GALEAS™ Tumor
Cancer Genomic Profiling
Features of GALEAS™ Tumor
Enhanced, Current and Clinically Relevant Content
Curated according to the guidelines of the UK NHS National Genomic Test Directory, NCCN, FDA, and ESMO, this panel profiles clinically significant biomarkers across 519 genes and provides Tumor Mutational Burden (TMB) and Microsatellite Instability (MSI) scores. It includes 64 pharmacogenomics SNPs, content related to hereditary and pediatric cancers, HLA profiling for solid tumors, structural variants, and enhanced CNV coverage.
Detection of Key Tumor Immune-Oncology biomarkers
GALEAS™ Tumor is designed with a focus on the analysis of TMB and MSI, providing integrated measurements of tumor genomic instability that can be used to predict positive responses to immunotherapy.
Support by GALEAS™ Analysis Software
The cloud-based GALEAS analysis software, developed in parallel with the panel, provides a solution for the rapid and accurate calling of SNV, INDEL, SV, CNV, TMB, and MSI.
Panel Design
This next-generation sequencing (NGS) solution covers driver mutations including SNV, INDEL, CNV, and several fusion genes across 519 genes. It also supports the analysis of immuno-oncology biomarkers such as TMB (tumor mutation burden) and MSI (microsatellite instability). While focusing on exons, a CNV backbone has been added to support the calling of copy number variations (CNV), and important intron and promoter regions are also covered.
This design, curated by Nonacus, includes:
- Common driver mutations including SNVs, CNVs and INDELs in 519 genes
- CNV backbone enabling enhanced CNV calling to a >1Mb resolution
- Enhanced coverage of the 1p/19q codeletion associated with Glioma
- Fusion/Structural rearrangements including: ALK, BRAF, EGFR, FGFR2, FGFR3, NTRK1, NTRK2, RET, ROS1, TMPRSS2
- 64 Pharmacogenomics (oncology) SNPs
- HLA genes relevant for solid tumors
- Identity tracking SNPs
High-Precision Detection of SNV and INDEL
The validation was evaluated using FFPE reference samples containing 23 SNVs and INDELs previously confirmed by ddPCR. A strong correlation was observed between the VAF (variant allele frequency) determined by NGS and ddPCR, yielding an R² of 0.99 at an average depth of 500x (Figure 1).
Variant Calls in Primary Tumors
GALEAS™ Tumor demonstrated a 100% reproducibility/accuracy rate when comparing somatic mutations in 50 CRC samples to other data*. (*Orthogonal data for BRAF, KRAS, and NRAS is available.)
High-Precision Detection of Copy Number Variants (CNV)
To accurately detect copy number variants (CNV), the system is equipped with a backbone that enhances CNV calls at a resolution greater than 1 Mb. A comparison between this CNV backbone data and sWGS (Shallow Whole Genome Sequencing) revealed a strong correlation between the profiles (Figure 3).
Scoring of Microsatellite Instability (MSI)
The GALEAS™ Tumor MSI scores for control reference samples, normal samples without cancer, and colorectal cancer (CRC) FFPE samples were compared to known MSI statuses. The GALEAS™ analysis software confirmed that all MSS (Microsatellite Stability) CRC and normal FFPE samples were indeed MSS and normal, respectively.
Furthermore, 23 out of 24 MSI-High CRC FFPE samples were confirmed as MSI-H (Figure 4).
To evaluate the sensitivity of CNV genotyping, samples with different copy numbers were assessed using GALEAS™ Tumor. The three samples evaluated had known copy number variations in EGFR and MET, containing 3, 6, and 12 copies, respectively (Figure 5).
Tumor Mutational Burden (TMB)
TMB is an important immuno-oncology biomarker and has been shown to have a strong correlation with MSI status in colorectal cancer. In a CRC cohort, a strong correlation was observed between the TMB scores derived from GALEAS™ Tumor (median TMB 28.24, log2 TMB 1.45) and the corresponding MSI status of the samples (Figure 6).
Achieving More Efficient Sequencing with High On-Target Rates and Excellent Coverage Uniformity
We provide high on-target rates, more uniform coverage, and enhanced coverage of clinically relevant genes. This superior technical performance enables high reproducibility and accuracy across a greater number of variants.
GALEAS™ Analysis Software
The GALEAS™ Analysis Software maximizes the performance of the panel. Developed in parallel with the panel, this software provides a robust and reliable bioinformatics solution.
In small panels, obtaining accurate and reproducible TMB values at low mutation levels can be challenging. However, GALEAS™ Tumor combines comprehensive genomic content with validated bioinformatics to deliver precise TMB scoring and indicators of MSI status.
Summary
GALEAS™ Tumor is a clinically validated comprehensive NGS solution that enables the analysis of SNV, CNV, INDEL, and TMB/MSI across 519 genes within a single NGS workflow.
Enhanced probe design, comprehensive gene coverage, and high coverage uniformity allow for accurate and sensitive detection of SNV, INDEL, SV, and CNV. When combined with the GALEAS™ Analysis Software solution, it offers a simple and user-friendly workflow from sample preparation to analysis.
References
- Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C. Emerging landscape of oncogenic signatures across human cancers. Nature genetics. 2013;10):1127-33.
- The ICGC/TCGA PanCancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Na- ture. 2020: 82-93.
- Endris V, Buchhalter I, Allgäuer M, Rempel E, Lier A, Vol- ckmar AL, et al. Measurement of tumor mutational bur- den (TMB) in routine molecular diagnostics: in silico and real-life analysis of three larger gene panels. International journal of cancer. 2019;144(9):2303-12.
- Schrock AB, Ouyang C, Sandhu J, Sokol E, Jin D, Ross JS, et al. Tumor mutational burden is predictive of response to immune checkpoint inhibitors in MSI-high metastatic colorectal cancer. Annals of Oncology. 2019;30(7):1096-103.
Panel Specifications
| Parameters | Specification |
|---|---|
| Enrichment method | Hybridization and capture |
| Number of genes | 519 |
| Capture Panel Size | 3.74Mb |
| Sequencing platform | Illumina |
| Targets | Genes associated with common cancers |
| Variant types | SNVs, CNVs and indels |
| Input DNA requirements | 10ng-200ng |
| Sample type | gDNA from FFPE, frozen tissue or blood |
| Multiplexing guidance for sequencing | 25M reads per sample required to achieve 500x. This equates to 5Gb per sample |
Ordering Information
| Product Name | Catalogue No. |
|---|---|
| GALEAS Tumor Kit Frag A (96 samples) | NGS_GAL_TCP_FR_96_A |
| GALEAS Tumor Kit Frag B (96 samples) | NGS_GAL_TCP_FR_96_B |
| GALEAS Tumor Kit Frag C (96 samples) | NGS_GAL_TCP_FR_96_C |
| GALEAS Tumor Kit Frag D (96 samples) | NGS_GAL_TCP_FR_96_D |
| GALEAS Tumor Kit Frag (16 samples) | NGS_GAL_TCP_FR_16 |
- A: Adapter plate with indexes 1–96
- B: Adapter plate with indexes 97–192
- C: Adapter plate with indexes 193–288
- D: Adapter plate with indexes 289–384
