By Dr. Chaitanya Ekkirala, Lab Director, NGS Operations, MedGenome Inc
The discovery of genetic and epigenetic mechanisms underlying the onset and progression of numerous diseases, including cancer, has helped redefine clinical research, diagnostic and treatment paradigms. Oncology research and diagnostics have undergone radical changes because of the development of next-generation sequencing (NGS). NGS has improved rationally designed personalized cancer medicine by identifying novel cancer mutations, detecting circulating tumor DNA (ctDNA), and discovering causative mutations for hereditary cancer syndrome. With NGS, it is now possible to sequence the whole genome, whole exome, whole transcriptome, or just targeted genes to provide detailed genomic landscape descriptions for many cancers.
MedGenome is committed to providing the highest-quality NGS services for research and clinical development. Our expert scientific team and laboratory facility with cutting-edge sequencing platforms, including NovaSeq, MiSeq, and 10X Chromium Controller, guarantee highly optimized protocols, customized solutions, and quick turnaround times.
Targeted panel for Oncology mutational profiling using TSO-500
MedGenome offers comprehensive genomic profiling of tumor samples using the TruSight Oncology 500 (TSO-500) from Illumina. The TSO-500 is a pan-cancer NGS assay with broad availability, rapid turnaround time, and a standardized bioinformatics pipeline that identify key genomic signatures for clinical research and immuno-oncology. The panel includes 523 cancer-relevant gene variants and 55 RNA variants that provide comprehensive coverage of biomarkers (Figure 1) frequently mutated in multiple cancer types.
The assay is designed to detect
- • Single nucleotide variants (SNVs)
- • Insertions/deletions (InDels)
- • Copy number variations (CNVs)
- • Novel transcript fusions
- • Splice variants
In addition, the TSO-500 panel also reports the key immunotherapy biomarkers, i.e. tumor mutational burden (TMB) and the microsatellite instability (MSI) status that correlates with response to immune-checkpoint inhibition.
TSO-500 employs a highly standardized single integrated workflow for both DNA and RNA input material. Library preparation involves a hybridization capture-based target enrichment strategy. High analytical specificity is achieved by adding unique molecular identifiers (UMIs) during library prep, which allows the detection of gene variants even at low variant allele frequency (VAF) while simultaneously suppressing errors. Sequencing reactions are carried out using fluorescence-labelled oligonucleotides, and an off-the-shelf bioinformatics pipeline provides robust and reliable results.
- • Variable sample types and throughput
MedGenome offers flexible and scalable genomic profiling from tumor biopsies, FFPE tissues, and liquid biopsies (to detect ctDNA) using the Illumina TruSight Oncology 500 portfolio (Figure 2). The platform also allows analysis of sample sizes ranging from 8-192 samples, even allowing accurate detection in low input samples (from 30ng DNA and 40ng RNA input material).
- • Easy ctDNA detection from liquid biopsies
Noninvasive plasma-based assays have emerged as an important complementary diagnostic approach to tissue-based assays which is not feasible for repeated sampling or inaccessible tissues. Further, single biopsies lack information on tumor heterogeneity. Blood plasma contains tumor cell fragments and DNA from apoptotic or necrotic cancer cells providing information on cancer aggressiveness, progression and therapeutic outcomes. The TSO-500 ctDNA assay enables non-invasive, comprehensive genomic profiling of ctDNA from simple blood draws to evaluate >500 gene variant classes in a single assay.
- • Optimized data Analysis
The variant calling algorithms are optimized to eliminate errors, artefacts, and germline variants for high accuracy and analytical specificity (99.9998%). Data interpretation and reporting are powered by PierianDx Clinical Genomics Workspace (CGW), which filters and prioritizes biologically relevant variants providing an automated and customizable genomic report.
- • Accurate TMB and MSI analysis
TSO-500 assay implements an error-corrected sequencing and informatic pipeline that provides an accurate quantitative score for MSI status and a precise and reproducible TMB value. TMB calculation involves the measurement of both nonsynonymous and synonymous SNVs and InDels based on specific criteria. The results were shown to have high concordance with whole-exome studies.
- • High sensitivity
Using the TSO-500 platform, we provide highly sensitive variant detection for CNVs with a limit of detection at 2.2× fold-change. In addition, the TSO-500 library prep protocol implements high binding specificity to hybridize to targets containing small mutations and SNVs, even from low-quality DNA samples and FFPE tissues. The assay reproducibility has been verified in FFPE samples with a VAF as low as 5%. Furthermore, with regards to the detection of RNA fusions, the hybrid-capture method accurately captures gene fusions from both known and novel fusion gene partners, even from FFPE samples where RNA yields can be >= 40ng.
The MedGenome Advantage
MedGenome offers end-to-end customized solutions for comprehensive genomic profiling of small and large-scale tumor samples to accelerate your clinical research and diagnostics R&D. We have expertise in processing a variety of sample types, including biopsies, FFPE tissue (DNA & RNA), and blood plasma (ctDNA) for DNA sequencing. Our scientific team can also provide solutions to challenging sample processing and high-throughput samples.
Utilizing the TruSight targeted panel we provide exclusive services and advantages:
- • Multiplexing solutions – Save time and samples by analyzing multiple tumor variant types in 523 genes in a single assay
- • Speed – Streamlined validated workflow with quick turnaround times for TSO-500 assay
- • Powerful bioinformatics pipelines – Additional insights on drug-gene interactions, identification of actionable mutations, and comprehensive reports
- • High-throughput processing – Scientific expertise and state-of-the-art lab facility for large sample sizes suitable for clinical research
- • TST170 Panel for ctDNA – We have validated the TruSight Tumor 170 panel on ctDNA samples for assessment of SNVs and indels in 151 genes, amplifications in 59 genes, and fusions plus splice variants in 55 genes.
Need more insights on tumor profiling using NGS?
- 1. Zhao, Chen & Jiang, Tingting & Ju, Jin & Zhang, Shile & Tao, Jenhan & Fu, Yao & Lococo, Jenn & Dockter, Janel & Pawlowski, Traci & Bilke, Sven. (2020). TruSight Oncology 500: Enabling Comprehensive Genomic Profiling and Biomarker Reporting with Targeted Sequencing. 10.1101/2020.10.21.349100.
- 2. https://sapac.illumina.com/content/dam/illumina-marketing/documents/products/technotes/trusight-umi-rare-variant-technote-1000000050426.pdf
- 3. https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/trusight-oncology-500-data-sheet-m-gl-00173/trusight-oncology-500-and-ht-data-sheet-m-gl-00173.pdf
- 4. Wei, B., Kang, J., Kibukawa, M., Arreaza, G., Maguire, M., Chen, L., Qiu, P., Lang, L., Aurora-Garg, D., Cristescu, R., & Levitan, D. (2022). Evaluation of the TruSight Oncology 500 Assay for Routine Clinical Testing of Tumor Mutational Burden and Clinical Utility for Predicting Response to Pembrolizumab. The Journal of molecular diagnostics: JMD, 24(6), 600–608. https://doi.org/10.1016/j.jmoldx.2022.01.008
##Tumor profiling, #Oncology, #Next-generation sequencing, #Whole genome, #Whole exome, #Whole transcriptome, #circulating tumor DNA, #ctDNA, #10X Chromium, #TSO-500, #TruSight Oncology, #Tumor mutational burden (TMB), #Microsatellite instability (MSI), #Genomic profiling, #Liquid biopsies, # Multiplexing solutions, #Powerful bioinformatics pipelines