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Next Generation Sequencing Finds More Gene Mutations for Leukemia

By LabMedica International staff writers
Posted on 18 Feb 2021
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Image: TruSight Oncology 500 is a next-generation sequencing (NGS) assay that enables in-house comprehensive genomic profiling of tumor samples it accurately measures key current immuno-oncology biomarkers: microsatellite instability (MSI) and tumor mutational burden (TMB) (Photo courtesy of Illumina).
Image: TruSight Oncology 500 is a next-generation sequencing (NGS) assay that enables in-house comprehensive genomic profiling of tumor samples it accurately measures key current immuno-oncology biomarkers: microsatellite instability (MSI) and tumor mutational burden (TMB) (Photo courtesy of Illumina).
Myeloid malignancies are characterized by uncontrolled proliferation and/or defects in differentiation of abnormal myeloid progenitor cells. Myelodysplastic syndromes (MDS) and myeloproliferative neoplasms (MPNs) are often thought to be precursors to a higher grade myeloid malignancies, namely acute myeloid leukemia (AML).

Many laboratories have used relatively small targeted panels that screen prominent mutation hotspots in less than 50 genes. Although this approach is cost- and time- effective with minimal data analysis and reporting complexity, it yields an incomplete mutational profile, omitting several important known hotspot mutations.

Pathologists at the Medical College of Georgia (Augusta, GA, USA) included 40 patient with myeloid neoplasms samples in a study, clinical information was available on 27 patients. The investigators retrospectively analyzed 61 bone marrow samples. DNA was isolated from bone marrow aspirates using the QIAamp DNA Blood Mini kit (QIAGEN, Hilden, Germany). Nanodrop spectrophotometer was used to analyze the DNA quality with an OD 260/280 value between 1.7 and 2.2 being considered acceptable.

Double stranded DNA was measured using Qubit dsDNA broad range assay kit (Invitrogen, Carlsbad CA, USA) and 120 ng gDNA was used for library preparation. The team evaluated the clinical performance and utility of a comprehensive 523 gene NGS panel (Illumina, San Diego, CA, USA) for screening myeloid neoplasms. The high-throughput comprehensive Next-Generation Sequencing (NGS) panel was validated for single-nucleotide variants (SNVs) and indels/duplications in myeloid neoplasms.

The scientists reported the larger panel identified 880 variants in 292 genes, and only 14.8% of the variants were in genes included in the smaller 54-gene panel currently in use by many laboratories. The remaining 749 variants are not typically assessed in a leukemia diagnosis or detected by the 54-gene panel. When they looked at the information available on those 749 variants in follow up, they found at least 14 of the variants in 10 genes likely could contribute to AML and 96.2% of the patients had at least one of the 14 novel variants. They also found 22 variants in five other genes associated with other tumor types in the vast majority of the patients with AML.

The authors concluded that the comprehensive panel employed in their study, demonstrated its ease of use and clinical utility for myeloid neoplasms. The panel has extensive coverage across the entire genome, for variants significantly beyond those captured on existing NGS platforms for hematological malignancies. The study was originally published on October 19, 2020 in the journal PLOS ONE.


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