^
    4d
    Role of somatic mutations in Homologous Recombination (HR) and DNA Damage Repair (DDR) genes in metastatic pancreatic ductal adenocarcinoma (mPDAC) (AIOM 2024)
    Background : First-line therapy’s (tx) choice between the two most efficacious approved regimens (FOLFIRINOX and Gemcitabine plus Nab-Paclitaxel - GemNab) in mPDAC is usually based on patients’ (pts) baseline characteristics... HR-DDR somatic alterations emerged as possible predictor of lower benefit from platinum-free regimens. Thus, platinum-based regimens should be preferred in this setting. Validation in wider cohorts and correlation with HR-DDR germline mutations are warranted.
    PARP Biomarker • Metastases
    |
    TruSight Oncology 500 Assay
    |
    gemcitabine • 5-fluorouracil • albumin-bound paclitaxel • irinotecan • leucovorin calcium
    4d
    Durvalumab plus cisplatin and gemcitabine as first line therapy for advanced biliary tract carcinoma (aBTC): a monocentric retrospective experience (AIOM 2024)
    The data presented in this study are consistent with the results of TOPAZ1 trial. However about a third of patients do not respond to CHT or have a short response duration. In our experience both NLR and basal elevated AST/ALT seem to be associated with an improved mPFS and a better outcome but further studies are needed.
    Retrospective data • PD(L)-1 Biomarker • IO biomarker • Metastases
    |
    KRAS (KRAS proto-oncogene GTPase) • TP53 (Tumor protein P53) • TMB (Tumor Mutational Burden)
    |
    TP53 mutation • KRAS mutation • TMB-H • TMB-L
    |
    TruSight Oncology 500 Assay
    |
    cisplatin • Imfinzi (durvalumab) • gemcitabine
    4d
    Tissue-based Next Generation Sequencing (NGS) for Patients with Advanced Solid Tumors: the experience of Verona University Hospital (AIOM 2024)
    Our study provides an example of implementation of molecular profiling in an academic pre-screening program. Further analysis will investigate treatment matching rates, drug access schemes, and their impact on treatment efficacy and survival.
    Clinical • Next-generation sequencing • BRCA Biomarker • Metastases
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • ER (Estrogen receptor) • ALK (Anaplastic lymphoma kinase) • TMB (Tumor Mutational Burden) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • FGFR2 (Fibroblast growth factor receptor 2) • PTEN (Phosphatase and tensin homolog) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1)
    |
    BRAF V600E • KRAS mutation • BRCA2 mutation • BRCA1 mutation • EGFR mutation • KRAS G12C • HER-2 amplification • PIK3CA mutation • BRAF V600 • NTRK1 fusion • PTEN mutation • KIT mutation • FGFR2 mutation • RET mutation • MET mutation • KRAS G12 • ESR1 mutation • NTRK1 mutation • BRAF amplification
    |
    FoundationOne® CDx • TruSight Oncology 500 Assay
    4d
    p53 pathway genes’ mutations (muts) as prognostic factors in patients (pts) with metastatic Pancreatic Ductal Adenocarcinoma (mPDAC): a single center study (AIOM 2024)
    Our study suggests an important prognostic role of p53 signaling muts in mPDAC pts; wt pts resulted in a longer OS than mutated pts, although some muts, in particular tp53 exon4 mut, seem to be associated with longer survival. Further studies are needed to investigate these findings, including an in-depth analysis of structural proteomics.
    Clinical • Metastases
    |
    KRAS (KRAS proto-oncogene GTPase) • CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) • CDKN2B (Cyclin Dependent Kinase Inhibitor 2B) • CHEK2 (Checkpoint kinase 2) • MDM4 (The mouse double minute 4) • CHEK1 (Checkpoint kinase 1) • TP53BP1 (Tumor Protein P53 Binding Protein 1)
    |
    TP53 mutation • KRAS mutation • TP53 wild-type • TP53 exon 4 mutation
    |
    TruSight Oncology 500 Assay
    4d
    Homologous recombination (HR) and DNA damage repair (DDR) somatic alterations in metastatic colorectal cancer (mCRC): results from the comprehensive genomic profiling (CGP) trial FPG500 (AIOM 2024)
    Background : Treatment (tx) of MSS/MMRp mCRC relies mainly on oxaliplatin (oxa)- or irinotecan-based doublet chemotherapy regimens, with no biomarker reported so far, allowing the selection of one tx over the other. HR-DDRa is associated with MSI-H or TMB-H. Pts with MSS HR-DDRa tumors benefit from oxa-based first line treatment. Longer FU, allowing mature OS data, and wider cohorts are warranted.
    Tumor mutational burden • BRCA Biomarker • MSi-H Biomarker • Metastases
    |
    TMB (Tumor Mutational Burden) • BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • MSI (Microsatellite instability) • BAP1 (BRCA1 Associated Protein 1) • PALB2 (Partner and localizer of BRCA2) • ATRX (ATRX Chromatin Remodeler) • CHEK2 (Checkpoint kinase 2) • FANCA (FA Complementation Group A) • BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1) • RAD50 (RAD50 Double Strand Break Repair Protein) • CHEK1 (Checkpoint kinase 1) • BARD1 (BRCA1 Associated RING Domain 1) • MRE11A (MRE11 homolog, double strand break repair nuclease) • NBN (Nibrin Nijmegen Breakage Syndrome 1 (Nibrin)) • FANCL (FA Complementation Group L) • FANCD2 (FA Complementation Group D2) • FANCE (FA Complementation Group E) • FANCC (FA Complementation Group C)
    |
    TMB-H • MSI-H/dMMR
    |
    TruSight Oncology 500 Assay
    |
    oxaliplatin • irinotecan
    5d
    Mutations of ARID1B, PIK3C2B, KMT2B, and FAT1 genes influence clinical outcome in newly diagnosed myeloma. (PubMed, Cancer Genet)
    Genetic alterations significantly influencing progression-free survival concerned PIK3C2B, ARID1B genes, and concomitant mutations in KMT2B, FAT1, and ARID1B. The findings underscore the potential of gene mutation-based prognostic tools in enhancing clinical decision-making and suggest that further exploration of identified genetic markers could pave the way for improved prognostic stratification and targeted therapeutic interventions in multiple myeloma.
    Clinical data • Journal
    |
    FAT1 (FAT atypical cadherin 1) • ARID1B (AT-Rich Interaction Domain 1B) • KMT2B (Lysine Methyltransferase 2B) • PIK3C2B (Phosphatidylinositol-4-Phosphate 3-Kinase Catalytic Subunit Type 2 Beta)
    |
    KRAS mutation • ARID1B mutation • KMT2B mutation
    |
    TruSight Oncology 500 Assay
    5d
    Assessing expression patterns of PTGR1, a potential biomarker for acylfulven sensitivity in urothelial carcinoma. (PubMed)
    13% in our cohort were identified as NER deficient and PTGR1 positive. Lower levels of PTGR1 indicates better outcome in this cohort.
    Journal • Retrospective data
    |
    TruSight Oncology 500 Assay
    8d
    Automation of the Pillar Biosciences oncoReveal Solid Tumor 22-Gene Panel Kit and the Illumina TruSight Oncology 500 DNA/RNA Kit on the Biomek NGeniuS Next-Generation Library Preparation System (AMP 2024)
    Automation of the Pillar Biosciences oncoReveal Solid Tumor 22 Gene Panel Kit and the Illumina TruSight Oncology 500 DNA/RNA kit on the Biomek NGeniuS Next Generation Library Preparation System shows the flexibility of the Biomek NGeniuS System in providing cancer researchers a range of applications to facilitate their research.
    KIT (KIT proto-oncogene, receptor tyrosine kinase)
    |
    TruSight Oncology 500 Assay • OncoReveal™ Solid Tumor Panel
    8d
    Characterization of Signaling Pathways in Solid Tumors Using Comprehensive Genomic Profiling (AMP 2024)
    Growth and proliferation pathways are altered more in certain cancers than in others; however, the CC pathway is altered to a lesser extent but across cancers. The HRR pathway is predominantly altered in ovarian and prostate cancers. RTK/Ras and PI3K pathways have been well studied with smaller panels and established genes; however, large panels allow for inclusion of additional components of these pathways, and assessment of HRR and CC pathways more effectively.
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • FGFR1 (Fibroblast growth factor receptor 1) • HRD (Homologous Recombination Deficiency)
    |
    KRAS mutation
    |
    TruSight Oncology 500 Assay
    8d
    Impact on the Diagnosis of Mesenchymal Tumors through the Use of a Customized NGS RNA Fusion Panel (AMP 2024)
    Implementing an expanded panel for fusion analysis contributed to defining or confirming the anatomical pathology diagnosis in approximately 74% of the tested cases. Additionally, enriching the panel with genes relevant to mesenchymal tumors increased the gene fusion detection rate by almost 50%.
    Next-generation sequencing
    |
    BCOR (BCL6 Corepressor) • FUS (FUS RNA Binding Protein) • TAF15 (TATA-Box Binding Protein Associated Factor 15) • JAZF1 (JAZF Zinc Finger 1) • SS18 (SS18 Subunit Of BAF Chromatin Remodeling Complex) • NCOA2 (Nuclear Receptor Coactivator 2)
    |
    TruSight Oncology 500 Assay
    8d
    Reporting the Discrete Data of Four NGS Panels into the EHR System: A Single-Institute Experience (AMP 2024)
    Since its initial proposal in December of 2022, discrete reporting at the University of California, San Diego genomic lab was an effort that took close to a year-and-a-half to accomplish. Although the process was not without its hardships, the decision to go with an in-house approach saved the lab both time and resources compared to an outside approach. By exploring the capabilities and functionalities of its current laboratory information systems and EHR systems, the lab built a discrete reporting system that is effective for its needs as well as a framework for converting other and future NGS assays to discrete reporting.
    Next-generation sequencing • Tumor mutational burden
    |
    TMB (Tumor Mutational Burden) • MSI (Microsatellite instability)
    |
    TruSight Oncology 500 Assay • Oncomine Precision Assay
    8d
    The Agena iPlex HS Lung Panel on the MassARRAY System Is Able to Robustly Characterize the Molecular Profile of FFPE-Derived Lung Tumor Samples Previously Deemed QNS on Multiple NGS Platforms (AMP 2024)
    The Agena iPlex HS Lung Panel on the MassARRAY System is highly tolerant of poor quantity and quality DNA, recovering and delivering accurate results on samples that would otherwise fail NGS-based analysis.
    Next-generation sequencing
    |
    EGFR (Epidermal growth factor receptor) • HER-2 (Human epidermal growth factor receptor 2) • KRAS (KRAS proto-oncogene GTPase) • BRAF (B-raf proto-oncogene) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha)
    |
    KRAS mutation • EGFR mutation • BRAF mutation • PIK3CA mutation • BRAF V600 • EGFR L858R • EGFR exon 19 deletion • KRAS G12V • KRAS G12 • KRAS G13 • KRAS Q61 • KRAS deletion
    |
    TruSight Oncology 500 Assay
    8d
    Clinical Validation of an In-House-Developed Somatic Copy Number Calling Pipeline to Use on the TruSight Oncology 500 Next-Generation Sequencing (TSO500) Kit in Solid Tumors (AMP 2024)
    The OncCNV pipeline accurately detects GAMP, HMZ, and BI beyond the reportable range validated by Illumina. Development of the OncCNV pipeline further enhances the clinical utility of the TSO500 assay, as demonstrated in this cohort of solid tumor samples.
    Clinical • Next-generation sequencing • Tumor mutational burden
    |
    TMB (Tumor Mutational Burden) • MSI (Microsatellite instability)
    |
    TruSight Oncology 500 Assay
    8d
    Comprehensive Genomic and Immune Profiling for the Detection of Clinically Significant Tumor Biomarkers (AMP 2024)
    Utilization of a multi-modal CGIP testing strategy resulted in a high rate of test success and detection of clinically relevant biomarkers and optimizing tissue usage.
    Clinical • Tumor mutational burden • IO Companion diagnostic • PD(L)-1 Biomarker • IO biomarker • PD(L)-1 companion diagnostic
    |
    PD-L1 (Programmed death ligand 1) • TMB (Tumor Mutational Burden) • MSI (Microsatellite instability)
    |
    PD-L1 expression • TMB-H
    |
    TruSight Oncology 500 Assay • Oncomine™ Immune Response Research Assay
    8d
    Detection of 1p/19q Co-deletion Using Hybridization-Capture-Based Targeted Next-Generation Sequencing (AMP 2024)
    Targeted hybridization-capture-based NGS assays can be a robust and reliable method for detecting 1p/19q co-deletion in gliomas. NGS methodologies provide enhanced resolution of copy number alterations but require a minimum tumor content.
    Next-generation sequencing
    |
    TP53 (Tumor protein P53) • IDH1 (Isocitrate dehydrogenase (NADP(+)) 1) • ATRX (ATRX Chromatin Remodeler)
    |
    TP53 mutation • IDH wild-type • IDH1 mutation + TP53 mutation
    |
    TruSight Oncology 500 Assay
    8d
    Use of %B Allele Frequency SNP Plots to Investigate Contamination Detection Flags in Next-Generation Sequencing (AMP 2024)
    This case series demonstrates the utility of BAF plots in distinguishing between true and spurious contamination flags in NGS assays. Integrating BAF plot analysis into routine NGS workflows can enhance the reliability of contamination detection and prevent misinterpretation of results.
    Next-generation sequencing
    |
    TruSight Oncology 500 Assay
    8d
    Analytical Validation of OmniSeq INSIGHT Whole-Exome Sequencing Assay to Facilitate Precision Oncology through Tumor-Only Testing in Solid Tumors (AMP 2024)
    This study demonstrates that the OmniSeq INSIGHT WES assay is a sensitive, specific, accurate, reproducible, and robust approach for genomic profiling of FFPE solid tumor specimens to support the precision oncology drug development continuum.
    Whole exome sequencing
    |
    TruSight Oncology 500 Assay • OmniSeq INSIGHT
    8d
    Novel SMAD4 MH2 Domain Inactivating Mutation in a Patient with Metastatic Malignant Melanoma (AMP 2024)
    SMAD4 p.G365S (c.1093G >A) is a novel inactivating missense mutation. Although this patient presented with aggressive disease, the clinical significance of this SMAD4 mutation is still uncertain. Additional meta-analytic studies are needed to determine the significance of SMAD4 alteration in patients with malignant melanoma.
    Clinical • Metastases
    |
    BRAF (B-raf proto-oncogene) • SMAD4 (SMAD family member 4) • TGFB1 (Transforming Growth Factor Beta 1) • SMAD2 (SMAD Family Member 2)
    |
    BRAF V600E • BRAF V600 • SMAD4 mutation
    |
    TruSight Oncology 500 Assay
    8d
    Analytical Performance of the New Illumina TruSight Oncology 500 V2 Assay for Comprehensive Genomic Profiling (AMP 2024)
    The new Illumina TSO500 v2 assay features a simplified workflow with improved performance and reduced turnaround time. Driven by innovations in assay design and bioinformatics, these capabilities can accelerate the democratization of actionable cancer biomarker detection, from small variants and copy number variants to RNA variants and complex biomarker outputs like TMB, MSI, and GIS scores.
    Tumor mutational burden • IO biomarker
    |
    TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • HRD (Homologous Recombination Deficiency)
    |
    HRD
    |
    TruSight Oncology 500 Assay
    8d
    Analytical Performance of TruSight Oncology 500 ctDNA v2 on the NovaSeq X Leading to Improved Turnaround Times (AMP 2024)
    Together, these results demonstrate that the NovaSeq X series of instruments generates equivalent analytical results with overall reduced sequencing time, enabling a <3.5-day turnaround time.
    Circulating tumor DNA
    |
    TruSight Oncology 500 Assay • TruSight Oncology 500 ctDNA v2
    8d
    Automation of the Illumina TruSight Oncology 500 ctDNA v2 Assay on the Hamilton Microlab NGS STAR MOA System (AMP 2024)
    The TSO500 ctDNA v2 assay with automated library prep on the NGS STAR MOA liquid handler has demonstrated performance comparable to manual library prep and offers a high-throughput solution to enable comprehensive genomic profiling with a faster chemistry, more flexible workflow, and easier-to-use reagent kit.
    Next-generation sequencing • Tumor mutational burden • Circulating tumor DNA
    |
    TMB (Tumor Mutational Burden) • MSI (Microsatellite instability)
    |
    TruSight Oncology 500 Assay • TruSight Oncology 500 ctDNA v2
    8d
    MET Transcript Quantification by a NanoString-Based Platform Guides Threshold for MET Exon 14 Splice Variant Reporting by Clinical Next-Generation Sequencing (AMP 2024)
    METex14 results by NGS and RNA STEP gene expression demonstrated strong correlation and were 100% concordant for 370 lung cases (25 positive) with a cut-off of ≥100 METex14 SRs for NGS and a METex14 log2 ratio cut-off of ≥4.0 for RNA STEP. Comparison of METex14 results with 2 assays, NGS and RNA STEP, provided practical insight into cutoffs for METex14 reporting with critical implications for clinical therapeutic decisions.
    Clinical • Next-generation sequencing
    |
    MET (MET proto-oncogene, receptor tyrosine kinase)
    |
    MET exon 14 mutation
    |
    TruSight Oncology 500 Assay
    8d
    ERBB2 RNA Expression Levels by NGS-Based Assay as an Alternate Measure for HER2 Overexpression (AMP 2024)
    RNA expression data from NGS panels may offer an additional assessment of HER2 status, as it correlates with ERBB2 DNA-level amplification and differentiates between HER2 0, 1+, 2+, and 3+ cases. Further studies to validate the clinical utility of RNA expression and its correlation with clinical outcome would be required. Our study also elucidates the potential use of RNA sequencing data from routine cancer NGS panels to assess biomarkers in addition to fusions.
    Next-generation sequencing
    |
    HER-2 (Human epidermal growth factor receptor 2)
    |
    HER-2 overexpression • HER-2 amplification • HER-2 expression
    |
    TruSight Oncology 500 Assay
    8d
    HRD Testing Using Illumina TSO500 and Comparison of Two Analysis Pipelines (AMP 2024)
    Our preliminary results indicate excellent concordance using Illumina 500+HRD kit with DRAGEN pipeline with previous test results. The concordance appears slightly lower using NxClinical, however, not statistically significant in this small sample set. Of particular interest, our findings suggest that, to reduce the testing costs, the standard TSO500 panel without the additional HRD probe pool, followed by analysis with NxClinical software, may serve as a suitable initial screen.
    HRD (Homologous Recombination Deficiency)
    |
    HRD
    |
    TruSight Oncology 500 Assay
    8d
    Validation of Automated Nucleic Acid Extraction Using Covaris Gen3 Extraction Methodology on the Assay-Ready Workstation (AMP 2024)
    The Covaris ARW provides an improvement on current nucleic acid extraction technology with greater sample yield and higher sample quality. Clinically, this decreases the number of quantity/quality not sufficient samples for testing, requires less tumor material to perform testing, and enhances the quality of library preparation and sequencing metrics to increase reporting and patient outcomes. Stem Cell Transplantation Clinically and Pathologically Presenting as Host-versus-Graft
    TruSight Oncology 500 Assay
    8d
    A Pilot Evaluation of the Workflow and Performance Characteristics of the Illumina TruSight Oncology 500 ctDNA v2 Assay (AMP 2024)
    In this pilot study, the TSO500 ctDNA v2 provided workflow enhancements with decreased overall turnaround time compared to TSO500 ctDNA v1, as well as low DNA input requirement, excellent sensitivity, and high accuracy.
    Tumor mutational burden • Circulating tumor DNA
    |
    TMB (Tumor Mutational Burden) • MSI (Microsatellite instability)
    |
    TruSight Oncology 500 Assay • TruSight Oncology 500 ctDNA v2
    8d
    Validation of a Homologous Recombination Deficiency (HRD) Assay for Use in Combination with Comprehensive Genomic Profiling (CGP) Testing (AMP 2024)
    The TruSight Oncology 500 comprehensive solid tumor next-generation sequencing panel with HRD assay demonstrated a high degree of sensitivity and specificity for deployment in a clinical setting.
    Combination therapy • BRCA Biomarker • PARP Biomarker
    |
    BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • HRD (Homologous Recombination Deficiency)
    |
    HRD
    |
    Myriad myChoice® CDx • TruSight Oncology 500 Assay • TruSight Oncology 500 HRD Assay
    8d
    Mutational Signature Comparison of Different Melanomas: Cutaneous versus Non-cutaneous (AMP 2024)
    In summary, targeted sequencing of a large NGS panel can detect predicted ultraviolet radiation mutational signatures in skin cancer with >99% specificity. This preliminary result warrants a potential application of mutational signature characterization in routine tumor profiling testing. Further investigation with larger data sets will follow up to determine the overall sensitivity and specificity for detection.
    TruSight Oncology 500 Assay
    8d
    Automation of the New Illumina TruSight Oncology 500 v2 Assay on the Beckman Coulter Biomek i7 Workstation (AMP 2024)
    The new TSO500 v2 assay with automated library prep on the Biomek i7 workstation was demonstrated to perform comparably to manual library prep and offers a high-throughput solution to enable comprehensive genomic profiling with a faster, more flexible workflow and easier-to-use reagent kit.
    Tumor mutational burden
    |
    TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • HRD (Homologous Recombination Deficiency)
    |
    HRD
    |
    TruSight Oncology 500 Assay
    8d
    Clinical Utility of Circulating Tumor DNA Profiling in Detecting Targetable Fusions in Non-small-Cell Lung Cancer (AMP 2024)
    Fusion detection using ctDNA CGP showed high concordance to tissue tests and high accuracy in predicting therapeutic response in NSCLC patients. The ctDNA CGP is expected to provide an important diagnostic option for fusion detection.
    Clinical • Circulating tumor DNA
    |
    ALK (Anaplastic lymphoma kinase) • FGFR2 (Fibroblast growth factor receptor 2) • ROS1 (Proto-Oncogene Tyrosine-Protein Kinase ROS)
    |
    ALK positive • FGFR2 fusion • ALK fusion
    |
    TruSight Oncology 500 Assay
    8d
    Genomic Landscape of Fusions in Solid Tumors Detected by DNA and RNA Comprehensive Genomic Profiling at a Large Community Health System (AMP 2024)
    The routine use of RNA-based CGP analysis allows for the comprehensive detection of oncogenic fusions in patients with cancer. The diversity of tumor types in which actionable fusions were detected supports the broader utilization of CGP to potentially increase targeted therapy usage and improve outcomes across cancer subtypes.
    Tumor mutational burden
    |
    ER (Estrogen receptor) • ALK (Anaplastic lymphoma kinase) • TP53 (Tumor protein P53) • PIK3CA (Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) • TMB (Tumor Mutational Burden) • RET (Ret Proto-Oncogene) • PTEN (Phosphatase and tensin homolog) • NTRK1 (Neurotrophic tyrosine kinase, receptor, type 1) • NTRK3 (Neurotrophic tyrosine kinase, receptor, type 3) • NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2) • NTRK (Neurotrophic receptor tyrosine kinase)
    |
    TMB-H • NTRK1 fusion • NTRK3 fusion • NTRK2 fusion • RET fusion • PTEN mutation • ALK fusion
    |
    TruSight Oncology 500 Assay
    8d
    A Retrospective Review of Clinical RNA Data from the Mayo Complete Solid Tumor Panel (MCSTP) Testing to Identify Best Strategies for Successful Repeat Testing (AMP 2024)
    For MCSTP failed RNA samples, repeating testing on RNA samples obtained from newly cut slides yielded a much higher success rate than repeating testing on existing RNA samples. In addition, the fact that samples with successful repeat testing by recut slides used statistically significantly more slides suggests insufficient tissue amount as the underlying factor for failed RNA testing on the initial attempt.
    Retrospective data • Review
    |
    TruSight Oncology 500 Assay
    8d
    Optimizing the Illumina TruSight Oncology 500 ctDNA v2 Workflow in a Clinical Lab with Automated Liquid Handling Systems (AMP 2024)
    This study successfully optimized the Illumina TruSight Oncology 500 ctDNA v2 library preparation using an automated liquid handling system. The experience may be beneficial for other laboratories in implementing the ctDNA NGS assay.
    Clinical • Circulating tumor DNA
    |
    TruSight Oncology 500 Assay • TruSight Oncology 500 ctDNA v2
    8d
    The Next Generation of Reference Materials for Analytical Validation of Liquid Biopsy Assays (AMP 2024)
    The performance of the Seraseq ctDNA v4 mutation mixes demonstrates that these materials would allow for assessment of complex and sensitive liquid biopsy NGS assays. Lot-to-lot consistency, minimal variance from intended VAF, expanded variant list, and stability of the product are likely to enable further advancements in the blood-based NGS clinical diagnostics space.
    Liquid biopsy • Biopsy
    |
    TruSight Oncology 500 Assay
    8d
    Validation of Cytology Specimens for Next-Generation Sequencing: An Institutional Experience (AMP 2024)
    Approximately 90% of cytology samples processed with 3 cyto-preparatory methods yielded sufficient DNA and RNA, confirming that cytology specimens alone may provide adequate yield for NGS sequencing. Clinical sequencing of cytology samples revealed equivalent results to FFPE tissue specimens.
    Clinical • Next-generation sequencing • Cytology
    |
    TruSight Oncology 500 Assay
    8d
    Comparison of Ovarian Tumor Homologous Recombination Deficiency (HRD) Status Generated from the Illumina TruSight Oncology 500 (TSO500) High-Throughput HRD Assay to the Myriad myChoice CDx Assay (AMP 2024)
    The FDA (US Food and Drug Administration) has approved olaparib as a front-line maintenance therapy in combination with bevacizumab for patients with newly diagnosed advanced ovarian, fallopian tube, or primary peritoneal cancer with HRD+ status. We have demonstrated that the TSO500-HRD assay can accurately determine HRD status in ovarian tumors.
    BRCA Biomarker • PARP Biomarker
    |
    BRCA1 (Breast cancer 1, early onset) • BRCA2 (Breast cancer 2, early onset) • HRD (Homologous Recombination Deficiency)
    |
    BRCA2 mutation • BRCA1 mutation • HRD
    |
    Myriad myChoice® CDx • TruSight Oncology 500 Assay • TruSight Oncology 500 HRD Assay
    |
    Avastin (bevacizumab) • Lynparza (olaparib)
    8d
    Effect of Genomic DNA Contamination in Cell-Free DNA on the Assay Performance of TSO500 ctDNA v2 (AMP 2024)
    This study suggests that gDNA contamination has minimal impact on the performance of TSO500 ctDNA v2, even with gDNA input 20 times higher than ctDNA. The high tolerance of TSO500 ctDNA v2 to gDNA contamination is likely due to its chemistry, which includes no initial fragmentation, size selection during bead cleanup, and a capture and hybridization process favoring shorter DNA fragments (cfDNA) over longer ones (gDNA).
    Circulating tumor DNA • Cell-free DNA
    |
    TruSight Oncology 500 Assay • TruSight Oncology 500 ctDNA v2
    8d
    Evaluation of Ancestry-Associated Bias in Tumor Mutational Burden Calculation in the TruSight Oncology 500 Platform (AMP 2024)
    Because no significant bias was identified in this limited cohort, an ancestry-based calibration constant or normalization procedure cannot be systematically applied. However, the TMB calling algorithm used by TSO500 relies upon population databases. Therefore, the underlying variants and calculations used to determine TMB should be manually evaluated on a case-by-case basis, particularly for tumors with TMBs close to treatment thresholds in patients of ancestries underrepresented in population databases.
    Tumor mutational burden • IO Companion diagnostic • IO biomarker
    |
    TMB (Tumor Mutational Burden)
    |
    TMB-H
    |
    FoundationOne® CDx • TruSight Oncology 500 Assay
    8d
    Automation of the New Illumina TruSight Oncology 500 v2 Assay on the Hamilton Microlab NGS STAR MOA System (AMP 2024)
    The new TSO500 v2 assay with automated library prep on the NGS STAR MOA liquid handler was demonstrated to perform comparably to manual library prep and offers a high-throughput solution to enable comprehensive genomic profiling with a faster, more flexible workflow and easier-to-use reagent kit.
    Next-generation sequencing • Tumor mutational burden
    |
    TMB (Tumor Mutational Burden) • MSI (Microsatellite instability) • HRD (Homologous Recombination Deficiency)
    |
    HRD
    |
    TruSight Oncology 500 Assay
    8d
    Clinical Utility of Whole-Genome Sequencing for Comprehensive Evaluation of Myeloid Cancers (AMP 2024)
    Overall, there was a high concordance between WGS and orthogonal methods across variant types, demonstrating the utility of WGS for clinical samples. Additionally, WGS identified small variants and CNAs not found in the other methods, although the clinical significance of these needs to be further explored. Given the importance of genomic profiling for AML, WGS should be considered with or in place of other methods.
    Clinical • Whole genome sequencing
    |
    TruSight Oncology 500 Assay
    11d
    Illumina MiSeq i100 Benchtop Sequencer Innovation (AMP 2024)
    As CGP indication and utilization grows, distributed solutions require more sensitive profiling from FFPE, faster, streamlined workflows and comprehensive content inclusive of IO biomarkers and HRD. Hear from experts about Illumina's efforts to further develop these aspects and democratize NGS biomarker profiling.
    TruSight Oncology 500 Assay
    14d
    Sequencing of DNA recovered from brain tumor biopsy surgical waste improves sensitivity of rapid IDH/TP53-mutant tumor diagnoses (SNO 2024)
    Surgical waste is an important diagnostic resource that should be leveraged for rapid diagnostic sequencing. Sufficient DNA can be easily recovered from surgical waste and sequenced within the same time-frame–but with increased sensitivity–to IHC.
    Biopsy
    |
    TP53 (Tumor protein P53)
    |
    TP53 mutation • IDH1 R132
    |
    TruSight Oncology 500 Assay