SureSeq™ Core MPN Panel

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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 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).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.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.

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