Biofluid Profiling Illumina Sequencers Biomarker Discovery Companion Diagnostics    Predictive Modeling


Examining Genetic Variants with Liquid Biopsy and Tumor Samples

Ocean Ridge Biosciences offers cost-effective ultra-deep sequencing of targeted genes to analyze genetic variants in solid tumors, cell-free DNA (cfDNA), and genomic DNA. Utilizing highly parallel multiplex next-generation sequencing of PCR amplicons, ORB's oncogene panel, or oncopanel, sequencing and analysis enables investigation of cancer-related genes or genomic regions, such as tumor suppressor genes such as BRCA1 or TP53, and oncogenes that can turn healthy cells into cancer cells. The focused nature of oncopanels can reduce costs and increase the speed of genomic studies because only a limited set of genes are interrogated. Additional benefits include advanced detection of low-frequency variants with deeper sequencing options and production of more manageable datasets than traditional whole genome sequencing studies.

Sample Types and Sample Submission Instructions

  • Tumor biopsies
  • Genomic DNA (gDNA)
  • Cell-free DNA (cfDNA)
 
Sample Type Minimum Input Requirement Sample Submission Checklist
Tumor tissue 10 mg Tissue
Genomic or cell-free DNA 10 ng gDNA / cfDNA 
Biofluid 4 ml Biofluid 
ORB provides cfDNA extraction services with blood-based biofluid samples and genomic DNA isolation from tumor tissues. ORB is a Biosafety Level 2 (BSL-2) laboratory, and can accept samples that contain agents associated with human diseases.


Common Oncology Areas Utilizing Oncopanels

  • Breast cancer
  • Melanoma
  • Colorectal cancer
  • Pancreatic cancer
  • Ovarian cancer
  • Prostate cancer
  • Non-small cell lung cancer
  • Renal cell carcinoma

ORB’s Oncogene Analysis Service

ORB offers analysis of numerous genetic variant types using oncopanels from industry leading manufacturers where starting materials are optimized for low-input and degraded samples, e.g. FFPE tissues. Many panels require as little as 10 ng of gDNA per sample, please see Table I for a list of available panels and associated variant types. Contact us to determine which panel would be most appropriate for your cancer investigation.

Table I. Oncopanels available for analysis using ORB's oncogene analysis service.

Manufacturer Panel Genes Cancer Type FFPE Variant Types
          Germline Somatic INDELS SNPs Gene Fusions Structural Copy Number Loss of Heterozygosity Chromosomal Abnormalities Short Tandem Repeats
Illumina TruSight Cancer Sequencing 94 Pan-Cancer   Yes                  
Illumina TruSight Tumor 15 15 Solid Tumor Yes   Yes Yes              
Illumina TruSight Myeloid Sequencing Up tp 54 Hematological     Yes Yes              
Illumina TruSeq Amplicon – Cancer 48 Pan-Cancer Yes   Yes Yes              
Illumina TruSight RNA Pan-Cancer 1385 Pan-Cancer Yes                    
Illumina TruSight Tumor 170 170 Solid Tumor Yes   Yes Yes Yes Yes Yes Yes      
Illumina TruSight RNA Fusion 507 gene fusion events Pan-Cancer Yes         Yes          
Illumina TruSight Custom Amplicon Low Input Up to 1536 amplicons Pan-Cancer Yes Yes Yes Yes Yes Yes Yes   Yes Yes Yes
Swift Biosciences Accel-Amplicon 56G Oncology Panel v2 56   Yes Yes Yes Yes              
Swift Biosciences Accel-Amplicon BRCA1 and BRCA2 2   Yes Yes Yes Yes              
Swift Biosciences Accel-Amplicon BRCA1, BRCA2, and PALB2 3   Yes Yes Yes Yes              
Swift Biosciences Accel-Amplicon Comprehensive TP53 1   Yes Yes Yes Yes              
Swift Biosciences Accel-Amplicon EGFR Pathway 4   Yes Yes Yes Yes              

Contact Us to learn how ORB’s oncopanel service can facilitate a deep view of the genetics in your oncology research!