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Company:
Thermo Fisher ScientificType:
Laboratory Developed Test
Related tests:
2ms
Detection of KMT2A-PTDs and KMT2A fusions using next generation sequencing (AACR 2024)
We characterize the KMT2A fusions present in myeloid malignant samples. We also describe the abundance of KMT2A PTDs in both healthy donor and myeloid samples, with myeloid cases showing significantly higher PTD read counts. KMT2A PTD read count >2000 is present only in malignant samples but not in healthy donors.
Next-generation sequencing
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KMT2A (Lysine Methyltransferase 2A) • MLLT3 (MLLT3 Super Elongation Complex Subunit)
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MLL rearrangement • MLL rearrangement • KMT2A-PTD • MLL fusion
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Oncomine Myeloid Assay GX
2ms
A comprehensive genomic profiling of myeloid malignancies demonstrates mutational spectrum of DNA variants, FLT3-ITDs, and gene fusions (AACR 2024)
The Oncomine Myeloid Assay is a fast, robust, and reproducible solution for comprehensive genomic profiling of myeloid malignancies. We describe the mutational spectrum of DNA variants and RNA fusions in a range of clinical research samples. (For research use only.
TP53 (Tumor protein P53) • FLT3 (Fms-related tyrosine kinase 3) • ABL1 (ABL proto-oncogene 1) • BCR (BCR Activator Of RhoGEF And GTPase) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • FGFR1 (Fibroblast growth factor receptor 1) • DNMT3A (DNA methyltransferase 1) • MYD88 (MYD88 Innate Immune Signal Transduction Adaptor) • RUNX1 (RUNX Family Transcription Factor 1) • ASXL1 (ASXL Transcriptional Regulator 1) • KMT2A (Lysine Methyltransferase 2A) • TET2 (Tet Methylcytosine Dioxygenase 2) • SRSF2 (Serine and arginine rich splicing factor 2) • CREBBP (CREB binding protein) • CEBPA (CCAAT Enhancer Binding Protein Alpha) • ZMYM2 (Zinc Finger MYM-Type Containing 2) • CALR (Calreticulin) • KAT6A (Lysine Acetyltransferase 6A) • ANKRD26 (Ankyrin Repeat Domain Containing 26)
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FLT3-ITD mutation • ASXL1 mutation • TET2 mutation • SRSF2 mutation • FGFR1 fusion
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Oncomine Myeloid Assay GX • Oncomine Myeloid Research Assay
2ms
Evaluation of Percentage of p53-Positive Dark Cells and Inter-Rater Reliability in Cases of TP53-Positive Myeloid Neoplasms: A Single Academic Institution Experience (USCAP 2024)
P53 IHC in BM has good to excellent interobserver reproducibility. IHC evaluation of p53 shows high sensitivity and specificity for TP53ms; further work validating cutoffs in specific disease entities is ongoing. A high negative predictive value could be helpful as a biomarker for real-time stratification based on TP53m+ status.
Clinical
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TP53 (Tumor protein P53)
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TP53 mutation
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Oncomine Myeloid Assay GX
4ms
Performing NGS Testing for Myeloid Malignancies in an Academic Medical Center Improves Turnaround Time and Cost (ACMG 2024)
Our experience demonstrates that a successful NGS-based testing program can be developed and executed within an academic medical center setting with quality, price, and TATs that are competitive with large commercial reference laboratories. The ability to implement NGS testing in smaller clinical settings continues to make the promise of personalized medicine more accessible to the patients that need it.
Next-generation sequencing
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Oncomine Myeloid Assay GX
5ms
A Comprehensive Genomic Profiling of Myeloid Malignancies Demonstrates Mutational Spectrum of DNA Variants Including FLT3-ITDs, and Gene Fusions (ASH 2023)
"Not for use in diagnostic procedures. )"
TP53 (Tumor protein P53) • FLT3 (Fms-related tyrosine kinase 3) • ABL1 (ABL proto-oncogene 1) • NRAS (Neuroblastoma RAS viral oncogene homolog) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • FGFR1 (Fibroblast growth factor receptor 1) • NPM1 (Nucleophosmin 1) • DNMT3A (DNA methyltransferase 1) • JAK2 (Janus kinase 2) • MYD88 (MYD88 Innate Immune Signal Transduction Adaptor) • RUNX1 (RUNX Family Transcription Factor 1) • SF3B1 (Splicing Factor 3b Subunit 1) • ASXL1 (ASXL Transcriptional Regulator 1) • KMT2A (Lysine Methyltransferase 2A) • TET2 (Tet Methylcytosine Dioxygenase 2) • SRSF2 (Serine and arginine rich splicing factor 2) • CREBBP (CREB binding protein) • RUNX1T1 (RUNX1 Partner Transcriptional Co-Repressor 1) • BCOR (BCL6 Corepressor) • PML (Promyelocytic Leukemia) • CEBPA (CCAAT Enhancer Binding Protein Alpha) • CALR (Calreticulin) • KAT6A (Lysine Acetyltransferase 6A) • MLLT3 (MLLT3 Super Elongation Complex Subunit) • ANKRD26 (Ankyrin Repeat Domain Containing 26)
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FLT3-ITD mutation • TET2 mutation • FGFR1 fusion
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Oncomine Myeloid Assay GX • Oncomine Myeloid Research Assay
5ms
Detection of KMT2A Partial Tandem Duplications ( KMT2A-PTDs) in Healthy Donors Using Next Generation Sequencing (ASH 2023)
"Not for use in diagnostic procedures. )"
Clinical
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KMT2A (Lysine Methyltransferase 2A)
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KMT2A-PTD • MLL fusion • MLL-PTD
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Oncomine Myeloid Assay GX
6ms
Rapid Clinical Mutation Screening for AML Using the Genexus Platform (ASH 2023)
The NMAv2 has high specificity, sensitivity, accuracy and reproducibility (inter-lab and intra-lab) with sequencing results generated within 48 hours of assay initiation. As such, the assay is well suited for use to rapidly categorize the genomic alteration of AML to support clinical care in patients with active myeloid malignancies, including those patients potentially enrolled in the myeloMATCH program. Table 1: Results of validation experiment results for the NMAv2 Figure 1: Harmonization results for the NMAv2 between MoCha and MO labs, Right Panel = Indel; Left panel = SNV
Clinical
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FLT3 (Fms-related tyrosine kinase 3) • KMT2A (Lysine Methyltransferase 2A)
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KMT2A-PTD
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Oncomine Myeloid Assay GX
6ms
Rapid NGS Detection of Gene Mutations and Fusions in Myeloid Neoplasms (AMP 2023)
We have validated an 80-gene DNA/RNA NGS panel for detection of both mutations and fusions, and thus offer a rapid comprehensive NGS test for myeloid neoplasms with an average TAT of five calendar days. More clinical data and comments will be added at the meeting presentation.
Next-generation sequencing
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DNMT3A (DNA methyltransferase 1) • JAK2 (Janus kinase 2) • RUNX1 (RUNX Family Transcription Factor 1) • SF3B1 (Splicing Factor 3b Subunit 1) • ASXL1 (ASXL Transcriptional Regulator 1) • KMT2A (Lysine Methyltransferase 2A) • TET2 (Tet Methylcytosine Dioxygenase 2) • SRSF2 (Serine and arginine rich splicing factor 2) • AFDN (Afadin, Adherens Junction Formation Factor)
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MLL mutation
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Oncomine Myeloid Assay GX
6ms
Overcoming Deficient ASXL1 Mutation Detection by Ion Torrent Oncomine Myeloid NGS Assays: Journey of a Molecular Pathology Lab (AMP 2023)
The ASXL1 c.1934dupG variant is now routinely detected in myeloid NGS data using Oncomine Myeloid Assay GX v2 at VAF ³ 10%. Variant calls between 5% and 10% VAF are confirmed by orthogonal testing using the PCR sizing assay. The updated pipeline and sizing assay protocol are available to other laboratories.
Next-generation sequencing
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ASXL1 (ASXL Transcriptional Regulator 1)
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ASXL1 mutation • ASXL1 G646Wfs*12
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Oncomine Myeloid Assay GX • TruSight Myeloid Sequencing Panel
6ms
ASXL1 p.G646Wfs*12 Detection Enabled and Integrated into a Rapid Automated Myeloid Variant Profiling Solution on Ion Torrent NGS Genexus System (AMP 2023)
Variant calling improvements were made in the OMAv2 assay to enable robust detection of challenging variants in low complexity regions including ASXL1 p.G646Wfs*12. The capability to accurately report ASXL1 p.G646Wfs*12 within OMAv2 is important to provide complete results. Within the context of a rapid automated profiling solution, OMAv2 facilitates comprehensive detection of key myeloid variants.
Next-generation sequencing
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ASXL1 (ASXL Transcriptional Regulator 1)
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ASXL1 mutation • ASXL1 G646Wfs*12
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Oncomine Myeloid Assay GX
6ms
Our experience with new integrated Genexus sequencer for simultaneous , detection of Somatic DNA and RNA Aberrations for myeloid neoplasms (AMP 2023)
The Genexus System offers an automated nucleic acid-to-report workflow in 30 hours, allowing an easy-to-use solution with faster turnaround time. When used with the Oncomine Myeloid GX v2 Assay, it provides accurate and comprehensive information on diverse mutations including fusions that are relevant to the study of myeloid cancers.
FLT3 (Fms-related tyrosine kinase 3) • CEBPA (CCAAT Enhancer Binding Protein Alpha)
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Oncomine Myeloid Assay GX
6ms
Clinical validation of the new OncomimeTM myeloid assay V2 panel for single-nucleotide variants, insertions/deletions, and fusion genes: challenges, performance and perspectives (AMP 2023)
This is a robust assay, which when paired with Genexus integrated sequencer allows for highly accurate and reproducible detection of common genetic alterations in myeloid neoplasms with a shorter turnaround time. The automated variant analysis may require adjustment for less strict filtering. The greatest limitation is the inability to detect variants in long homopolymer regions.
Clinical
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MET (MET proto-oncogene, receptor tyrosine kinase)
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Oncomine Myeloid Assay GX
6ms
Automated Purification for Robust Sample Performance on Ion Torrent Genexus System for Detection and Research of Myeloid Malignancies (AMP 2023)
The Ion Torrent GeneXus System provides a fully automated purification and sequencing workflow for sample to report in <2 days. The integrated workflow was optimized for fresh and frozen blood or bone marrow, thereby supporting the major sample types important in myeloid cancer research. Purified samples demonstrated reliable sequencing and variant calling outcomes.
Oncomine Myeloid Assay GX
6ms
Analytical validation of an automated semiconductor-based next-generation sequencing assay for detection of DNA and RNA alterations in myeloid neoplasms. (PubMed, J Mol Diagn)
The Myeloid GX v2 panel is highly accurate and reproducible for the detection of SNVs, indels, and gene fusions in myeloid neoplasms. The ability to deliver clinically relevant results in a short time is key to providing personalized treatments.
Journal • Next-generation sequencing
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Oncomine Myeloid Assay GX
7ms
Pitfalls of using polymerase chain reaction-based assays for JAK2 and CALR exon 9 variant testing in myeloproliferative neoplasms: Knowing when to go the extra mile! (PubMed)
These cases highlight the importance of understanding the pitfalls of molecular techniques in current practice.
Journal • Polymerase Chain Reaction
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ABL1 (ABL proto-oncogene 1) • JAK2 (Janus kinase 2) • CALR (Calreticulin)
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JAK2 V617F
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Oncomine Myeloid Assay GX
10ms
Unraveling the Somatic Mutational Landscape in Myelodysplastic Syndrome: A Single-Center Experience (AMP Europe 2023)
We studied the genetic profile of 46 MDS cases using NGS. The mutation frequency of MDS at our center was 61%, which was concordant with published literature. TET2 and RUNX1 genes were the most frequently mutated genes, and TP53 gene-mutated patients showed progression and poor outcomes.
Clinical
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TP53 (Tumor protein P53) • RUNX1 (RUNX Family Transcription Factor 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • SRSF2 (Serine and arginine rich splicing factor 2)
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TP53 mutation • TET2 mutation • SRSF2 mutation
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Oncomine Myeloid Assay GX
10ms
STAT5B-RARa Fusion Positive Variant Acute Promyelocytic Leukemia: Role of Next-Generation Sequencing in Detection of a Rare Malignancy (AMP Europe 2023)
The patient received ATO, steroid, and azacytidine; however, within 7 days he developed respiratory distress followed by cardiac arrest which proved fatal... STAT5B-RARa t(17;17) is a rare variant of APML. It exhibits diagnostic, therapeutic, and prognostic difference with the common PML-RARa positive APL and, hence, the need for its prompt identification. Our case demonstrates the valuable role of NGS in reaching a definite diagnosis of such challenging and rare malignancy.
Next-generation sequencing
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BCR (BCR Activator Of RhoGEF And GTPase) • KIT (KIT proto-oncogene, receptor tyrosine kinase) • CD33 (CD33 Molecule) • PML (Promyelocytic Leukemia) • CD34 (CD34 molecule) • PTPRC (Protein Tyrosine Phosphatase Receptor Type C) • NCAM1 (Neural cell adhesion molecule 1) • STAT5B (Signal Transducer And Activator Of Transcription 5B) • GATA2 (GATA Binding Protein 2) • ANPEP (Alanyl Aminopeptidase, Membrane) • MPO (Myeloperoxidase)
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STAT5b-RARA fusion • RARA positive
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Oncomine Myeloid Assay GX
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azacitidine
10ms
Severe Systemic Auto-Inflammation in an Elderly Woman with Clonal Hematopoiesis (AMP Europe 2023)
The discovery of clonal hematopoiesis in this elderly woman with a wide spectrum of severe auto-inflammatory conditions supports a potentially intriguing link between somatic blood mutations and her adult- onset rheumatologic disorders. Mechanistically, disrupted SRSF2-mediated splicing may be driving aberrant antigen presentation by bone marrow-derived dendritic cells in her skin and other organs. Causal relationships between somatic blood mutations and autoimmune/auto-inflammatory conditions have been established in patients with hematologic malignancies and conditions like VEXAS syndrome.
Clinical
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MAP2K1 (Mitogen-activated protein kinase kinase 1) • SRSF2 (Serine and arginine rich splicing factor 2)
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IDH2 mutation • SRSF2 mutation • MAP2K1 C121S • IDH2 R140Q • SRSF2 P95L • IDH2 mutation + SRSF2 mutation
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Oncomine Focus Assay • Oncomine Myeloid Assay GX • TruSight Myeloid Sequencing Panel
12ms
ATYPICAL CHRONIC MYELOID LEUKEMIA. CLINICAL AND MOLECULAR FEATURES. A SINGLE CENTER EXPERIENCE. (EHA 2023)
Palliative drugs commonly used are AML-like chemotherapy, hypomethylating agents, hydroxyurea (HU), or PEG– IFN–α, ruxolotinib and trametinib. Atypical Chronic Myeloid Leukemia, BCR::ABL1 negative (aCML) is a rare hematological entity, with a dismal prognosis. Molecular landscape is heterogenous. Further comprensive molecular profiling may allow to find new targeted treatments in the next future.
Clinical
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KRAS (KRAS proto-oncogene GTPase) • ABL1 (ABL proto-oncogene 1) • NRAS (Neuroblastoma RAS viral oncogene homolog) • FGFR1 (Fibroblast growth factor receptor 1) • PDGFRA (Platelet Derived Growth Factor Receptor Alpha) • JAK2 (Janus kinase 2) • RUNX1 (RUNX Family Transcription Factor 1) • ASXL1 (ASXL Transcriptional Regulator 1) • PDGFRB (Platelet Derived Growth Factor Receptor Beta) • TET2 (Tet Methylcytosine Dioxygenase 2) • SRSF2 (Serine and arginine rich splicing factor 2) • CSF3R (Colony Stimulating Factor 3 Receptor) • U2AF1 (U2 Small Nuclear RNA Auxiliary Factor 1) • STAG2 (Stromal Antigen 2) • SETBP1 (SET Binding Protein 1) • PHF6 (PHD Finger Protein 6) • ETNK1 (Ethanolamine Kinase 1) • IFNA1 (Interferon Alpha 1) • ZRSR2 (Zinc Finger CCCH-Type, RNA Binding Motif And Serine/Arginine Rich 2)
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KRAS mutation • ASXL1 mutation • CBL mutation • SRSF2 mutation • U2AF1 mutation • FGFR1 rearrangement • TET2 deletion
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Oncomine Myeloid Assay GX
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Mekinist (trametinib) • hydroxyurea
12ms
AML AND MDS WITH RARA OVEREXPRESSION: MOLECULAR AND CLINICAL FEATURES OF PATIENTS ENROLLED IN A PHASE 2 TRIAL EVALUATING TAMIBAROTENE-BASED THERAPY (EHA 2023)
AML and MDS with RARA overexpression present with molecular features similar to those described in published datasets. Notably, SRSF2 was the most common mutation in the ND older unfit AML cohort, consistent withpublished series. While the small number of RARA -positive MDS patients precludes definitive characterization of molecular profiles, data in AML patients suggest that RARA overexpression may be agnostic to known molecular features.
P2 data • Clinical
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TP53 (Tumor protein P53) • NRAS (Neuroblastoma RAS viral oncogene homolog) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • NPM1 (Nucleophosmin 1) • DNMT3A (DNA methyltransferase 1) • RUNX1 (RUNX Family Transcription Factor 1) • SF3B1 (Splicing Factor 3b Subunit 1) • ASXL1 (ASXL Transcriptional Regulator 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • ETV6 (ETS Variant Transcription Factor 6) • PTPN11 (Protein Tyrosine Phosphatase Non-Receptor Type 11) • RARA (Retinoic Acid Receptor Alpha) • SRSF2 (Serine and arginine rich splicing factor 2) • BCOR (BCL6 Corepressor) • U2AF1 (U2 Small Nuclear RNA Auxiliary Factor 1) • CEBPA (CCAAT Enhancer Binding Protein Alpha) • STAG2 (Stromal Antigen 2)
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SRSF2 mutation • U2AF1 mutation • RARA overexpression • RARA positive
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Oncomine Myeloid Assay GX
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Venclexta (venetoclax) • azacitidine • Amnolake (tamibarotene)
12ms
RUNX1 GERMLINE VARIANT AND CLONAL EVOLUTION TO ACUTE MYELOID LEUKEMIA – A FPDMM FAMILY STUDY (EHA 2023)
The identification of a heterozygous germline LP variant in RUNX1 in a family with a clinical suspicion of a germline risk of myeloid malignancies allowed us to establish the diagnosis of RUNX1 - FPDMM, an autosomal dominant disease. Mild-to-moderate thrombocytopenia is the highest penetrant feature of this disorder, and was present in the proband, the father and the grandfather. The identification of these pre- leukemic conditions is very important for a closer surveillance of the family and, in case of eventual malignant transformation, provides the opportunity for a selection of a matched-related donor that does not carry the pathogenic variant.
TP53 (Tumor protein P53) • RUNX1 (RUNX Family Transcription Factor 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • PHF6 (PHD Finger Protein 6)
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Oncomine Myeloid Assay GX
12ms
CO-MUTATION PROFILE IN A REAL-LIFE COHORT OF ACUTE MYELOID LEUKEMIA (AML) (EHA 2023)
Overall survival analysis showed a statistically significant difference when ELN 2022 risk groups were compared to ELN2017, as well as among WHO 2022 AML classes, confirming an improvement of the new classification and risk stratification systems.TP53 variants occurred in the absence of other gene mutations and were associated with a shorter OS, as expected. The triple mutation pattern of FLT3 ITD- NPM1 mut - DNMT3A mut was the most frequent combination both in young and older patients without impact on outcomes. DTAS mutations did not affect OS in our setting.
Clinical
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TP53 (Tumor protein P53) • FLT3 (Fms-related tyrosine kinase 3) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • NPM1 (Nucleophosmin 1) • DNMT3A (DNA methyltransferase 1) • RUNX1 (RUNX Family Transcription Factor 1) • ASXL1 (ASXL Transcriptional Regulator 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • SRSF2 (Serine and arginine rich splicing factor 2)
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TP53 mutation • FLT3-ITD mutation • NPM1 mutation • DNMT3A mutation • RUNX1 mutation • ASXL1 mutation • TET2 mutation • SRSF2 mutation • DNMT3A R882
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Oncomine Myeloid Assay GX
12ms
BASELINE HLA-DR-RESTRICTED NEOANTIGEN BURDEN OF AML BLASTS IMPACTS ON HLA-DR GENE EXPRESSION AT RELAPSE AFTER ALLOGENEIC STEM CELL TRANSPLANT (EHA 2023)
These novel findings demonstrate that higher HLA-DR-restricted neoantigen burden at diagnosis is associated with a longer time to relapse post-AHSCT, consistent with a contribution to immune mediated graft-versus- leukemia effects. Furthermore, the increased downregulation of HLA-DR at relapse in patients with higher baseline HLA-DR neoantigen burden suggests the latter may drive this mechanism of immune escape known to contribute to relapse post-AHSCT. Diagram Description automatically generated Immune response, Allogeneic hematopoietic stem cell transplant, Acute myeloid leukemia
Tumor mutational burden
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TMB (Tumor Mutational Burden) • CD8 (cluster of differentiation 8) • CD4 (CD4 Molecule) • HLA-B (Major Histocompatibility Complex, Class I, B) • HLA-C (Major Histocompatibility Complex, Class I, C)
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MHC-II expression
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Oncomine Myeloid Assay GX
1year
Molecular mutation profiling of patients with suspected myelodysplastic syndromes using Next Generation Sequencing - a single centre experience (ISLH 2023)
Conclusions MDS is genetically complex and highly heterogeneous in clinical presentation and molecular/cytogenetics profile. Integration of NGS panels in the diagnosis of MDS, in addition to morphology, aids in accurate classification, prognostication and determination of targeted therapy.
Clinical • Next-generation sequencing
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TP53 (Tumor protein P53) • DNMT3A (DNA methyltransferase 1) • RUNX1 (RUNX Family Transcription Factor 1) • SF3B1 (Splicing Factor 3b Subunit 1) • ASXL1 (ASXL Transcriptional Regulator 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • SRSF2 (Serine and arginine rich splicing factor 2) • U2AF1 (U2 Small Nuclear RNA Auxiliary Factor 1)
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TP53 mutation • DNMT3A mutation • TET2 mutation • SF3B1 mutation • SRSF2 mutation • U2AF1 mutation
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Oncomine Myeloid Assay GX
over1year
Determining the Role of Germline Polymorphisms in the Development of Myeloid Neoplasms (USCAP 2023)
Our findings demonstrate that MNs are associated with an increased number of polymorphisms. More specifically, polymorphisms present at low frequency in the general population are over-represented in MN patients compared to controls, suggesting the importance of specific polymorphic variants in MN development. Expanding the study cohort is warranted to further define the role of specific polymorphisms in MN pathogenesis and clinical outcomes.
Oncomine Myeloid Assay GX
over1year
Rapid and Automated Semiconductor-Based Next Generation Sequencing for Simultaneous Detection of Somatic DNA and RNA Aberrations in Myeloid Neoplasms. (PubMed, J Mol Diagn)
Reanalysis of exported, unfiltered Ion Torrent Genexus data revealed 15 DNA variants not called by the filtered on-board bioinformatics pipeline, yielding a 92% potential detection rate. These results hold promise for the implementation of an integrated NGS system to rapidly detect genetic aberrations, facilitating accurate, genomics-based diagnoses and accelerated time to precision therapies in myeloid neoplasms.
Journal • Next-generation sequencing
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Oncomine Myeloid Assay GX
over1year
Molecular Aberrations in Acute Myeloid Leukemia (AML) and Myelodysplastic Syndrome with Excess Blast II (MDS-EB II) in Kuwait (ASH 2022)
We have noticed an increased PTPN11 mutation, detected in 17.5% of the cases.Conclusion : This is an important study showing extensive molecular abnormalities in AML patients in the region. This will facilitate more understanding of the disease biology and potentially guide therapeutic options
FLT3 (Fms-related tyrosine kinase 3) • PTPN11 (Protein Tyrosine Phosphatase Non-Receptor Type 11)
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PTPN11 mutation • FLT3 D835
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Oncomine Myeloid Assay GX
over1year
Evolutionary Portrait of Adult Core-Binding Factor Leukemia Patients Treated with a Continuation Therapy with Midostaurin: Preliminary Results (ASH 2022)
Method Patients with de-novo CBFL received standard induction therapy with an anthracycline containing regimen ("7+3"-like) + Mido, three cycles of post-remission consolidation chemotherapy with high-dose cytarabine + Mido, and 12 months of Mido as Maintenance. Conclusion In patients with CBFL, we found FLT3 and/or KIT mutations actionable by a regimen consisting of intensive chemotherapy and Mido in 47% of cases. In two out of three relapsed cases the KIT mutation is maintained, although frequency of the mutant allele is lower at relapse, while all FLT3 and NRAS mutated patients lose the mutation upon disease relapse.
Clinical
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FLT3 (Fms-related tyrosine kinase 3) • NRAS (Neuroblastoma RAS viral oncogene homolog) • RUNX1 (RUNX Family Transcription Factor 1) • RUNX1T1 (RUNX1 Partner Transcriptional Co-Repressor 1) • CEBPA (CCAAT Enhancer Binding Protein Alpha)
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NRAS mutation • FLT3-ITD mutation • FLT3 mutation • KIT mutation • KIT positive • CEBPA mutation
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Oncomine Myeloid Assay GX
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cytarabine • Rydapt (midostaurin)
over1year
Acute Myeloid Leukemia (AML) Risk Stratification Using the European Leukemianet 2022 Classification in a Real-Life Cohort of Patients from Sardinia, Italy (ASH 2022)
Re-classification according to ELN 2022 showed shifting from favorable to a worse category in the 10% of AML patients <60 years of age, who could have been eligible to a more intensive treatment. Furthermore, the implementation of the AML screening gene panel through NGS analysis allows to identify molecular abnormalities, such as IDH1/IDH2 mutations, susceptibles of target therapies.
Clinical
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TP53 (Tumor protein P53) • FLT3 (Fms-related tyrosine kinase 3) • NRAS (Neuroblastoma RAS viral oncogene homolog) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • NPM1 (Nucleophosmin 1) • RUNX1 (RUNX Family Transcription Factor 1) • ASXL1 (ASXL Transcriptional Regulator 1) • BCOR (BCL6 Corepressor) • STAG2 (Stromal Antigen 2)
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TP53 mutation • FLT3-ITD mutation • IDH2 mutation • NPM1 mutation • ASXL1 mutation • BCOR mutation • STAG2 mutation
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Oncomine Myeloid Assay GX
over1year
Clinical Features and Mutational Landscape of Patients Referred for Suspected Essential Thrombocytosis: A Descriptive Study Using a 'Real-World' Database (ASH 2022)
Overall yield of molecular testing for this population of patients referred for thrombocytosis was high (55.0%), suggesting appropriate use of NGS testing, but the identification of clinical factors predicting secondary causes might suggest further improvement in utilization. In our cohort, CBC parameters did not readily distinguish between ET and secondary thrombocytosis. Clinical factors such as smoking, active malignancy, chronic inflammatory disease and post splenectomy and iron deficiency are associated with secondary thrombocytosis.
Real-world evidence • Clinical
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JAK2 (Janus kinase 2) • CALR (Calreticulin)
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Oncomine Myeloid Assay GX
over1year
SF3B1, RUNX1 and TP53 Mutations Significantly Impact the Outcome of Patients with Lower-Risk Myelodysplastic Syndrome (ASH 2022)
Incorporation of molecular testing in LR-MDS identified a subset of pts with expected poorer outcome, either due to lower survival or probability of leukemic progression. Results herein reported may help prognosis stratification in this set of pts with low-risk disease and support the recommendation of molecular testing in pts with MDS.
Clinical
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KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • TP53 (Tumor protein P53) • FLT3 (Fms-related tyrosine kinase 3) • NRAS (Neuroblastoma RAS viral oncogene homolog) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • NPM1 (Nucleophosmin 1) • HRAS (Harvey rat sarcoma viral oncogene homolog) • DNMT3A (DNA methyltransferase 1) • RB1 (RB Transcriptional Corepressor 1) • NF1 (Neurofibromin 1) • JAK2 (Janus kinase 2) • MYD88 (MYD88 Innate Immune Signal Transduction Adaptor) • RUNX1 (RUNX Family Transcription Factor 1) • SF3B1 (Splicing Factor 3b Subunit 1) • ASXL1 (ASXL Transcriptional Regulator 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • PTPN11 (Protein Tyrosine Phosphatase Non-Receptor Type 11) • IKZF1 (IKAROS Family Zinc Finger 1) • SRSF2 (Serine and arginine rich splicing factor 2) • WT1 (WT1 Transcription Factor) • BCOR (BCL6 Corepressor) • CSF3R (Colony Stimulating Factor 3 Receptor) • U2AF1 (U2 Small Nuclear RNA Auxiliary Factor 1) • CEBPA (CCAAT Enhancer Binding Protein Alpha) • STAG2 (Stromal Antigen 2) • SETBP1 (SET Binding Protein 1) • GATA2 (GATA Binding Protein 2) • PHF6 (PHD Finger Protein 6) • CALR (Calreticulin) • SH2B3 (SH2B Adaptor Protein 3) • ZRSR2 (Zinc Finger CCCH-Type, RNA Binding Motif And Serine/Arginine Rich 2)
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TP53 mutation • RUNX1 mutation • TET2 mutation • SF3B1 mutation • SRSF2 mutation • U2AF1 mutation
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Oncomine Myeloid Assay GX
over1year
Bone Marrow Microenvironment Changes in Myelodysplastic Neoplasms and Its Relationship with Clonal Hematopoiesis and Disease Progression (ASH 2022)
Our study suggests the presence of immunosuppressive profile of NK cells on MDS, with gain of expression of NKG2A and higher expression of IL10 on high risk MDS. Interestingly, 63.6% CUS subjects were CCUS and showed increase cytotoxic profile. The increase of CD244 expression, at one year control, may be related to an exhausted environment leading to immunosuppression and progression.
PD(L)-1 Biomarker • IO biomarker
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PD-L1 (Programmed death ligand 1) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • CD19 (CD19 Molecule) • PD-1 (Programmed cell death 1) • SF3B1 (Splicing Factor 3b Subunit 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • CD33 (CD33 Molecule) • TIGIT (T Cell Immunoreceptor With Ig And ITIM Domains 2) • PTPRC (Protein Tyrosine Phosphatase Receptor Type C) • IL10 (Interleukin 10) • CD14 (CD14 Molecule) • ITGAM (Integrin, alpha M) • PVR (PVR Cell Adhesion Molecule) • KIR2DS4 (Killer Cell Immunoglobulin Like Receptor, Two Ig Domains And Short Cytoplasmic Tail 4) • HLA-C (Major Histocompatibility Complex, Class I, C) • KIR2DL1 (Killer Cell Immunoglobulin Like Receptor, Two Ig Domains And Long Cytoplasmic Tail 1) • KLRC1 (Killer Cell Lectin Like Receptor C1) • NKG2D (killer cell lectin like receptor K1)
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TET2 mutation
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Oncomine Myeloid Assay GX
over1year
Mutational Landscape of Patients Referred for Elevated Hemoglobin Level. (PubMed, Curr Oncol)
The presence of additional mutations, such as ASXL1 mutations, in this population has implications for prognosis. Both the incidence and mutation type identified in patients with secondary erythrocytosis likely reflects incidental, age-associated clonal hematopoiesis of indeterminate potential (CHIP).
Journal
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TP53 (Tumor protein P53) • ABL1 (ABL proto-oncogene 1) • IDH2 (Isocitrate Dehydrogenase (NADP(+)) 2) • DNMT3A (DNA methyltransferase 1) • JAK2 (Janus kinase 2) • ASXL1 (ASXL Transcriptional Regulator 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • SRSF2 (Serine and arginine rich splicing factor 2) • BCOR (BCL6 Corepressor) • ZRSR2 (Zinc Finger CCCH-Type, RNA Binding Motif And Serine/Arginine Rich 2)
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BCR-ABL1 fusion • IDH2 mutation • DNMT3A mutation • ASXL1 mutation • TET2 mutation • SRSF2 mutation • JAK2 V617F • JAK2 mutation
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Oncomine Myeloid Assay GX
over1year
Using NGS to Detect the MYD88 p.L265P Mutation Often Requires Distinguishing Low-Level Mutation from Background Using Bioinformatic Analysis and Visual Review in IGV (AMP 2022)
MYD88 is being included on many NGS-based panels. However, our results show that the MYD88 p.L265P mutation can occur at a very low level, especially in cases that cannot be definitively classified as LPL. It is worthwhile for laboratories using NGS to interrogate the specific chr3:38182641 site bioinformatically and/or use IGV visualization to identify a low-level p.L265P mutation.
Review • Next-generation sequencing
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MYD88 (MYD88 Innate Immune Signal Transduction Adaptor)
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MYD88 mutation • MYD88 L265P
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Oncomine Myeloid Assay GX
over1year
Workflow Assessment for the Oncomine Myeloid NextGeneration Sequencing Panel (AMP 2022)
Automated sequencing systems such as the Ion Chef and S5 systems, utilized by the Oncomine Myeloid assay, assist in processing samples quickly and effectively. Greater system automation made it easier for technologists to maintain proficiency and facilitated additional staff coverage for the assay due to lower amount of hands-on time.
Next-generation sequencing
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Oncomine Myeloid Assay GX
over1year
Unraveling the Somatic Mutational Landscape in Myelodysplastic Syndrome: A Single Center Experience (AMP 2022)
Patients were treated as per WHO classification and IPSS-R risk stratification with either hypomethylating agents alone or in combination (with Venetoclax), Lenalidomide and supportive care. We studied the genetic profile of 42 MDS cases using NGS. The mutation frequency of MDS at our center was 60%, which was in concordance with published literature. TET2 and STAG2 genes were the most frequently mutated genes and TP53 gene mutated patients showed progression and poor outcomes
Clinical
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TP53 (Tumor protein P53) • TET2 (Tet Methylcytosine Dioxygenase 2) • SRSF2 (Serine and arginine rich splicing factor 2) • STAG2 (Stromal Antigen 2)
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TP53 mutation • TET2 mutation • SRSF2 mutation • STAG2 mutation
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Oncomine Myeloid Assay GX
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Venclexta (venetoclax) • lenalidomide
over1year
STAT5B-RARa Fusion Positive Variant Acute Promyelocytic Leukemia: Role of Next-Generation Sequencing in Detection of a Rare Malignancy (AMP 2022)
The patient received ATO, steroid and azacytidine; however, within seven days he developed respiratory distress followed by cardiac arrest which proved fatal... STAT5B-RARa t(17; 17) is a rare variant of APML. It exhibits diagnostic, therapeutic, and prognostic difference with the common PML-RARa positive APL and hence the need for its prompt identification. Our case demonstrates the valuable role of NGS in reaching a definite diagnosis of such challenging and rare malignancy.
Next-generation sequencing
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BCR (BCR Activator Of RhoGEF And GTPase) • KIT (KIT proto-oncogene, receptor tyrosine kinase) • CD33 (CD33 Molecule) • PML (Promyelocytic Leukemia) • CD34 (CD34 molecule) • PTPRC (Protein Tyrosine Phosphatase Receptor Type C) • NCAM1 (Neural cell adhesion molecule 1) • STAT5B (Signal Transducer And Activator Of Transcription 5B) • GATA2 (GATA Binding Protein 2) • ANPEP (Alanyl Aminopeptidase, Membrane)
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STAT5b-RARA fusion • RARA positive
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Oncomine Myeloid Assay GX
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azacitidine
over1year
Evaluation of the Oncomine Myeloid Assay GX v2 NGS Panel on the Ion Torrent Genexus System with Previously Benchmarked Clinical Nucleic Acid Samples (AMP 2022)
OMAv2 panel variant detection was consistent with current benchmarked assays down to 5% AF. Serial dilutions provided AF calls down to 1.6% for FLT3 and TET2 variants. Variant calls below 5% AF were more inconsistent.
Clinical • Next-generation sequencing
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FLT3 (Fms-related tyrosine kinase 3) • ABL1 (ABL proto-oncogene 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • CEBPA (CCAAT Enhancer Binding Protein Alpha) • STAG2 (Stromal Antigen 2)
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Oncomine Myeloid Assay GX
over1year
Evaluation of Genexus System for Rapid Comprehensive Genomic Profiling of Myeloid Malignancies in Clinical Samples (AMP 2022)
Based on our evaluation, the Ion Torrent Genexus system ultra-rapid NGS assay produces highly reproducible data, which is highly concordant with our in-house NGS assay but obtained in a single day with minimal specimen manipulation. In addition, difficult-to-sequence targets, such as NPM1, GC-rich CEBPA, and FLT3-ITDs, were identified without orthogonal specimen triaging and at lower expense because of the elimination of multiple workflows.
Clinical
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FLT3 (Fms-related tyrosine kinase 3) • NPM1 (Nucleophosmin 1) • CEBPA (CCAAT Enhancer Binding Protein Alpha) • CALR (Calreticulin)
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Oncomine Myeloid Assay GX
over1year
FLT3 ITD Gene Detection by PCR/CE and NGS Method: Performance Comparison (AMP 2022)
The analytical correlation between both assays for detection of FLT3-ITD was satisfactory; however, based on ACL data NGS Myeloid panel should not be used as an independent method for AR calculation. PCR/CE method has been the gold standard for unbiased AR determination. For the best interest of the patient, ACL Lab retained PCR/CE method for detection of ITD variants and determination of AR values.
Next-generation sequencing
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FLT3 (Fms-related tyrosine kinase 3)
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FLT3-ITD mutation • FLT3 wild-type
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Oncomine Myeloid Assay GX
over1year
AML-419 Molecular Aberrations in Acute Myeloid Leukemia (AML) and Myelodysplastic Syndrome With Excess Blast II (MDS-EB II) in Kuwait. (PubMed, Clin Lymphoma Myeloma Leuk)
This is an important study showing extensive molecular abnormalities in AML patients in the region. This will facilitate more understanding of the disease biology.
Journal
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FLT3 (Fms-related tyrosine kinase 3) • PTPN11 (Protein Tyrosine Phosphatase Non-Receptor Type 11)
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FLT3 mutation • PTPN11 mutation • FLT3 D835
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Oncomine Myeloid Assay GX
over1year
Molecular Aberrations in Acute Myeloid Leukemia (AML) and Myelodysplastic Syndrome With Excess Blast II (MDS-EB II) in Kuwait (SOHO 2022)
This is an important study showing extensive molecular abnormalities in AML patients in the region. This will facilitate more understanding of the disease biology.
FLT3 (Fms-related tyrosine kinase 3) • PTPN11 (Protein Tyrosine Phosphatase Non-Receptor Type 11)
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FLT3 mutation • PTPN11 mutation • FLT3 D835
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Oncomine Myeloid Assay GX
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