC exon 15 coverage. Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).
Approximately 8-15% of colorectal cancers involve mutations in the BRAF gene, with up to 90% of these a result of a mutation at V600E, located on exon 155. In TP53, another frequently mutated cancer gene, point mutations are predominantly located in exons 5-82, however sequencing 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.
Illustration of the excellent uniformity of coverage of (Figure 3) BRAF exon 15 and TP53 exons 3 - 9 (Figure 4). 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 colorectal whole gene or exonic content below:
| APC | CDH1 | ERBB2 | KRAS | MSH6 | PIK3CA | STK11 |
| BRAF | CHEK2 | HRAS | MET | NRAS | PTEN | TP53 |
Getting started with your next SureSeq myPanel Custom Cancer Panel could not be simpler...
Talk to us about your custom colorectal NGS panel requirements and let our expertise work in helping advance your cancer research.
Let's talk about panel content >
Ordering Information
| Product | Contents | Cat. No. | Price |
|---|---|---|---|
| SureSeq myPanel NGS Custom Colorectal 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
1. http://globocan.iarc.fr/Pages/fact_sheets_cancer.aspx
2. Han et al, PLoS One. 2013; 8(5): e64271
3. Tan et al, World J Gastroenterol. 2012 Oct 7; 18(37): 5171–51804
4. More, et al, Hum Mol Genet (1992) 1 (4): 229-233
5. https://www.mycancergenome.org/content/disease/colorectal-cancer/braf/54/
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.
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
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.
Catalogue
Gene list
Lab Programme
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.