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3ms
Analytical validation of a 37-gene next generation sequencing panel for myeloid malignancies and review of initial findings, including reclassification of Acute Myeloid Leukemias and Myelodysplastic Syndromes using the 2022 WHO/ICC/ELN guidelines. (PubMed, J Mol Diagn)
A retrospective analysis of 535 clinical specimens tested with the Archer NGS panel showed a frequency and pattern of mutations across myeloid malignancies that were similar to other published studies. A review of the diagnostic classification of patients with acute myeloid leukaemia and myelodysplastic syndrome using the World Health Organisation 2017/2022 and International Consensus Classification 2022 guidelines, in addition to European LeukemiaNet 2017/2022 risk stratification of AML patients, was also performed to assess the utility of the molecular information provided by the Archer NGS panel.
Journal • Review • Next-generation sequencing
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Archer® VariantPlex® Myeloid panel
7ms
A comparison study of mutation detection and allele frequency calling between unbiased genome-wide approaches and targeted NGS in pediatric myeloid neoplasms (AMP 2023)
Our study demonstrated that the sensitivity of WGS in detecting clinically relevant mutations is comparable to high-depth panel assays despite the overall lower coverage. Given that WGS is a truly unbiased genome-wide molecular profiling platform, our data further support the importance of WGS in oncology molecular diagnostics.
Clinical • Next-generation sequencing
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Archer® VariantPlex® Myeloid panel
11ms
Validation of a New Next-Generation Sequencing Library Prep Kit for the Detection of Mutations in Hematological Neoplasms (AMP Europe 2023)
The Archer panel presented high performance and good coverage in GC-rich regions as CEBPA gene being a promising test in accuracy of somatic analysis and was validated in our laboratory.
Next-generation sequencing
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TP53 (Tumor protein P53) • CEBPA (CCAAT Enhancer Binding Protein Alpha)
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TP53 amplification
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Archer® VariantPlex® Myeloid panel • TruSight Myeloid Sequencing Panel
1year
The role of next-generation sequencing in myeloproliferative neoplasms associated with splanchnic vein thromboses (MPN-SVT) (BSH 2023)
Additional mutations were detected in 12.2% of 41 MPN-SVT patients, lower than reported elsewhere. Explanations for this include methodologic differences: the lower sensitivity of older NGS technologies and different thresholds for reporting abnormal NGS. The presence of additional mutations by NGS was associated with higher JAK2V617F VAF, whilst rising VAF was seen alongside clinical disease progression; these findings concur with those seen elsewhere.
Next-generation sequencing
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TP53 mutation • JAK2 V617F • CALR mutation
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Archer® VariantPlex® Myeloid panel
1year
Assessing clonal evolution of myeloid neoplasms by flow cytometry guided, cell-enriched next generation sequencing (AACR 2023)
Using a combination of flow cytometry, magnetic cell sorting, and NGS, variants specific to the tumor fraction of samples were identified. For patient specimens, the presence of ARCH/CHIP mutations in both enriched and residual cell populations indicate these variants evolved prior to the emergence of true leukemic progenitor cells; the identification of the flow-matched mutations only in the enriched population indicates the key role of these changes in the disease progression. Together, flow cytometry and cell-enriched NGS have the potential to enhance detection of disease-driving mutations earlier, thus, could be used as novel approaches to identify and treat myeloid neoplasms early with existing therapies and/or support development of new investigational agents.
Next-generation sequencing
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Archer® VariantPlex® Myeloid panel
over1year
Integrated DNA Technologies Acquires ArcherDX Next Generation Sequencing Research Assays from Invitae Corporation (Integrated DNA Technologies Press Release)
"Integrated DNA Technologies, Inc....announced it closed on the purchase of Next Generation Sequencing (NGS) research assays from Invitae Corporation (NYSE: NVTA) under the trademarked name Archer. The integration of IDT’s portfolio with the acquired NGS research assays—which have been foundational in researching novel cancer fusions—will empower labs with an all-in-one solution to uncover biomarkers and advance cancer discoveries. The transaction enables IDT to expand its existing operations, build upon the legacy Archer portfolio, and welcome more than 100 new associates globally....Transaction Details-IDT purchased Archer NGS research assays—which reported high double-digit growth since 2019—from Invitae for cash consideration of approximately $48 million, subject to certain adjustments. The transaction is structured as an asset deal and includes a license to intellectual property related to the AMP technology."
M&A
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Archer® FusionPlex® Comprehensive Thyroid & Lung (CTL) Kit • Archer® FusionPlex® Acute Lymphoblastic Leukemia (ALL) • Archer® FusionPlex® Lung Kit • Archer® FusionPlex® Lymphoma • Archer® FusionPlex® Myeloid Kit • Archer® FusionPlex® Oncology Research Kit • Archer® FusionPlex® Sarcoma kit • Archer® VariantPlex® Comprehensive Thyroid and Lung (CTL) kit • Archer® VariantPlex® Myeloid panel • Archer® VariantPlex® Solid Tumor Kit • FusionPlex® Dx • FusionPlex® Pan Solid Tumor v2 panel • FusionPlex™ Heme v2 panel • FusionPlex™ Pan-Heme panel • LiquidPlex™
over1year
Clonal Hematopoiesis Prevalence and Mutational Spectrum in Patients with Plasma Cell Disorders at the Time of Diagnosis and Its Impact on Clinical Features, Cardiovascular Complications, and Survival (ASH 2022)
"CH was associated with more A Fib and atherosclerosis in PCD patients, but overall survival was not significantly different for CH patients in the MM subgroup. Our data indicate an increase in CH prevalence with PCD disease progression highlighting the need for additional studies to evaluate the factors responsible."
Clinical
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KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • DNMT3A (DNA methyltransferase 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • U2AF1 (U2 Small Nuclear RNA Auxiliary Factor 1) • GNAS (GNAS Complex Locus) • PPM1D (Protein Phosphatase Mg2+/Mn2+ Dependent 1D)
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U2AF1 mutation • PPM1D mutation
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Archer® VariantPlex® Myeloid panel
2years
ACUTE MYELOID LEUKEMIA SUPPRESSION BY PALBOCICLIB AND PONATINIB IN PATIENT-DERIVED XENOGRAFT (EHA 2022)
Aims To test palbociclib and ponatinib, along with reference drugs – venetoclax, azacitidine, cytarabine+doxorubicine (chemotherapy) on 2 primary AML samples in a patient-derived xenograft model. Effect of ponatinib was only limited. This encourages further investigation of treatment efficacy in different AML subtypes and in combination with other drugs.
Clinical • IO biomarker
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KRAS (KRAS proto-oncogene GTPase) • FLT3 (Fms-related tyrosine kinase 3) • NRAS (Neuroblastoma RAS viral oncogene homolog) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • CD38 (CD38 Molecule) • WT1 (WT1 Transcription Factor) • CD34 (CD34 molecule) • PTPRC (Protein Tyrosine Phosphatase Receptor Type C)
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KRAS mutation • NRAS mutation • IDH1 mutation • WT1 mutation
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Archer® VariantPlex® Myeloid panel
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Venclexta (venetoclax) • Ibrance (palbociclib) • cytarabine • Iclusig (ponatinib) • doxorubicin hydrochloride • azacitidine
over2years
Clinical Validation of a Web Application to Create Nomenclature of FLT3 Internal Tandem Duplication from Next Generation Sequencing Result (USCAP 2022)
Our free web application can correctly create HGVS FLT3-ITD nomenclature from next generation sequencing results, as long as there is no error or mutation at the 3’ end of the sequence. RNA-based sequencing is required to definitively determine how the intronic sequence in ITD is translated into amino acids.
Clinical • Next-generation sequencing
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FLT3 (Fms-related tyrosine kinase 3)
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FLT3 wild-type
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Archer® VariantPlex® Myeloid panel
over2years
Evaluation of a Rapid Automated Next Generation Sequencing Assay for Precision Medicine in Acute Myeloid Leukemia (ASH 2021)
NMA is an automated sample-to-results workflow that can identify myeloid disorder-associated genomic variants in less than 48 hours from library preparation to clinical reporting. We show that NMA is highly concordant with a standard DNA NGS assay for detecting mutations within recurrently mutated AML genes. Accurate rapid genotyping is required for assignment to initial treatment with targeted therapy, and this technology may be a valuable tool for upcoming clinical trials for patients with myeloid malignancies.
Next-generation sequencing
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KRAS (KRAS proto-oncogene GTPase) • 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) • JAK2 (Janus kinase 2)
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NRAS mutation • NPM1 mutation
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Archer® VariantPlex® Myeloid panel • Oncomine Myeloid Assay GX
over2years
Utilization of Non-Invasive Sample Sources for Identification of Somatic and Germline Mutations in Hematologic Malignancies and Clonal Hematopoiesis (ASH 2021)
These methods of sample collection are non-invasive, amenable to in home collection, and are temperature stable. Collection of saliva and nails could be easily utilized for remotely administered studies by mailing collection kits to participants, thus avoiding the cost and labor of a blood draw.
JAK2 (Janus kinase 2)
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JAK2 V617F
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Archer® VariantPlex® Myeloid panel
over2years
[VIRTUAL] Cross-Platform Comparison of Next-Generation Sequencing Assays for Myeloid Variant Profiling (AMP 2021)
There was an inverse relationship between cost/workflow time and analytical performance of assays. The analytical assessments results across the 3 platforms were comparable for inter-run reproducibility, LOD, accuracy, and specificity. Areas of differentiation among the assays included sensitivity and intra-patient concordance, with VariantPlex showing the highest values for each.
Next-generation sequencing
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FLT3 (Fms-related tyrosine kinase 3)
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Archer® VariantPlex® Myeloid panel • Oncomine Myeloid Assay GX
over2years
Predictive Biomarkers of Response to the Polo-like Kinase 1 (PLK1) Inhibitor, Onvansertib, in Combination with Decitabine in Relapsed or Refractory Acute Myeloid Leukemia (R/R AML) (ASH 2021)
In our cohort, we confirmed the association between clinical response to ONV-DAC and SF mutations. These analyses support further investigation of the ONV-DAC combination in R/R AML patients with SF mutations and the potential use of ONV-DAC for other hematological diseases with high prevalence of SF mutations such as myelodysplastic syndrome and chronic myelomonocytic leukemia.
Combination therapy
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TP53 (Tumor protein P53) • SF3B1 (Splicing Factor 3b Subunit 1) • TET2 (Tet Methylcytosine Dioxygenase 2) • SRSF2 (Serine and arginine rich splicing factor 2) • PLK1 (Polo Like Kinase 1)
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TP53 mutation • TET2 mutation • SF3B1 mutation • SRSF2 mutation
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Archer® VariantPlex® Myeloid panel
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decitabine • onvansertib (PCM-075)
over2years
Molecular Responses Are Observed across Mutational Spectrum in Treatment-Naïve Higher-Risk Myelodysplastic Syndrome Patients Treated with Venetoclax Plus Azacitidine (ASH 2021)
Pts with higher-risk MDS treated with Ven + Aza had rapid, durable responses and high remission rates. Pts across key mutational profiles achieved meaningful clinical and molecular responses, supporting an all-comers approach. Updated data will be presented, which will provide more follow up time and durability of responses among mutational subsets.
Clinical • IO biomarker
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TP53 (Tumor protein P53) • RUNX1 (RUNX Family Transcription Factor 1) • ASXL1 (ASXL Transcriptional Regulator 1) • U2AF1 (U2 Small Nuclear RNA Auxiliary Factor 1)
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TP53 mutation • ASXL1 mutation • U2AF1 mutation
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Archer® VariantPlex® Myeloid panel
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Venclexta (venetoclax) • azacitidine
over2years
[VIRTUAL] Detection of pathogenic germline variants following somatic panel-based next-generation sequencing (BLOOD 2021)
Familial myeloid predisposition syndromes may be suspected following somatic NGS testing, however our data shows that the rate of confirmatory germline testing is low. This has implications for stem cell donor selection and cascade screening of relatives. For genes that are rarely somatically mutated in MDS/AML such as DDX41 and ANKRD26, the likelihood of germline transmission is high and clinical vigilance is essential to ensure timely confirmatory sequencing.
Next-generation sequencing
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TP53 (Tumor protein P53) • RUNX1 (RUNX Family Transcription Factor 1) • ETV6 (ETS Variant Transcription Factor 6) • CEBPA (CCAAT Enhancer Binding Protein Alpha) • GATA2 (GATA Binding Protein 2)
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Archer® VariantPlex® Myeloid panel