An NGS-Based Test for Myeloid Leukemia
What is OncoTarget®Myeloid68
Next-Generation sequencing (NGS) performs massively parallel sequencing of genomes, allowing for the analysis of a significant number of genomic targets with a single test. Critically, NGS allows for the detection of aberrations that may only be present at very low levels, but which may have important clinical relevance for the patient’s diagnosis and prognosis.

GoPath’s MyeloidNGS68 Panel provides actionable information for improved diagnosis, prognosis, and risk stratification for myeloid malignancies including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN).
Clinical Values of OncoTarget® Myeloid68
Clinical Utility
The majority of myeloid tumors harbor high numbers of somatic mutations, which are not inherited but created within the tumor itself. Thus, unlike germline mutations these somatic mutations are not transmitted to offspring. Somatic mutations significantly contribute to the pathogenesis, progression and prognosis of myeloid malignancies.


GoPath’s MyeloidNGS68 Panel consists of 68 genes that targets known mutations associated with acute myeloid leukemia (AML), myeloproliferative neoplasms (MPN), myelodysplastic syndrome (MDS), chronic myelogenous leukemia (CML), chronic myelomonocytic leukemia (CMML) and juvenile myelomonocytic leukemia (JMML). Testing using this panel can aid in making therapy decisions, predicting prognosis, and can be used in clinical research. This is a generic and comprehensive profiling of myeloid neoplasms.
Comprehensive and Targeted Panel of Genes
ABL1, ASXL1, ASXL2, ATRX, BCOR, BCORL1, BRAF, BRINP3, CALR, CBL, CBLB, CEBPA, CSF3R, CUX1, DNMT1, DNMT3A, EED, ELANE, ETNK1, ETV6, EZH2, FLT3, GATA1, GATA2, GNAS, HNRNPK, HRAS, IDH1, IDH2, IKZF1, JAK1, JAK2, JAK3, KDM6A, KIT, KMT2A, KRAS, LUC7L2, MAP2K1, MPL, MYD88, NOTCH1, NPM1, NRAS, NSD1, PHF6, PRPF8, PRPF40B, PTEN, PTPN11, RAD21, RUNX1, SETBP1, SF1, SF3A1, SF3B1, SMC1A, SMC3, SRSF2, STAG2, SUZ12, TET1, TET2, TP53, U2AF1, U2AF2, WT1, ZRSR2 
Validation
Design: GoPath MyeloidNGS68 panel is designed for analyzing clinically significant genetic alterations in hematological specimens from whole blood and bone marrow. GoPath MyeloidNGS68 panel is designed to detect single nucleotide variant, small sequence deletion, insertion and duplication. GoPath MyeloidNGS68 panel is performed using GoPath Laboratory established NGS standard laboratory platforms. MyeloidNGS68 panel is designed to enrich selected genes and regions using fresh DNA and 2872 primer mixes. The assay is designed to provide efficient coverage of all coding exons of each gene in the panel. Variant calling, detections, clinical annotations of detected variants and reporting are conducted by our established clinical-grade NGS bioinformatics platform. The assay provides high density coverage of sequencing reads (≥ 300x) for all targeted coding exons of myeloid malignancy genes. 

Results: The variants of known (and unknown) significance in 15 myeloid malignancies DNA from Reference Lab (referred to as ref lab) and variants of known significance in 12 myeloid malignancies DNA from GoPath Labs were included in the validation study. These variants were analyzed by 37 replicated tests. No false negative variant was observed. However, one variant reported by the ref lab and one variant reported by GoPath Labs were not confirmed by this assay. Accuracy was assessed by comparing the analysis result of NGS panel tested in GoPath Labs to the results of the same samples from the reference lab. 

A total of 54 variants were analyzed and 52 variants were identified by this assay and the results are in 96.3% concordance with the confirmed results. The assay performance characteristics of sensitivity and specificity were calculated by the following formulas (Table 02): 
Myeloid Leukemia Cells
Table 02. Assay performance for detection of the Myeloid panel variants
Assay Sensitivity: 97,4%; Assay Specificity: 100%; Positive Predictive Value (PPV): 100%; Negative Predictive Value (NPV): 100%
True Positive (based on ref data)
MyeloidNGS68 Detected (%)
False Positive
False Negative
Ref Lab Variants
Counts:42 Replicates: 66
65 (98,5%)
0
0
GoPath Variants
Counts:12 Replicates: 12
11 (91,7%)
0
0
Total
Counts:54 Replicates: 78
76 (97,4%)
0
0

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