Principle of operation
The SOPHiA DDM™ Community Liquid Biopsy Solution 21 genes
has been developed and tested by genomic experts. The solution combines
a capture-based targeted enrichment kit with the advanced analytical
capabilities of the SOPHiA DDM™ platform, which detects, annotates and
pre-classifies genomic alterations in the genes included in the panel.
The workflow starts with cfDNA extracted from peripheral blood and requires
an input of more than 20 ng of cfDNA. Library preparation incorporates
CUMIN® molecular barcodes to support the sensitive detection of
low-frequency variants. The method uses hybridisation-based capture
enrichment and deep 20,000× coverage in selected regions.
Gene list
21 genes: AKT1, ALK, BRAF, BRCA1, BRCA2, EGFR, ERBB2,
ESR1, FGFR2, FGFR3, IDH1, KIT, KRAS, MET, NRAS, PALB2, PDGFRA, PIK3CA,
RET, ROS1 and TP53.
Clinical applications
The panel covers 21 oncogenes and tumour suppressor genes selected
according to ESMO recommendations and expert knowledge. It is intended
for research into alterations associated with multiple tumour types,
including breast, colorectal, prostate, non-small cell lung, thyroid,
melanoma, ovarian, pancreatic, gastric, cholangiocarcinoma, urothelial,
GIST and hepatocellular carcinoma, among others listed in the association
table included in the document.
MSI-H: the solution also includes MSI-H as an indication
associated with immunotherapy. However, MSI status is investigational
and has not been verified or validated in cfDNA.
Benefits
The SOPHiA DDM™ platform facilitates the assessment and reporting of
genomic variants through algorithm-assisted variant pre-classification,
fully customisable filters and comprehensive report generation. These
functions allow users to focus the analysis on relevant genomic
alterations and tailor reports to their requirements.
The optional OncoPortal™ Knowledge Base module links tumour molecular
profiles with clinical associations and available clinical trials,
using expert-curated evidence and content powered by the Genomenon
Cancer Knowledgebase.
The solution is also supported by the SOPHiA GENETICS™ community,
where genomic experts from multiple institutions interpret findings
and assign pathogenicity levels to variants, securely enriching the
shared knowledge base for research purposes.
Intended users
This solution is intended for genomic research users and laboratories
working with liquid biopsy samples that require analysis of somatic
alterations in cfDNA, with assisted interpretation, configurable filters
and integrated reporting within SOPHiA DDM™.
The document also highlights the support provided through the SOPHiA DDM™
MaxCare Program, including assistance with assay implementation, local
support and access to bioinformaticians for troubleshooting workflow issues.
Considerations and limitations
For Research Use Only; not for use in diagnostic
procedures.
MSI analysis is investigational and has not been verified or
validated in cfDNA.
CNV detection is limited to selected genes.
The reported sensitivity performance for SNVs and Indels is based on
15 real samples. Specificity, precision and accuracy are based on
reference materials.
For Research Use Only. Not for use in diagnostic procedures.
Key features
Panel covering 21 oncogenes and tumour suppressor genes.
Designed for cfDNA extracted from peripheral blood.
Required input: more than 20 ng of cfDNA.
Detection of SNVs, Indels, selected CNVs, fusions and MSI status.
Reporting threshold for SNVs and Indels: above 0.2% VAF.
CUMIN® molecular barcodes for sensitive detection of low-frequency
variants.
Capture-based targeted enrichment with deep 20,000× coverage in
selected regions.
Library preparation and capture completed in 1.5 days when overnight
hybridisation is performed.
Integration with SOPHiA DDM™ for detection, annotation,
pre-classification, filtering and report generation.
Implementation support through the SOPHiA DDM™ MaxCare Program.
Product details
| Product type |
Bundle solution: wet-lab reagents and credits for the
cloud-based SOPHiA DDM™ web platform.
|
| Product ID (CE-IVD) |
BS0121ILLCSMY08-32 |
| Product ID (RUO) |
BS0127ILLRSMY10-16
BS0127ILLRSMY10-32
BS0127ILLRSMY10-48
|
| Sample type |
FFPE |
What does the solution include?
SOPHiA GENETICS Universal Library Prep reagents for library
preparation from fragmented DNA.
Hybridisation probes for targeted capture.
Full access and credits for secondary and tertiary analysis on the
SOPHiA DDM™ platform.
Required reagents and materials not included in the kit
Genomic DNA extraction kits for FFPE samples.
Equipment and reagents for fluorometric quantification and nucleic
acid quality control, such as Qubit™, TapeStation™ or equivalent
systems.
Platform-specific Illumina sequencing reagents and Illumina PhiX v3
control.
