Source:IVD Professional Self-MediaIVD Tool Person
Roche is preparing to launch the fully automated version of its tissue-based Comprehensive Genomic Profiling (CGP) sequencing kit, which the company claims will enable translational oncology researchers toComplete library preparation and target enrichment within 24 hours, with only 3.5 hours of hands-on operation time.
The upcoming Avenio Tumor Tissue CGP Automation Suite will also include a new pan-cancer Homologous Recombination Deficiency (HRD) signature score.Called HRDsig. This score is trained based on the pan-cancer genomic database of Roche's subsidiary, Foundation Medicine, covering more than 100 unique genomic features.
Researchers from Roche and early user Circulogene presented early data of the planned products at the company-sponsored workshop and several posters during the Annual Meeting of Molecular Pathology held last week in Vancouver, British Columbia.
At the seminar, Austen Cohen, international business leader of Roche Diagnostics, stated that automated assays would beFebruary 2025 launch.
The kit will follow the launch of the Avenio Tumor Tissue CGP Kit V2, which was quietly released in July this year as an update to the first-generation kit launched in 2021.
The update already includes the HRDsig score, and its interpretation is supported by Roche's Navify Mutation Analysis software.
HRD as a Biomarker is Becoming Increasingly Important in Several Cancer Types
Roche’s Global Head of Medical Affairs and Strategy, Muriel De Vos, noted at the symposium that HRDsig is a comprehensive scar-based signature that provides a functional pan-cancer HRD readout (HRD “scars” typically refer to a series of genetic alterations or patterns in the cancer cell genome indicative of HRD). Importantly, De Vos pointed out: HRDsig is designed to provide "Independent of genetic alteration predictions, enabling the detection of HRD through non-genomic mechanisms."Therefore,This signature captures the majority of biallelic BRCA cases, as well as other homologous recombination repair (HRR) gene mutations and HRR wild-type cases, which may have true HRD.
In addition to HRDsig, the current Avenio CGP V2 and the upcoming automation kit also examine single nucleotide variants, insertions and deletions, copy number alterations, and selective gene rearrangements in tumor tissue samples, covering 355 genes, and provide additional genomic signatures such as microsatellite instability, tumor mutation burden, and loss of heterozygosity.
Automated CGP WorkflowIncluding the Avenio kit, Roche Avenio Edge liquid handling system, Illumina NovaSeq 6000 sequencing, and FoundationOne data analysis software, all of which are coordinated through the Avenio Connect software.
Cohen pointed out that the Avenio Edge instrument is an open platform that can be used with any NGS workflow, but "is very well optimized for this new workflow." The kit reagents come preloaded in cartridges, and users only need to remove the packaging and place them on the instrument, making it "different from any CGP workflow on the market," he said.
Roche pointed out that this workflow improves laboratory efficiency, minimizes human errors, and reduces the total turnaround time, with complete reports available in less than five days.
This appears to be similar or superior to other commercially available CGP kits or services currently on the market. For instance, Illumina notes on its website that its TruSight Oncology Comprehensive kit is run in local laboratories, such as Roche’s kit, with a sample-to-report turnaround time of four to five days.
Meanwhile, the Labcorp Tissue Complete service, supported by the PGDx Elio assay, advertises a turnaround time of six to thirteen days, while the Guardant Health Guardant360 TissueNext service states a turnaround time of less than two weeks from sample receipt to results.
The primary competitive test in HRD is Myriad Genetics' MyChoice HRD test, an FDA-approved service that helps identify HRD patients and may assist in determining whether patients with breast or ovarian cancer are suitable candidates for PARP inhibitor therapy. Myriad advertises that results can be returned "within 14 days or less" after receiving the tumor specimen.
Moreover, just last week, Myriad announced that Illumina is adding its Genomic Instability Score (GIS) to the Illumina TruSight Oncology 500 v2 assay currently under development, which is scheduled for global release in mid-2025. The updated assay will feature a faster turnaround time and reduced hands-on time compared to earlier versions, along with sensitive variant calling and Myriad’s GIS for determining HRD status, the two companies noted.
At the AMP conference, Eric Thompson, vice president of translational research at liquid biopsy developer and early adopter Circulogene, noted that CGP is a "very complex workflow" that is both time-consuming and labor-intensive, involving large gene panels and constant changes. He said his company primarily uses CGP because it offers greater insight than single-gene testing.
When evaluating the reproducibility of the Avenio automated CGP assay, Circulogene researchers found their data to be highly consistent with that produced by Roche, particularly for genomic signature scores. He also reported that the average time to load and run the assay was less than an hour, even shorter than advertised by Roche.
"It works in our hands - completely - with very high consistency and very robust results," he said. "Just discussing with my team... about bringing this assay into our lab, the first thing is: it works. That's key. We can't compromise on quality when testing samples from subjects. The automation kit is truly reliable."
Thompson pointed out that one of the disadvantages of the system is that a failed run can invalidate the reagents on standby on the platform, and the barcoded cartridges prevent future use. Additionally, he noted that if there is an error, clearing the loading check error takes a long time.
In an email, Sunandini Chopra, Senior Product Manager at Roche, stated that this was "a deliberate feature to ensure that any observed errors have been corrected, and then prompt users to rerun the loading check process from the beginning, ensuring all errors are cleared. Designing the system in this way helps ensure that failures in subsequent processes can be avoided and operations can proceed as intended."
Chopra said that other early users include laboratories in Belgium and Ireland, although Roche is currently unable to disclose their identities. She also pointed out that other features of the automation suite include an overall pass rate of 99.3% from FFPE tissue DNA extraction to sequencing results, compatibility with small biopsy samples, a very low contamination rate of 0.11%, and high analytical sensitivity in detecting small mutations, with a limit of detection ranging from 1% to 3.1% — all of which were provided by the company in its AMP poster.
Roche emphasized that the Avenio CGP V2 Kit and Automation Kit are for research use only.
"In the short term, providing internal CGP testing, software, and systems for research use allows us to continuously improve and innovate our assays, helping our customers stay at the forefront of scientific advancements," said Chopra.
"Roche’s intention is to align with all regulatory bodies in markets interested in our solutions," she added. "As the regulatory landscape for laboratory-developed tests and the implementation in different countries remains an evolving environment, we are carefully evaluating when and how to pursue IVD for each of our solutions and welcome partnerships."
Summary
Roche's Avenio Tumor Tissue CGP Automated Kit has the following advantages:
Rapid library preparation and target enrichment: This kit can complete library preparation and target enrichment in approximately 24 hours, with only 3.5 hours of manual operation time, significantly improving research efficiency.
Comprehensive Genomic Analysis: The kit can detect single nucleotide variants, insertions and deletions, copy number alterations, and selective gene rearrangements in tumor tissue samples, covering 355 genes, and provides additional genomic signatures such as microsatellite instability, tumor mutational burden, and loss of heterozygosity.
New HRD Signature Score: Includes a new pan-cancer homologous recombination deficiency signature score HRDsig, which helps determine HRD status across multiple cancer types, particularly in breast or ovarian cancer patients, potentially aiding in identifying suitability for PARP inhibitor therapy.
High Consistency and Robust Results: Circulogene researchers found in the evaluation that this automated kit is highly consistent with Roche's data, especially in terms of genomic signature scores.
Reduce Human Errors and Improve Lab Efficiency: Automated workflows reduce the possibility of human error and improve laboratory efficiency.
Rapid Report Generation: The complete report can be obtained in less than five days, which is competitive compared to other commercial CGP kits or services on the market.
Open Platform: The Avenio Edge instrument is an open platform that can be used with any NGS workflow and is highly optimized for this new workflow.
Preloaded Reagents: The kit reagents are preloaded in the cartridge, and the user only needs to remove the packaging and place it on the instrument, simplifying the operation process.
High Compatibility and Sensitivity: The kit is compatible with small-sized biopsy samples, featuring a very low contamination rate and high analytical sensitivity, capable of detecting minor variations.
Research Use: Currently, the Avenio CGP V2 Kit and Automation Kit are for research use only, providing Roche with the opportunity to continuously improve and innovate its assays.
These advantages indicate that Roche's automated sequencing kits are designed to enhance the efficiency and accuracy of translational oncology research while reducing time and resource consumption in laboratory workflows.
Industry Group
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