Detecting Complex Mutations in Myeloid Leukemia Using the GeneReader NGS System and QIAact Myeloid DNA UMI Panel

Introduction

Somatic mutations acquired in key signalling pathway, transcription factor, spliceosome, epigenetic and tumor suppressor genes are of central importance in the development and progression of myeloid malignancies including myeloproliferative neoplasms (MPN), myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). To date, in order to evaluate all relevant genetic alterations, multiple tests are needed, requiring large amounts of DNA. As tests are typically performed sequentially this unnecessarily extends the time between sample acquisition and mutation detection.

The QIAact Myeloid DNA UMI Panel in combination with the QIAGEN GeneReader NGS System provides a single solution to simultaneously test for actionable mutations, whilst also saving sample material (only 40ng DNA input required per sample), shortening test time and enabling simplification of lab operations.

The QIAact Myeloid DNA UMI Panel is a multi-gene targeted sequencing panel designed to detect complex mutations throughout the most informative genes linked to myeloid disease. This allows reliable and sensitive detection of single nucleotide variants (SNV) and large Insertion/Deletion (InDel) mutations.

Methods

The QIAact Myeloid DNA UMI Panel targets 25 genes known to be important in myeloid leukemia. A key feature of the panel is the addition of a unique molecular index (UMI) to tag each individual original DNA molecule prior to target enrichment by PCR. UMIs enable sequencing and PCR bias corrections, allowing sensitive detection of mutations.

To assess the assay performance, reference standards and blood and bone marrow samples were used. Following target enrichment, libraries were sequenced on the GeneReader NGS System and mutations analyzed using the QIAGEN Clinical Insight (QCI) Analyze software suite.

Results

To confirm DNA mutation detection, Horizon Discovery and SeraCare Reference Standards containing variants typical of myeloid malignancies were used. The anticipated DNA mutations were consistently identified both within and between runs.

The samples used, including blood and bone marrow samples, demonstrated the ability of the assay to detect important large indels (52 bp deletion CALR type 1 variant) and key SNVs down to a minor allele fraction (MAF) of 1% for JAK2 (e.g. exon 12, 13, 14 & 15) and KIT (exon 8, 9, 10, 11 & 17). A sensitive variant detection of allele frequency <0.5% for the KIT D816V was also achieved. For the other genes covered by the panel, including ASXL1, RUNX1, NPM1, DNMT3A, IDH1/2, results show sufficiently uniform amplification and sequencing coverage to support mutation detection with a MAF of 5%.

Conclusion

The QIAact Myeloid DNA UMI Panel in combination with the QIAGEN GeneReader NGS System offer a fully integrated DNA to variant detection and interpretation solution. The optimized chemistry allows superior analytical sensitivity resulting in accurate and efficient mutation detection of highly relevant genetic alterations for myeloid malignancy research.