^
    Contact us  to learn more about
    our Premium Content:  News alerts, weekly reports and conference planners

    TEST:
    Ion AmpliSeq™ Cancer Hotspot Panel v2

    Company:
    Thermo Fisher Scientific
    Type:
    Laboratory Developed Test
    Related tests:
    Details
    Evidence

    News

    5d
    Detection of a Novel MET Intronic Insertion in NSCLC, Leading to an Exon 14 Skipping Variant: An Interruption in the Pattern of Deletions (AMP 2024)
    Thus, for variants within the MET gene in patients with NSCLC, particular attention is required to assess for possible intronic variants that may lead to the METex14, especially if only sequencing DNA. The novelty of the intronic variant herein identified is heightened by being a net insertion rather than a deletion, as all reported intronic variants in the Catalogue of Somatic Mutations in Cancer (COSMIC) within this region are deletions. If sequencing DNA and RNA, both the intronic variant and RNA consequence should be used synergistically as evidence for the presence of METex14 skipping variant.
    MET (MET proto-oncogene, receptor tyrosine kinase)
    |
    MET exon 14 mutation
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2
    4ms
    Unusual PEComa With PRCC::TFE3 Fusion Mimicking Sinonasal Tract Melanoma. (PubMed)
    "This report emphasis the importance of molecular testing in the differential diagnosis between PEComa and melanoma, especially when the tumor arises in a site typical of melanoma but showing an unusual morphology and immunophenotype. The detection of TFE3 fusion transcripts suggested the diagnosis of SNT PEComa, although it cannot be excluded that this and similar tumors represent a distinct diagnostic category."
    Journal
    |
    FusionPlex® Pan Solid Tumor v2 panel • Ion AmpliSeq™ Cancer Hotspot Panel v2
    9ms
    Genetic characterization of intramuscular myxomas. (PubMed, Pathol Oncol Res)
    Secondly, the presence of the rare pathogenic variants R201S, p.R201G and p.Q227E in 26% (5 out of 19) of myxomas with GNAS pathogenic variants shows that methodologies designed to detect only the common "hotspot" of p.R201C and p.R201H will give false negative results. Finally, a comparison between Ion AmpliSeq Cancer Hotspot Panel v2 and direct cycle Sanger sequencing showed that direct cycle Sanger sequencing provides a quick, reliable, and relatively cheap method to detect GNAS pathogenic variants, matching even the most cutting-edge sequencing methods.
    Journal
    |
    GNAS (GNAS Complex Locus)
    |
    GNAS R201C
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2
    10ms
    Genome-wide analysis of DNA methylation in pseudomyxoma peritonei originated from appendiceal neoplasms. (PubMed)
    These findings may help the understanding of the molecular mechanism(s) of PMP and contribute to the development of therapeutic strategies for this life-threatening disease.
    Journal • Epigenetic controller
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2
    10ms
    Comparative Analysis of Ion Torrent Sequencing Platforms: Unveiling Enhanced Performance and Precision with the GenexusTM integrated sequencer in Clinical Applications (ACMG 2024)
    Taken together, our comparison ofIon PGMTM Dx system and GenexusTM integrated sequencer indicates that the latter exhibits superior performance with significantly higher total reads, mapped reads, and mean depth, leading to a faster turnaround time and improved detection of clinically relevant variants. This underscores its potential for enhanced precision in clinical applications.
    Clinical
    |
    EGFR (Epidermal growth factor receptor) • NRAS (Neuroblastoma RAS viral oncogene homolog)
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2 • Oncomine Precision Assay
    1year
    Next-generation sequencing of pancreatic cyst wall specimens obtained using micro-forceps for improving diagnostic accuracy. (PubMed, Endosc Int Open)
    "Conclusions NGS data correlate well with histology and may aid in diagnosis and risk stratification of pancreatic cysts. Cyst wall biopsy performs well in diagnosing cysts but was inadequate in five of 24 patients."
    Journal
    |
    KRAS (KRAS proto-oncogene GTPase) • GNAS (GNAS Complex Locus)
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2
    1year
    Dideoxy Sequencing Enhances Detection of KIT Variants in GISTs Initially Evaluated by NGS Hotspot Panels (AMP 2023)
    Our results suggest that short read NGS-based assays may miss a significant number of clinically actionable KIT variants, and that follow-up of KIT and PDGFRA NGS-negative cases by alternative testing modalities should be considered.
    Next-generation sequencing
    |
    BRAF (B-raf proto-oncogene) • KIT (KIT proto-oncogene, receptor tyrosine kinase) • PDGFRA (Platelet Derived Growth Factor Receptor Alpha)
    |
    BRAF V600E • BRAF V600 • KIT exon 11 mutation • KIT exon 9 mutation • KIT exon 17 mutation
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2 • Oncomine Precision Assay
    1year
    Effect of Heated EDTA Decalcification on Quality and Quantity of DNA for Molecular Testing (AMP 2023)
    Bone samples heated to 50o to 60oC showed histology comparable to those not heated, decalcified faster than those not heated, had adequate quantity of DNA for molecular analysis, and next-generation sequencing was successfully performed on select samples. Samples heated above this demonstrated poor-quality histology. The study is limited by heterogeneity in formalin fixation times, variable bone and DNA content of specimens, and small number of samples.
    Ion AmpliSeq™ Cancer Hotspot Panel v2
    over1year
    Mutation spectrum in Bulgarian patients with thyroid cancer and struma nodosа (EACR 2023)
    NSF,MES:D01-395/18.12.2020, D01-278-14.12. 2022, D01-302/17.12.2021, D01 165/28.07.2022; NSF,MES: KP06-H23/9.18.12.2018
    Clinical
    |
    EGFR (Epidermal growth factor receptor) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • ABL1 (ABL proto-oncogene 1) • NRAS (Neuroblastoma RAS viral oncogene homolog) • FGFR2 (Fibroblast growth factor receptor 2) • PTEN (Phosphatase and tensin homolog) • FGFR3 (Fibroblast growth factor receptor 3) • STK11 (Serine/threonine kinase 11) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • RB1 (RB Transcriptional Corepressor 1) • PTPN11 (Protein Tyrosine Phosphatase Non-Receptor Type 11) • SMAD4 (SMAD family member 4) • CTNNB1 (Catenin (cadherin-associated protein), beta 1) • FBXW7 (F-Box And WD Repeat Domain Containing 7) • ERBB4 (erb-b2 receptor tyrosine kinase 4) • GNAS (GNAS Complex Locus) • HNF1A (HNF1 Homeobox A)
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2
    over1year
    Multicentric prospective study assessing clinical benefit of targeted treatment for patients with biliary tract cancers (ESMO-GI 2023)
    Targeted therapy was actually started for 95 pts (16%), with 15 (16%) pts treated with ivosidenib for IDH1 mutations, 63 (66%) with FGFR2 inhibitors for FGFR2 alterations, 3 (3%) with immune checkpoint inhibitors (ICIs) for MSI-H, 9 (10%) with BRAF+MEK inhibitors for BRAFV600E mutations and 4 (4%) with HER2 inhibitors for HER2 amplification... NGS is feasible in daily clinical practice and it should be performed, as recommended, for all pts affected by advanced BTC, since biomarker-directed treatment for BTCs has clinically meaningful benefit in pretreated patients.
    Clinical • MSi-H Biomarker • IO biomarker
    |
    MSI (Microsatellite instability) • FGFR2 (Fibroblast growth factor receptor 2) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1)
    |
    BRAF V600E • MSI-H/dMMR • HER-2 amplification • BRAF V600 • IDH1 mutation • FGFR2 mutation
    |
    FoundationOne® CDx • Archer® FusionPlex® Oncology Research Kit • Ion AmpliSeq™ Cancer Hotspot Panel v2 • Oncomine™ Comprehensive Assay Plus
    |
    Tibsovo (ivosidenib)
    over1year
    A case report of a FGFR activation and genetic variability in metastatic sinonasal mucosal melanoma (EADO 2023)
    "A switch to second-line Lenvatinib and Pembrolizumab followed due to progressive disease...According to these results, we have received approval to start Erdafitinib (Balversa®), a specific FGFR1-4 inhibitor... We present the case of a 44-year-old male patient with stage IV metastasized sinonasal mucosal melanoma. Treatment included primary tumor resection, followed by adjuvant radiotherapy and adjuvant systemic therapy with a PD-1 inhibitor. After a local recurrence, first-line therapy with combination immunotherapy (ipilimumab and nivolumab) was initiated."
    Clinical
    |
    KRAS (KRAS proto-oncogene GTPase) • NRAS (Neuroblastoma RAS viral oncogene homolog) • FGFR3 (Fibroblast growth factor receptor 3) • FGFR (Fibroblast Growth Factor Receptor) • TACC3 (Transforming acidic coiled-coil containing protein 3)
    |
    KRAS mutation • NRAS mutation • KIT mutation • FGFR3 mutation • FGFR mutation
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2
    |
    Keytruda (pembrolizumab) • Opdivo (nivolumab) • Yervoy (ipilimumab) • Lenvima (lenvatinib) • Balversa (erdafitinib)
    over1year
    Comparison between Three Different Techniques for the Detection of EGFR Mutations in Liquid Biopsies of Patients with Advanced Stage Lung Adenocarcinoma. (PubMed, Int J Mol Sci)
    "Our results evidenced an equivalent detection ability between PCR-based techniques for circulating EGFR mutations. The NGS assay allowed detection of a wider range of EGFR mutations but showed a poor ability to detect T790M."
    Journal • Liquid biopsy
    |
    EGFR (Epidermal growth factor receptor)
    |
    EGFR mutation • EGFR L858R • EGFR exon 19 deletion • EGFR T790M • KIT mutation
    |
    therascreen® EGFR RGQ PCR Kit • Idylla™ ctEGFR Mutation Assay • Ion AmpliSeq™ Cancer Hotspot Panel v2
    almost2years
    Exploring the Molecular Landscape of Advanced Gallbladder Cancer by Targeted Next-Generation Sequencing on Cytologic Aspirates: Cytology at the Molecular Frontier (USCAP 2023)
    To date, this is the first study to describe the mutational spectrum of AGBC on cytologic aspirates. Most of the variants detected in our study are actionable with FDA-approved targeted therapies that can be used to improve outcomes in these patients.
    Next-generation sequencing • Metastases • Cytology
    |
    KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • FLT3 (Fms-related tyrosine kinase 3) • NRAS (Neuroblastoma RAS viral oncogene homolog) • FGFR2 (Fibroblast growth factor receptor 2) • PTEN (Phosphatase and tensin homolog) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • STK11 (Serine/threonine kinase 11) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • RB1 (RB Transcriptional Corepressor 1) • GNAQ (G Protein Subunit Alpha Q) • KDR (Kinase insert domain receptor) • SMAD4 (SMAD family member 4) • CTNNB1 (Catenin (cadherin-associated protein), beta 1) • FBXW7 (F-Box And WD Repeat Domain Containing 7) • HNF1A (HNF1 Homeobox A)
    |
    TP53 mutation • KRAS mutation • NRAS mutation • PIK3CA mutation • PTEN mutation • STK11 mutation • RET mutation • CDKN2A mutation • CTNNB1 mutation • SMAD4 mutation
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2
    almost2years
    Circulating tumor cells and cell-free tumor DNA analyses in urothelial cancer using the LiquidBiopsy platform. (PubMed, Curr Urol)
    "The Ion Torrent platform efficiently detected CTCs compared with previous reports. NGS with the present system also allowed for detection of gene alterations which are likely to be therapeutic targets and provided an attractive tool to guide personalized therapy for patients with advanced UC."
    Journal • Liquid biopsy • Circulating tumor DNA
    |
    CELLSEARCH® • Ion AmpliSeq™ Cancer Hotspot Panel v2
    over2years
    Molecular Heterogeneity of Compound Epidermal Growth Factor Receptor (EGFR) Mutations in Lung Adenocarcinoma (LAC) (IASLC-WCLC 2022)
    5 pts were treated with afatinib, 3 pts with osimertinib, 4 pts with gefitinib and 1 pt with erlotinib). EGFR LAC with compound mutations is a heterogeneous group. The incidence of common mutations was lower than expected. The most frequent uncommon mutations involved EGFR exons 20 and 21.
    EGFR (Epidermal growth factor receptor) • ALK (Anaplastic lymphoma kinase) • TP53 (Tumor protein P53) • PTEN (Phosphatase and tensin homolog) • SMAD4 (SMAD family member 4) • CTNNB1 (Catenin (cadherin-associated protein), beta 1)
    |
    TP53 mutation • EGFR mutation • EGFR L858R • EGFR exon 19 deletion • EGFR T790M • PTEN mutation • ALK translocation • EGFR exon 20 mutation • SMAD4 mutation
    |
    Ion AmpliSeq™ Cancer Hotspot Panel v2
    |
    Tagrisso (osimertinib) • erlotinib • Gilotrif (afatinib) • gefitinib