SureSeq™ Core MPN Panel
The SureSeq Core MPN Panel delivers accurate detection of somatic variants in 3 clinically relevant myeloid-associated genes, JAK2, MPL and CALR.
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Details
The SureSeq Core MPN Panel has been designed by Oxford Gene Technology (OGT) in collaboration with recognised cancer experts to deliver accurate detection of somatic variants in 3 clinically relevant myeloid-associated genes, JAK2, MPL and CALR, for research into the diagnosis, aetiology and prognosis of MPN.
The SureSeq Core MPN Panel offers:
- Hybridisation-based panel delivering unparalleled coverage uniformity — detect low frequency variants consistently down to 1% VAF at a read depth of >1000x with confidence
- Time and cost saving solution — replace multiple single gene assays with a single NGS panel
- Focused panel content — sequence only what’s relevant for your cancer research, increase throughput and save on sequencing reagents
- Hybridisation quality — Amplicon speed – streamlined library preparation, rapid 30 minute hybridisation step, 1 day from sample to sequencer
- Excellent coverage uniformity — >99% of targeted regions are covered to at least 50% of mean target coverage
Reliable Detection of SNVs, Insertions and Deletions
The SureSeq Core MPN Panel in combination with the enhanced library preparation workflow is able to reliably detect single nucleotide variants (SNVs) as well as insertions (5 bp insertion in JAK2 exon 12 and CALR exon 9) and deletions (5 bp deletion in JAK2 exon 12 and 52 bp deletion in CALR exon 9) (Figures 1 and 2).
Figure 1: Detection of a 52 bp deletion (exon 9 CALR). Wild-type sample (top panel) is compared to a 52 bp somatic deletion (bottom panel).
Figure 2: Detection of a 5 bp deletion (exon 12 JAK2). Wild-type sample (top panel) is compared to a 5 bp somatic deletion (bottom panel).
Panel Coverage
The panel covers sites of relevance in the following 3 genes:
| Gene | Exon | Mutation |
|---|---|---|
| MPL |
10 | W515 |
| CALR | 9 | insertions/deletions |
| JAK2 | 12 | insertions/deletions amino acid substitutions |
| JAK2 | 14 | V617F |
If you are looking for an extended myeloid panel, choose our SureSeq Myeloid Panel covering 25 genes of interest, or customise your own panel with our SureSeq myPanel service.
Ordering Information
| Product | Contents | Cat. No. | Price |
|---|---|---|---|
| SureSeq Core MPN Panel (16) | Enrichment baits; sufficient for 16 samples; SureSeq Interpret Software | 602002 | Get a quote |
| SureSeq Core MPN Panel (96) | Enrichment baits; sufficient for 96 samples; SureSeq Interpret Software | 602001 | Get a quote |
| SureSeq Myeloid Panel (16 reactions) | Enrichment baits sufficient for 16 samples; SureSeq Interpret Software | 600075 | Get a quote |
| SureSeq Myeloid Panel (96 reactions) | Enrichment baits sufficient for 96 samples; SureSeq Interpret Software | 600076 | 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 |
* Only for use with SureSeq NGS panels
For more information about the SureSeq Core MPN Panel or any cancer analysis products contact us at products@ogt.com.
We would like to thank Professor Nick Cross (National Genetics Reference Laboratory - Wessex, UK) for providing the validated research samples.
SureSeq: For research use only; not for use in diagnostic procedures.
Resources
Gene list
Lab Programme
Flyer
White paper
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The importance of enrichment assay choice and optimisation for confident variant detection
This white paper discusses the main strategies employed to optimise the enrichment step, depending on the type of assay chosen.
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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
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.
Product profile
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SureSeq myPanel™ NGS Custom AML Panels
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SureSeq myPanel™ NGS Custom Cancer Panels
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SureSeq™ Core MPN Panel
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SureSeq™ Myeloid Panel
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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.