Search
First slide
Sureseq Logo

Product summary

  • Technology NGS
  • Application Haematology
  • Areas of interest AML
  • Gene Targets 1 - 29+
  • Aberration Types SNV, indel, ITD, PTD, translocation
  • Product Code Various
  • Regulatory Status For research use only; not for diagnostic procedures.

Documentation

Ancillary products

Overview

Introduction

Acute myeloid leukaemia (AML) is the most common type of acute leukaemia in adults. Our understanding of AML has been transformed in recent years to a disease classified largely based on genetic, genomic and molecular characteristics. Key genes implicated in AML progression include CEBPA, NPM1, FLT3 and KMT2A (MLL) with mutations in multiple additional genes identified in recent research1.

Choose your perfect AML NGS panel from our range of fully tested and optimised panel content. Simply mix and match the genes or individual exons you require for your research and get the most out of your sequencing runs.

Getting started with your SureSeq myPanel™ NGS Custom Panel could not be simpler, find out more in this video…

SureSeq myPanel process Image

SureSeq myPanel process

Zopom Icon
Select from any of the following SureSeq myPanel AML gene or exonic content Image

Select from any of the following SureSeq myPanel AML gene or exonic content

Zopom Icon
Features
  • Unparalleled coverage uniformity across all content including CEBPA — confidently detect AML variants and remove the requirement for supplementary fill-in approaches
  • Bespoke panels with pre-optimised content — create your ideal AML panel and sequence only what’s relevant for your AML research
  • Robust detection of FLT3-ITDs and KMT2A-PTDs — streamline your laboratory workflow with a single NGS assay for comprehensive aberration detection in AML
  • Complimentary Interpret NGS data analysis software — easy-to-use analysis solution for accurate detection of all variants

Gene targets

Select a gene to view exon coverage examples:

* Exon examples not yet available

ASXL1 Exon 1 (hg19 chr20:30946147-30946635). Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

ASXL1 Exon 1

ASXL1 Exon 11 (hg19 chr20:31021087-31021720). Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

ASXL1 Exon 11

ASXL1 Exon 12 (hg19 chr20:31022235-31027122). Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

ASXL1 Exon 12

Want to customise these gene targets?

We have a regularly updated, expert-curated library of pre-optimised cancer panel content for you to select from. Simply mix and match the gene, exonic or intronic content you need to create an AML NGS cancer panel that meets your exact requirements.

Customise this panel

Capabilities

Excellent coverage uniformity of the CEBPA gene

Mutations in the CEBPA gene are among the most common molecular alterations in AML. 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, even in difficult to sequence genes, 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. Depth of coverage per base (grey). Targeted region (green). Gene coding region as defined by RefSeq (blue). GC percentage (red).

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).

Zopom Icon
Sophisticated bait design strategies allowing reliable FLT3-ITD and KMT2A-PTD detection

The most prevalent type of FLT3 mutations in AML are internal tandem duplications (ITDs). FLT3-ITDs are challenging to target 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 generate a complete picture of the genetic makeup of AML. To provide optimal results OGT employs sophisticated bait design strategies to generate uniform coverage across, as well as upstream and downstream of the repetitive region, allowing easy detection of FLT3-ITDs ranging from a handful of base pairs to >200 bp (Figure 2).

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 exons 3 to 9, exons 3 to 10 and exons 3 to 11 being the most commonly found in AML2. With OGT’s expertise in hybridisation-based panel design, your SureSeq myPanel offers robust detection of all sizes of KMT2A-PTDs, alleviating the burden of running multiple assays (Figure 3).

Figure 2: Facilitated by OGT’s expert bait design, 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.

Figure 2: Facilitated by OGT’s expert bait design, 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.

Zopom Icon
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.

Zopom Icon
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, you’ll be able to accurately detect all SNVs, indels, ITDs and PTDs covered by your SureSeq myPanel Custom AML Panel. Additionally, if you choose to expand your panel further, our Interpret software can reliably detect copy-number variations (CNVs), loss-of-heterozygosity (LOH) and translocations, for example BCR-ABL. Following detection, all variants can be readily visualised in the user-friendly variant browser, for an effortless translation of all your AML data into meaningful results.

SureSeq myPanel NGS Custom AML panel workflow

Content selection Image

Content selection

Sure Seq Bar 1
  • SureSeq myPanel NGS Custom AML panel
Library preparation Image

Library preparation

Sure Seq Bar 2
Sequencing Image

Sequencing

Sure Seq Bar 3
Data analysis Image

Data analysis

Sure Seq Bar 4

What our customers say

We were delighted with the performance of the SureSeq panel. It showed complete concordance with our other techniques, detecting all known mutations with excellent sensitivity down to 1% [MAF (minor allele frequency)], including, in one case, a JAK2 V617F mutation which was not detected by ddPCR due to a second mutation under the primer. The panel also demonstrated mutations in other genes in samples with low level JAK2 V617F and good correlation between allele frequencies and quantitative analysis by ddPCR. We are planning to adopt the panel in the near future.

Anna S Quote Image

Dr Anna Skowronska

R&D Scientist, Haemato-Oncology Team, West Midlands Regional Genetics Laboratory, Birmingham Women’s NHS Foundation Trust, UK

References

  1. Döhner et al., Blood 2017; 129(4):424–447
  2. Steudel et al., Genes Chromosomes Cancer 2003; 37(3):237-51

Request a quote for this product

Customise this panel
View all products

NGS resources & support

Basics Icon

NGS basics

Tips Icon

NGS tips & troubleshooting

Videos Icon

NGS tutorial videos & webinars

Literature Icon

NGS scientific literature