SureSeq myPanel™ NGS Custom AML Panel

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.

SureSeq myPanel Custom AML Panels offer:

• 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

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).

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).

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.

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 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 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.

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

Offering comprehensive content covering a wide range of aberrations, you can now design your perfect SureSeq myPanel Custom AML Panel and generate a comprehensive genetic picture of all your AML samples using a single streamlined workflow.

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References

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

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.