SOPHiA Hereditary Cancer Solutions

Confidently assess genetic variants predisposing to cancer
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SOPHiA Hereditary Cancer Solutions are NGS-based applications that enable you to accurately characterize the complex mutational landscape associated with major hereditary cancer disorders.


All the solutions have been conceived to overcome sequencing bias, maximize performance, combining an expertly designed capture-based target enrichment kit with the analytical capabilities and interpretation-support functionalities of the SOPHiA DDM™ platform. Our pre-designed applications help you increase the efficiency of your laboratory, offering an end-to-end approach (from sample to variant report) to turn high-quality data into valuable insights.
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Highlights

  • Ready-to-sequence target enriched library in just 1.5 days
  • Optimized automation protocols for a variety of liquid handling robots to support high-throughput analyses
  • Customizable content with 143 cancerpredisposing genes to meet your specific research laboratory needs
  • Accurate detection and annotation of challenging variants, including SNVs, long Indels and CNVs in a single assay
  • Streamlined interpretation through intuitive variant filters, machine learning-based variant classification (complementing the ACMG ranking), and access to one of the largest networks of connected healthcare institutions to gain and share knowledge on relevant variants
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Specifications

Parameters HCS Community panels
Covered genes 26 + PMS2CL 37 + PMS2CL 50 143
Target regions 105 kb 92 kb 177 kb 405 kb
Sample source Blood Blood Blood Blood
DNA input 200 ng 200 ng 200 ng 200 ng
Sequencer compatibility - Illumina MiniSeq™, MiSeq®, NextSeq® 500/550 - Thermo Fisher Scientific: Ion Proton™, Ion S5™ Illumina MiSeq® Illumina MiSeq® Illumina NextSeq®500/550
Library Prep Time 1.5 days 1.5 days 1.5 days 1.5 days
Analysis time from FASTQ file 4 hours 4 hours 4 hours 4 hours
Detected Variants - SNVs - Indels - CNVs - Alu insertions - PMS2 vs PMS2CL variants - Boland inversion - SNVs - Indels - CNVs - Alu insertions - PMS2 vs PMS2CL variants - SNVs - Indels - CNVs -Alu insertions   - SNVs - Indels - CNVs - Alu insertions  

Please note that the SOPHiA Hereditary Cancer Solutions cover exclusively germline mutations.

Deeply assessed to not miss any variant


The SOPHiA Hereditary Cancer Solution (HCS) accuracy has been assessed through a multicenter performance evaluation study on 159 samples with 373 unique variants coming from 7 sequencing centers. The study showed:

  • High on-target rates and coverage uniformity

  • High-confidence calling of SNVs, Indels and CNVs in all genes of the panel

  • Reliable detection of complex variants, such as Alu insertions

  • PMS2 and PMS2CL variants

Performance
measurement

Observed

Lower 95% CI

Sensitivity 100% 99.20%
Specificity 100% 99.99%
Accuracy 100% 99.99%
Precision 99.86% 96.42%
Repeatability 99.98% 99.98%
Reproducibility 99.93% 99.93%

Values have been calculated for SNVs and Indels only from a total of 159 samples processed on MiSeq®

Dedicated features to ease variant interpretation

The SOPHiA DDM™ platform features intuitive variant filters and prioritization options to streamline the interpretation process and help you significantly reduce turnaround time.

Dual Variant Pre-classification to improve assessment of variants pathogenicity based on both ACMG scores and our machine learning predictions
Virtual Panels to restrict the interpretation to sub-panels of genes using the HPO or OMIM browser
Cascading Filters to apply custom filtering options for quicker screening of relevant variants and save strategies for future analyses

Through SOPHiA DDM™, you can also have access to Alamut Visual Plus, a fullgenome browser that integrates numerous curated genomic and literature databases, guidelines, missense and slicing predictors, thus enabling a deeper variant exploration.

Data pooling and knowledge sharing

Automated workflow to increase your productivity

HCS can be coupled with leading liquid handling robots for a fully automated library preparation. As a result, you can benefit from a standardized workflow, that provides high quality libraries for reliable sequencing while also increasing sample throughput and decreasing required hands-on time to as little as 1.45 hours.

Read the experience of an Italian genomic laboratory, that easily automated the library preparation workflow of HCS on the Hamilton STARlet robot. The automated workflow shows a very uniform coverage of the target region with high-on target rate read percentage and robust detection of multiple type of variants, including long Indels and gene
conversion events.

Discover the experience of a French client, who efficiently adopted an automated the HCS library preparation protocol on the Zephyr® G3 NGS workstation. The resulted workflow enables high throughput sample processing without any decrease in data quality compared to manual preparation – but also increases productivity of the workforce with minimal hands-on time, freeing staff.

Read More

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New germline mutations in BRCA1, ATM, MUTYH, and RAD51D genes in Tuvans early-onset breast cancer patients.

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A Novel ATM Pathogenic Variant in an Italian Woman with Gallbladder Cancer.
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Automated Capture-Based NGS Workflow: One Thousand Patients Experience in a Clinical Routine Framework.

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Characterization of New ATM Deletion Associated with Hereditary Breast Cancer.
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