SureSeq™ Pan-Myeloid Panel

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The SureSeq Pan-Myeloid Panel has been designed with input from recognised cancer experts to detect key variants in 70 genes implicated in a wide range of myeloid disorders, including AML, MPN and MDS.

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Details

The SureSeq Pan-Myeloid Panel accurately detects SNVs and indels in genes such as CEBPA, JAK2, CALR and MPL, as well as structural variants including FLT3-ITDs and KMT2A-PTDs, providing researchers with a single NGS workflow delivering a comprehensive picture of the genetic make-up of each myeloid sample.

 

The SureSeq Pan-Myeloid Panel offers:

  • Comprehensive panel content designed by experts — investigate key variants in 70 genes implicated in a variety of myeloid malignancies
  • Unparalleled coverage uniformity, even in difficult regions — confidently detect low-frequency SNVs and indels down to 1% VAF
  • Robust detection of FLT3-ITDs and KMT2A-PTDs — streamline your laboratory workflow with a single NGS assay
  • Complimentary Interpret NGS data analysis software — easy-to-use analysis solution for accurate detection of all variants in your panel

 

ABL1 all exons CEBPA all exons ETNK1 all exons IDH1 exon 4 KRAS exons 2, 3 PHF6 all exons SRSF2 exon 1
ASXL1 exon 12 CHEK2 all exons ETV6 all exons IDH2 exons 4, 5 MPL exon 10 PLCG2 exons 19, 20, 24 STAG2 all exons
BCOR all exons CREBBP all exons EZH2 all exons IKZF1 all exons MYD88 exons 3, 5 PPM1D all exons STAT3 exons 19-21
BCORL1 all exons CSF3R exons 14-17 FBXW7 exons 9-11 IRF1 all exons NF1 all exons PTEN all exons STAT5B exon 16
BIRC3 all exons CTNNA1 all exons FLT3 exons 13-15, 20 JAK1 all exons NFE2 all exons PTPN11 exons 3, 13 TET2 exons 3-11
BRAF exon 15 CUX1 all exons GATA1 all exons JAK2 exons 12, 14 NOTCH1 exons 26-28, 34, 3'UTR RAD21 all exons TP53 all exons
BTK exon 15 CXCR4 all exons GATA2 exons 2-6 JAK3 all exons NPM1 exon 12 RUNX1 all exons U2AF1 exons 2, 6
CALR exon 9 DDX41 all exons GNAS exons 8-10 KIT exons 2, 8-11, 13, 17 NRAS exons 2, 3 SETBP1 exon 4 WT1 exons 7, 9
CBL exons 8, 9 DNMT3A all exons GNB1 exons 5-6 KMT2A all exons PAX5 all exons SF3B1 exons 13-16 XPO1 all exons
CDKN2A all exons EP300 all exons HRAS all exons KMT2C all exons PDGFRA all exons SH2B3 all exons ZRSR2 all exons

Table 1: The SureSeq Pan-Myeloid Panel targets 70 genes implicated in a variety of myeloid disorders

 

Contains the latest evidence-based content

Myeloid malignancies are a heterogenous group of diseases, associated with a wide variety of variants ranging from mutations to structural variations. The hybridisation-based SureSeq Pan-Myeloid Panel is able to consistently detect clinically relevant variants down to 1% variant allele frequency (VAF) in 70 key genes implicated in myeloid malignancies.

 

Robust detection of CEBPA variants, FLT3-ITDs and KMT2A-PTDs

Mutations in the CEBPA gene are among the most common molecular alterations in AML, which itself is the most common type of acute leukaemia in adults1,2. Sequencing of CEBPA is challenging due to the presence of repeat regions and the high GC-content of the gene, leading to poor coverage across these regions and potentially missed variants. OGT’s expert bait design overcomes these issues and provides exceptional coverage uniformity, enabling reliable detection of variants and eliminating the requirement for supplementary fill-in with Sanger sequencing (Figure 1).

Figure 1: Illustration of the excellent coverage uniformity of the CEBPA gene.Figure 1: Illustration of the excellent coverage uniformity of the CEBPA gene. Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

 

FLT3 internal tandem duplications (ITDs) are challenging to target, and subsequently detect, because they are by nature repetitive and can be very long. As a result, FLT3-ITDs are generally masked in most panel designs, necessitating additional techniques to obtain a comprehensive genetic picture. OGT employs sophisticated bait designs to generate uniform coverage across, as well as upstream and downstream of the repetitive region. In combination with our complimentary NGS analysis software Interpret, this allows easy detection of FLT3-ITDs ranging from a handful of base pairs to >200 bp (Figure 2).

Figure 2: FLT3-ITDs of various sizes and even regions containing multiple ITDs can be confidently detected.Figure 2: FLT3-ITDs of various sizes and even regions containing multiple ITDs can be confidently detected. ITD sizes are [A] 174 bp, [B] 225 bp, [C] 195 bp with additional 6 bp, [D] 120 bp and [E] 168 bp with additional 69 bp.

 

Other tandem duplications frequently observed in AML are partial tandem duplications (PTDs) in KMT2A (MLL). Similar to ITDs, KMT2A-PTDs are notoriously difficult to detect due to their size, with duplications spanning multiple exons. With OGT’s expertise in hybridisation-based panel design, SureSeq offers robust detection of all sizes of KMT2A-PTDs, alleviating the burden of running multiple assays (Figure 3).

Figure 3: PTD detected spanning exons 2-8 of KMT2A by OGT’s Interpret NGS analysis software.Figure 3: PTD detected spanning exons 2-8 of KMT2A by OGT’s Interpret NGS analysis software.

 

Complimentary Interpret NGS analysis software

Interpret is OGT’s powerful and easy-to-use NGS 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 Pan-Myeloid Panel, delivering fast and accurate detection of all SNVs, indels, ITDs and PTDs covered by the panel. Following detection, all variants can be easily visualised in the user-friendly variant browser, for an effortless translation of all your myeloid data into meaningful results.

 

Bespoke panel content

You never have to sequence genes you’re not interested in and can always modify each panel to what’s relevant to your research. If the SureSeq Pan-Myeloid Panel doesn’t meet your exact requirements, you can choose from our regularly updated, expert-curated library of pre-optimised cancer content to create your ideal custom SureSeq myPanel™ Myeloid Panel. Alternatively, have a look at the other myeloid panels we have available, including our focused 3-gene SureSeq Core MPN Panel and the SureSeq myPanel Custom Myeloid Panel - 49 gene plus, or our disease-specific content, such as our SureSeq myPanel NGS Custom AML panels.

 

The SureSeq Pan-Myeloid Panel in numbers

Feature

Specification

Number of genes 70
Panel size 215 kb
Mean target coverage >1000x
Coverage uniformity >99% of bases at >20% of mean target coverage
DNA input recommended >500ng high quality DNA
Limit of detection SNVs/ indels: 1% VAF
Samples per MiSeq® v2 run* 12 samples / run

 

 

Ordering information

Product

Contents

Cat. No.

Price

SureSeq Pan-Myeloid Panel (16 reactions) Enrichment baits sufficient for 16 samples; SureSeq Interpret Software 602024-16 Get a quote
SureSeq Pan-Myeloid Panel (96 reactions) Enrichment baits sufficient for 96 samples; SureSeq Interpret Software 602024-96
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

 

Discover more products in our SureSeq range

Product

Contents

Cat. No.

Price

SureSeq Core MPN Panel (16) Enrichment baits sufficient for 16 samples; Interpret Software 602002 Find out more
SureSeq Core MPN Panel (96) Enrichment baits sufficient for 96 samples; Interpret Software 602001 Find out more
SureSeq Myeloid Panel (16 reactions) Enrichment baits sufficient for 16 samples; Interpret Software 600075 Find out more
SureSeq Myeloid Panel (96 reactions) Enrichment baits sufficient for 96 samples; Interpret Software 700076 Find out more
SureSeq myPanel Custom Myeloid Panel - 49 gene plus (16 reactions) Enrichment baits sufficient for 96 samples; Interpret Software 602017-16 Find out more
SureSeq myPanel Custom Myeloid Panel - 49 gene plus (96 reactions) Enrichment baits sufficient for 96 samples; Interpret Software 602017-96 Find out more

 

* Metrics calculated with 1000 ng DNA using Covaris and Speedvac options in the protocol. Contact support for specific information based on your laboratory workflow.

References

  1. Siegel et al., CA Cancer J Clin 2015; 65(1):5-29.
  2. Pabst et al., Nat Genet 2001;27:263-270

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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