Expanded Sequencing Panel Supports Myeloid Malignancy Variant Profiling

Myeloid malignancies require molecular profiling to detect variants relevant to disease characterization and research. FLT3 internal tandem duplications occur in an estimated 20–30% of de novo acute myeloid leukemia cases and are associated with poor prognosis, but longer repetitive insertions can be difficult for short-read sequencing assays to size accurately. Now, a newly launched research-use-only panel expands myeloid gene coverage while improving detection of long and multiple FLT3 internal tandem duplications.

Pillar Biosciences (Natick, MA, USA) has launched the oncoReveal Myeloid v2 Panel, an expanded research-use-only (RUO) DNA next-generation sequencing (NGS) panel for myeloid malignancies. The panel expands the original oncoReveal Myeloid Panel from 58 to 80 gene targets. It adds 22 genes while retaining all prior content, giving laboratories broader guideline-relevant coverage without disrupting existing workflows.

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The new version uses Pillar’s proprietary SLIMamp chemistry and VersaTile primer design tool to support panel scaling. Only four of the original 766 amplicons covering the original 58 genes were changed to accommodate the expanded content. The panel is also paired with PiVAT informatics to support detection and sizing of FLT3 internal tandem duplications using standard 2 x 150 bp short-read sequencing.

In an independent evaluation of 111 samples, including 23 FLT3-ITD-positive samples with internal tandem duplications ranging from 12 bp to 279 bp, the panel and PiVAT informatics accurately detected and sized these variants. The evaluation included internal tandem duplications up to 279 bp and nine samples with two to four concurrent internal tandem duplications. FLT3 internal tandem duplications were detected to 1% or lower variant allele frequency. NGS-derived variant allele frequencies trended consistently with allelic ratios from orthogonal capillary electrophoresis-based fragment analysis across the evaluated internal tandem duplication lengths.

Detection of long and multiple internal tandem duplications in a single NGS run can identify distinct clonal populations within the same sample. Each population may have its own internal tandem duplication length and variant allele frequency. This level of detail can be obscured by a single capillary electrophoresis-based allelic ratio.

“With oncoReveal Myeloid v2, we significantly expanded our myeloid gene content while preserving the trusted panel content laboratories already rely on. We also invested significant effort in FLT3-ITD detection so laboratories can obtain accurate, base-pair-resolved calls for long and multiple ITDs without defaulting to a separate fragment-analysis workflow,” said ShiPing Zou, Senior Director, Product Management at Pillar Biosciences.

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