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
Myeloproliferative neoplasms (MPNs) are a heterogeneous group of diseases characterised by the overproduction of one or more types of blood cells. The SureSeq Core MPN Panel has been designed in collaboration with recognised cancer experts to detect somatic variants in 3 clinically relevant MPN-associated genes; JAK2, MPL and CALR (Table 1). The SureSeq Core MPN Panel provides researchers with a single, 1-day NGS workflow for studies into the diagnosis, aetiology and prognosis of MPNs.
The SureSeq Core MPN Panel offers:
- Unparalleled uniformity and high depth of coverage — detect low frequency SNVs and indels with confidence
- Time and cost savings — replace multiple single gene assays with a focused NGS panel
- 1 day from sample to sequencer — streamlined library preparation and rapid 30-minute hybridisation
- Additional BCR-ABL fusion gene detection — customise your panel by adding BCR-ABL translocation content
- Complimentary Interpret NGS data analysis software — easy-to-use analysis solution for accurate identification of all variants and translocations
Reliable Detection of SNVs, Insertions and Deletions
The hybridisation-based SureSeq Core MPN Panel is able to consistently detect SNVs and indels down to 1% minor allele frequency (MAF), using a streamlined 1-day workflow. Facilitated by OGT’s expert bait design, the panel delivers the turn-around time of an amplicon-based protocol with the superior coverage uniformity of a hybridisation-based panel, enabling confident detection of key MPN variants including a 52 bp deletion in CALR exon 9 and a 6 bp deletion in JAK2 exon 12 (Figures 1 and 2).
Gene |
Exon |
Key variants |
| MPL | 10 | W515 |
| CALR | 9 | insertions / deletions |
| JAK2 | 12 | insertions / deletions, amino acid substitutions |
| JAK2 | 14 | V617F |
Table 1: The SureSeq Core MPN Panel targets 4 exons in 3 genes implicated in MPNs, covering various key MPN driver mutations.
Figure 1: Detection of a 52 bp deletion (type 1) in exon 9 of CALR (bottom panel), compared to a wild-type sample (top panel).
Figure 2: Detection of a 6 bp deletion in exon 12 of JAK2 (bottom panel), compared to a wild-type sample (top panel).
Bespoke panel content including BCR-ABL fusion detection
The BCR-ABL gene fusion is formed following a balanced translocation of chromosome 9 and 22, generating the Philadelphia chromosome. Most MPNs are negative for BCR-ABL, however this translocation is a hallmark of chronic myeloid leukaemia (CML) (Figure 3).
Figure 3: BCR-ABL translocation reported in Interpret. Split-reads covering both BCR (left panel) and ABL1 (right panel) are detected, indicative of the BCR-ABL gene fusion.
With SureSeq myPanel™, our regularly updated, expert-curated library of pre-optimised cancer content, you can customise your SureSeq Core MPN Panel and add BCR-ABL fusion gene detection, as well as other myeloid content, to create your ideal custom SureSeq myPanel MPN Panel. Combine SNV and indel detection with translocation content and replace multiple assays with a single streamlined NGS workflow for a more comprehensive picture of all your MPN samples.
Complimentary Interpret NGS analysis software
Interpret is OGT’s powerful and easy-to-use data analysis solution, facilitating analysis and visualisation of a wide range of somatic variants and structural aberrations. Designed to work seamlessly with all SureSeq panels, Interpret perfectly complements the SureSeq Core MPN Panel, delivering fast and accurate detection of SNVs and indels, as well as BCR-ABL and other translocation events for customised panels. Following detection, all variants can be readily visualised in the user-friendly variant browser, for an effortless translation of all your MPN data into meaningful results.
The Core MPN Panel in numbers
Feature |
Specification |
| Target regions |
JAK2 exons 12 and 14 CALR exon 9 MPL exon 10 |
| Panel size | 1kb |
| Mean target coverage | >1000x |
| Coverage uniformity | 100% of bases at >20% of mean target coverage |
| DNA input recommended | >500ng high quality DNA |
| Limit of detection | SNVs / indels: 1% MAF |
| Workflow | 30 minutes hybridisation, 1-day sample-to-sequencer |
| Samples per MiSeq® v2 run | 48 samples / run |
If you are looking for an extended myeloid panel or want to create your own custom SureSeq myPanel, talk to us and let our expertise help you advance your cancer research.
Ordering Information
Product |
Contents |
Cat. No. |
Price |
|---|---|---|---|
| SureSeq Core MPN Panel (16) | Enrichment baits sufficient for 16 samples; Interpret Software | 602002 | Get a quote |
| SureSeq Core MPN Panel (96) | Enrichment baits sufficient for 96 samples; Interpret Software | 602001 | 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 |
We would like to thank Professor Nick Cross (National Genetics Reference Laboratory - Wessex, UK) for providing the validated research samples and West Midlands Regional Genetic Laboratory, Birmingham, for providing the BCR-ABL samples.
Disclaimer
SureSeq: For Research Use Only; Not for Diagnostic Procedures. This webpage and its contents are © Oxford Gene Technology IP Limited – 2020. All rights reserved. OGT™ and SureSeq™ are trademarks of Oxford Gene Technology IP Limited. The SureSeq NGS Library Preparation Kit was jointly developed between Oxford Gene Technology and Bioline Reagents Limited. Dynabeads is a trademark of Thermo Fisher Scientific and AMPure® is a registered trademark of Beckman Coulter Inc.
Resources
Catalogue
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OGT Product Catalog - USA and Canada
Including Cytocell® FISH probes for Constitutional Cytogenetics and Hematology/Pathology Cytogenetics, CytoSure™ NGS and Array Products for Cytogenetics and Rare Disease Research and SureSeq™ NGS Products for Hematology and Solid Tumor Cancer Research.
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OGT Product Catalogue
Including Cytocell® FISH Probes for Cancer and Inherited Genetic Disease, CytoSure™ NGS and Array Products for Cytogenetics and Rare Disease, and SureSeq™ NGS Products for Haematology and Solid Tumour Cancers.
Flyer
Brochure
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An integrated approach to tumour profiling
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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
This poster illustrates the SureSeq™ hybridisation-based approach as a robust method for the identification of germline and somatic mutations in TP53, BRCA1, and BRCA2.
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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.
Gene list
Handbook
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
This white paper describes 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 app 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.