Detailed description
Operating principle
Comprehensive solution based on hybrid capture technology for the targeted analysis of genes involved in the homologous recombination repair (HRR) pathway.
The assay provides an efficient workflow starting with a recommended input of 50 ng of DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tumour tissue or fresh-frozen tissue. Library preparation produces sequencing-ready libraries in just 1.5 days, with an automation option and minimal hands-on time.
The portfolio can be flexibly scaled across three capture-panel configurations according to the laboratory’s objectives:
| Feature | mini HRS | HRS | Extended HRS (ExtHRS) |
|---|---|---|---|
| Genes included | 4 genes BRCA1, BRCA2, RAD51C, TP53 |
16 genes ATM, BARD1, BRCA1, BRCA2, BRIP1, CDK12, CHEK1, CHEK2, FANCL, PALB2, PPP2R2A, RAD51B, RAD51C, RAD51D, RAD54L, TP53 |
28 genes AKT1*, ATM, BARD1, BRCA1, BRCA2, BRIP1, CCNE1, CDK12, CHEK1, CHEK2, ESR1*, FANCA, FANCD2, FANCL, FGFR1*, FGFR2*, FGFR3*, MRE11, NBN, PALB2, PIK3CA*, PPP2R2A, PTEN, RAD51B, RAD51C, RAD51D, RAD54L, TP53 |
| Sample type | FFPE, fresh-frozen tissue | FFPE, fresh-frozen tissue | FFPE, fresh-frozen tissue |
| DNA input | 50 ng recommended | 50 ng recommended | 50 ng recommended |
| Reads per sample (2×150 bp) | 1.6 million | 4.7 million | 8 million |
| Compatible sequencing platforms |
Illumina MiSeq® (v3)
Illumina MiSeq® (v2)
Ion Torrent™ Ion S5™ System
|
Illumina MiniSeq™
Illumina MiSeq® (v3)
Illumina MiSeq® (v2)
|
Illumina® NextSeq® 500/550a Also compatible with NovaSeq® sequencers |
HRD analysis and how GIInger™ works
Although all three panels can identify point mutations and indels in HRR pathway genes, only the Extended HRS (ExtHRS) solution can assess overall Homologous Recombination Deficiency (HRD) status. This assessment requires the complementary use of GIInger™, an advanced algorithm based on deep learning.
GIInger™ has been specifically trained to recognise genomic signatures and “scars” characteristic of DNA damage (genomic scars).
The algorithm analyses genomic instability (GI) profiles obtained through low-coverage whole-genome sequencing (lpWGS, low-pass Whole Genome Sequencing).
Based on these large-scale structural instability patterns, the system objectively calculates genomic integrity status and classifies the sample as HRD-positive or HRD-negative. This provides key predictive information that goes beyond the isolated detection of variants in susceptibility genes.
Clinical applications
This tool is intended for research into the mutational profile of the homologous recombination repair (HRR) pathway in FFPE or fresh-frozen tissue samples. Its applications include in-depth molecular characterisation of several types of cancer, such as ovarian, breast, prostate, colorectal, lung and pancreatic cancer.
Benefits
Technology
SOPHiA DDM™ HRS solutions use targeted hybrid capture technology and next-generation sequencing (NGS) to analyse genes involved in the homologous recombination repair (HRR) pathway. The assays incorporate SOPHiA GENETICS™ Universal Library Prep for library preparation and specific capture probes to enrich the coding regions and splice sites of the genes included in each panel. Bioinformatic analysis is performed using the SOPHiA DDM™ platform, enabling the detection of SNVs, indels and gene amplifications, as well as automated interpretation of the identified alterations.
Intended users
Additional considerations
Key features
Product details
| Feature | SOPHiA DDM™ mini HRS | SOPHiA DDM™ HRS | SOPHiA DDM™ ExHRS |
|---|---|---|---|
| Samples |
Up to 24 samples for Illumina MiniSeq™ kit
Up to 32 samples for Illumina MiSeq® kit v3
Up to 24 samples for Illumina MiSeq® kit v2
|
Up to 8 samples for Illumina MiSeq® kit v3
Up to 4 samples for Illumina MiSeq® kit v2
Up to 16 samples for Ion Torrent™ Ion S5™ System
|
Up to 32 samples for Illumina® NextSeq® 500/550 Mid Output Kita |
| Product codes |
BS0111ILLRSMY05-16; BS0111ILLRSMY05-32; BS0111ILLRSMY05-48 |
MiSeq®: BS0108ILLRSMY05-16; BS0108ILLRSMY05-32; BS0108ILLRSMY05-48 IonTorrent™: BS0108TFSRSML03-016; BS0108TFSRSML03-032 |
BS0128ILLRSMY10-16; BS0128ILLRSMY10-32; BS0128ILLRSMY10-48; BS0128ILLRSMY10-96 |
BS0111ILLRSMY05-32;
BS0111ILLRSMY05-48
BS0108ILLRSMY05-16;
BS0108ILLRSMY05-32;
BS0108ILLRSMY05-48
IonTorrent™:
BS0108TFSRSML03-016;
BS0108TFSRSML03-032
BS0128ILLRSMY10-32;
BS0128ILLRSMY10-48;
BS0128ILLRSMY10-96
