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Evaluation of Rapid Next-Generation Sequencing for the Study of Acute Myeloid Leukemia

In a recent GenomeWeb webinar, Rapid next-generation sequencing for the study of acute myeloid leukemia (AML), Dr. Diana Morlote from The University of Alabama at Birmingham presented an overview of the disease and its molecular testing challenges.

After reviewing why molecular testing in AML research is essential, Dr. Morlote emphasized the importance of efficiently profiling AML samples for key mutations, including single nucleotide variants, indels, tandem duplications, and gene fusions.

Morlote-Diana-webinar-feature
Dr. Diana Morlote, MD
Assistant Professor Hematopathology, Molecular Genetic Pathology,
Division of Genomics, Diagnostics, and Bioinformatics,
Department of Pathology UAB Medicine, The University of Alabama at Birmingham

 

While multiple modalities are commonly used for molecular testing in AML, Dr. Morlote noted the clear advantage of next-generation sequencing (NGS) for simultaneously testing of multiple genetic abnormalities.

She pointed out 2 of the key challenges of NGS testing— turnaround time (1-2 weeks from sample collection to results) and interpretation of variants requiring bioinformatics experience.

Dr. Morlote detailed her lab’s experience with 2 leading NGS systems, the Illumina MiSeq and the Ion Torrent Genexus System, highlighting the latter’s dramatic workflow and turnaround time advantages.

NGS Workflow Illumina MiSeq Hybrid Capture Ion Torrent Genexus System
Number of instruments 4 2
Total hands-on-time 10.5 hours <20 minutes
Library preparation ~3 days for manual prep Automated
Data analysis & Reporting ~1 day
Requires bioinformatics expertise
~1 hour 15 minutes Automated variant calling, analysis, and reporting with Oncomine pipeline matching
Total turnaround time 5-6 days 1-2 days

 

Dr. Morlote reviewed some of the features and benefits of the Genexus purification and quantitation system, the Genexus Integrated Sequencer, and the Oncomine Myeloid Assay GX v2. She noted the versatility of the Oncomine Myeloid Assay GX v2 to run both DNA and RNA simultaneously, which eliminates the need for batching, saving significant time.

Dr. Morlote concluded that the automated variant analysis of the Oncomine Myeloid Assay GX v2 takes the guesswork out of interpretation, enabling smaller labs without bioinformatics expertise to conduct AML sequencing both efficiently and effectively.

Finally, Dr. Morlote shared her lab’s evaluation of the Oncomine Myeloid Assay GX v2 sequencing 29 archival samples of AML and other myeloid neoplasms using the Oncomine Myeloid Assay GX v2.

Overall, the lab was impressed by the speed and simplify of the assay workflow and noted that it performed very well for detecting variants in key genes like FLT3, NPM1, and CEBPA--a high GC-rich target that is notoriously challenging for NGS.

Dr. Morlote's Conclusions

  • Robust assay with very little hands-on time and superb turnaround time for rapid AML analysis
  • 100% of FLT3 and NPM1 variants detected
  • 92% of CEBPA variants detected
  • Archival sample age and or concentration may have affected results
  • Variant filtering works well for AML

Learn more by watching Dr. Morlote's full presentation.

 

For Research Use Only. Not for use in diagnostic procedures.

 

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