1. Home
  2. Solutions
  3. Laboratories
  4. Specialty Biomarker Laboratories
  5. Genomics

Genomics

Robust technical proficiency in genomics for retrospective and prospective biomaker analysis.

ICON utilises robust technical proficiency in genomics, including NGS, ddPCR, and qPCR, along with over ten years of experience in developing and validating clinical trial assays, to meet sponsors' needs for both retrospective and prospective biomarker analysis in clinical trials. 

Delivering value for your clinical trial:

  • Extensive expertise in genomic assay design, validation, and bioinformatics.
  • Thorough validation processes to assess product strengths and weaknesses, enhancing assay performance through additional data analysis beyond commercial software capabilities
  • A wide range of commercially validated assays ready for immediate use in clinical trials
  • Development and validation of assays tailored to sponsors' specific needs
  • Proven success in custom assay development, securing approvals from regulatory bodies such as NY state, FDA IDE, and PMA.
  • High-quality deliverables with fast turnaround times.
  • Flexibility, agility, and strong collaboration with clients

 

Broad NGS testing 

ICON has multiple types of NGS instruments to address different biomarker needs. Our Illumina sequencers include MiSeq, MiSeq Dx, NextSeq 550 Dx, and NovaSeq 6000; ThermoFisher platforms include Ion S5xl sequencer and Genexus. Using these platforms, ICON offers broad NGS tests to address variable biomarker testing requirements.

 

Whole exome (WES) and transcriptome (RNASeq)

  • WES: ICON offers Agilent SureSelect Max human All Exon v8 kit on NovaSeq 6000 for FFPE and fresh DNA. Illumina Dragen Enrichment and Molecular Health and or Illumina Connected Insight are used for secondary analysis and ternary annotation, respectively. The assay can detect small variants, TMB, HLA (class I and III), CNV and gene fusion.
  • RNASeq: ICON offers Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus, which provides accurate measurement of gene and transcript abundance (gene expression) and detects both known and novel features in coding and multiple forms of noncoding RNA. The assay can also be used for the discovery of alternative transcripts, gene fusions, and allele-specific expression. Sample types include fresh and FFPE samples. DRAGEN Differential Expression is used for differential analysis.

Targeted NGS panels

  • TSO500 solid tumor and ctDNA v2 panels: ICON offers Illumina TSO500 solid tumor panel and ctDNA v2 panel for biomarker profiling in 523 genes from DNA/RNA (FFPE or fresh) and ctDNA, respectively. Both assays report full-coding region small variants, TMB, MSI, CNV and fusion. The assays offer highly sensitive and specific biomarker results by using error reduction through Duplex sequencing.
  • Archer Anchored Multiplex PCR based DNA and RNA NGS assays: ICON has more than 10 years of experiencing on Archer DNA and RNA NGS assays, including validation of commercial assay, custom assay development and validation, and clinical trial testing. Our offerings include panels for myeloid disease (Archer Core Myeloid Panel and Myeloid Panel for mutation detection) and Archer FUSIONPlex Pan Solid Tumor v2 panel for gene fusion. Benefit of the Archer assays include robust performance, full coding region coverage, and overcoming of challenging mutation regions.
  • Oncomine assays: ICON has 10 years of experience on running Oncomine assay for targeted mutations and gene fusions. Benefit of Oncomine assays includes low-input (DNA/RNA), robustness to FFPE, and fast TAT.  

 

Custom NGS to address unmet need

  • Add-on gene to existing NGS panel: ICON has years of successful experience on adding gene not covered by existing targeted NGS panels to backbone Archer NGS panel e.g. Archer Core Myeloid panel. This helps to address the unmet biomarker need at lower cost and more focused results than WES.
  • A novel custom BCR::ABL1 NGS test: Molecular monitoring of CML patients faces challenges such as the identification of atypical BCR::ABL1 transcripts and detecting low-level TKI resistance mutations. Qualitative RT-PCR detects transcript type but not mutation, and NGS mutation assays, while sensitive, can yield low-level false positives. ICON NGS team developed a novel custom RNA-based NGS assay that identifies both common and atypical BCR::ABL1 transcripts and detects resistance mutations from both common and atypical transcript types with high sensitivity and specificity. This assay also streamlines molecular testing workflow in the clinical management of CML patients by consolidating multiple assays into a single comprehensive test. The assay is being utilized for biomarker testing in multiple CML clinical trials.  
     

 

Selective assays

 

Comprehensive genomic profiling

  • Illumina TruSight Oncology 500 Panel: for solid tumor and CHiP mutation
  • Illumina TruSight Oncology 500 ctDNA v2 Panel: for liquid biopsy

  • Illumina TruSeq RNA exome: gene expression and fusion

     

Focused targeted panels

  • ArcherDx Core Myeloid Panel (37 genes) and Myeloid Panel (75 genes)*: myeloid cancer and CHiP mutation
  • ArcherDx Solid Tumor VariantPlex Panel*: solid tumor
  • ArcherDx Solid Tumor FusionPlex Panel*: solid tumor
  • ThermoFisher Oncomine Comprehensive Assay v3: solid tumor
  • ThermoFisher Oncomine cfDNA Panel: for liquid biopsy
In this section

Connect with us