Accelerating and empowering our customers’ clinical cancer research decisions with cost-effective, accurate and fast in-house results.

This week is marking one year from the official launch of the SOPHiA DDM™ Homologous Recombination Deficiency (HRD) Solution. This is a milestone to celebrate, as with the introduction of our SOPHiA DDM™ HRD Solution, we introduced a cutting-edge, novel approach to HRD detection and supporting clinical researchers in their decision-making.

What is Homologous Recombination Deficiency (HRD) and why does it matter in cancer?

Homologous Recombination (HR) is a cellular process that repairs double-stranded breaks (DSBs) arising from DNA replication process or resulting from the exposure to DNA-damaging agents. Homologous Recombination Deficiency (HRD) is a condition that hinders the ability of cells to repair the double-stranded DNA break damage, therefore ultimately triggering oncogenesis¹.

Damaged or falsely repaired DNA double strands lead to the accumulation of genomic scars which can be assessed by means of a Genomic Instability (GI)¹. Deficiency in one (or more) homologous recombination genes, increases the risk for multiple malignancies², while HRD is identifiable in multiplecancer types^4-7. Some of the Homologous Recombination Repair (HRR) pathways genes most prevalently involved in the HRD phenotype are: BRCA1, BRCA2, RAD51C and PALB2.

How does the SOPHiA DDM™ HRD Solution allow clinical researchers to accelerate HRD detection?

At SOPHiA GENETICS, we are leveraging target capture technology and low-pass Whole Genome Sequencing (WGS) to isolate somatic and germline mutations in HR-associated genes.This permits the end user to identify pathogenic variants, such as SNPs and Indels, that could be potential causes of HRD.

In a single workflow, the SOPHiA DDM™ HRD Solution combines identification of mutations in 28 homologous recombination repair (HRR) genes beyond BRCA1 and BRCA2.

The unique value proposition of the SOPHiA DDM™ HRD Solution lies in the possibility of HRD testing in a decentralized format, supporting accurate detection of HRD status in a simple and intuitive platform that reduces turnaround time and costs.

We are extremely proud of having designed a sample-to-report application as a powerful tool for data-driven decision making by HCPs for the benefit of the ovarian cancer patients globally. In 2022, our expert bioinformatics and technical implementation teams facilitated over 30 SOPHiA GENETICS Set-Up Programs, supporting rapid adoption of the workflow across the globe, demonstrating high analytical performance and customer benefit maximization leveraging the capabilities of the SOPHiA DDM™ Platform.

SOPHiA DDM™ HRD Solution: A commitment to science, our customers and the world.

We, at SOPHiA GENETICS, are committed to improving science and healthcare outcomes across the world, developing cutting-edge technologies for our global customers and partners. To mark this 1-year celebration, we spoke to one of our partners, Diagnosticos da America (Dasa), about their experience with the SOPHiA DDM™ HRD Solution. Here are some insights from our collaboration:

SOPHiA GENETICS and Dasa celebrate a great milestone: 2,000 samples analyzed in less than two years!

Dasa is the largest integrated health network in Brazil, serving more than 20 million patients per year through more than 250,000 medical partners. Dasa became one of the frontrunners, introducing SOPHiA GENETICS's Solution for HRD as the first decentralized solution in Latin America.

“With such a large regional network, we needed a cost-effective HRD solution that helped improve our workflow efficiency. The decentralized approach of SOPHiA GENETICS has enabled us to increase our scalability and output – in less than two years, we've tested the HRD status of over 2,000 in-house samples. The powerful analytics of SOPHiA DDM™ have helped us to maximize genomic insights from these samples and advanced our clinical research capabilities.”, said Ana Gabriela, Dasa’s Genomic Business Unit Sr. Manager.

SOPHiA DDM™ HRD Solution: Going beyond BRCAness

SOPHiA GENETICS is expanding its capabilities by launching an extended Homologous Recombination Solution which allows to explore deficient HRR genes resulting in the HRD phenotype. The panel relies on high accuracy and coverage uniformity, while giving the user the ability to have their library ready for sequencing in 1.5 days.

Our extended solution delivers a comprehensive coverage of 28 genes involved in the HRR pathway, encompassing SNVs, indels and gene amplifications, while providing access to OncoPortal™ Plus, to classify variants leveraging evidence-based annotations from the JAX-CKB database.

Our aim is to expand our offerings in a platform-agnostic approach, that will further empower healthcare professionals to continuously improve their data-driven decision making.

We want to thank everyone who contributed to this success and looking forward to the next milestones to come. Together, we always achieve more!

References :

1. Ngoi NYL, Tan DSP. ESMO Open 2021;6(3):100144.
2. Mekonnen N, Yang H and Shin YK (2022) Homologous Recombination Deficiency in Ovarian, Breast, Colorectal, Pancreatic, Non-Small Cell Lung and Prostate Cancers, and the Mechanisms of Resistance to PARP Inhibitors. Front. Oncol. 12:880643. doi: 10.3389/fonc.2022.880643
3. Biomarkers of Homologous Recombination Deficiency in the era of PARP inhibitors, C. Piombino, L. Cortesi, Vol. 2 (No. 2) 2022 June, Review, 138-148, doi: 10.48286/aro.2022.48
4. Robson ME, Tung N, Conte P, et al. Ann Oncol 2019;30(4):558–66.
5. González-Martín A, Pothuri B, Vergote I, et al. N Engl J Med 2019;381(25):2391–402.
6. de Bono J, Mateo J, Fizazi K, et al. N Engl J Med 2020;382(22):2091–102.
7. Mekonnen N, Yang H and Shin YK. Front Oncol.  202212:880643. 
8. Li, S., Wang, L., Wang, Y. et al. The synthetic lethality of targeting cell cycle checkpoints and PARPs in cancer treatment. J Hematol Oncol 15, 147 (2022). https://doi.org/10.1186/s13045-022-01360-x
9. Testing for homologous recombination repair or homologous recombination deficiency for poly (ADP-ribose) polymerase inhibitors: A current perspective Thomas J. Herzog ^a,*, Ignace Vergote ^b, Leonard G. Gomella ^c, Tsveta Milenkova ^d, Tim French ^d, Raffi Tonikian ^e,1, Christian Poehlein ^e, Maha Hussain ^f

Newsletter - March 2022 SOPHiA GENETICS at BARCLAYS Healthcare Conference We were back in person at the BARCLAYS Global Healthcare Conference in Miami earlier this month! You can listen to the replay of our CEO Dr. Jurgi Camblong's fireside chat.   READ MORE 4th Quarter and 2021 Financial Results Take a look at the full report of our fourth quarter and entire 2021 financial results reported earlier this month.  READ MORE ACMG Recap: Food for Thought We're recapping our highlights from our time at this year's ACMG conference.    LEARN MORE Protean BioDiagnostics & SOPHiA GENETICS In this blog, you'll learn how Protean BioDiagnostics utilizes our technology for more comprehensive genomic analysis and research  READ MORE Overcoming Challenges of Exome Sequencing  Whole exome sequencing has the potential to accelerate the diagnosis of rare diseases, but without the right tools, achieving comprehensive coverage and sifting through tens of thousands of variants is a challenge. READ MORE Upcoming events AACR - New Orleans April 8, 2022 – April 13, 2022 In-person, Virtual EHA 2022 June 9, 2022 – June 12, 2022 In-person, Virtual ASCO 2022 - Chicago June 3, 2022 – June 7, 2022 In-person, Virtual In The News GenomeWeb SOPHiA GENETICS, Realm IDx Sign Letter of Intent to Expand NGS in Cancer Care   More BioSpectrum Asia SOPHiA GENETICS HRD Solution Makes Way In Asia Pacific More GEN Cancer Genomics: Streamlined Workflows for Reading and Writing DNA More FIERCE Biotech SOPHiA GENETICS, Realm IDx to Pool Sequencing Tools for Cancer Care More Health Professional Radio SOPHiA GENETICS - Genomic Data and AI-Powered Software as a Service (SaaS) Platform More DISCLAIMER The information included in this document has been prepared for and is intended for viewing by a global audience. This document contains information about products and services which may or may not be available in different countries and if applicable, may or may not have received approval or market clearance by a governmental regulatory body for different indication for use. Please consult local sales representative.   unsubscribe from this list | update subscription preferences

This week, President Joe Biden described his plans to supercharge the American Cancer Moonshot to significantly cut the cancer death rate in half over the next 25 years. In a White House news conference Wednesday, he challenged the medical research community to come together in new, data-driven, collaborative efforts.

SOPHiA GENETICS supports democratizing data-driven medicine for the ultimate benefit of patients and their loved ones. We continue to deliver to our global community by advancing their cancer research capabilities through our technology and our amazing people who work closely with researchers every day.

Why the priority for cancer research now?

Fewer people are visiting their doctors. This means it’s less likely they’re catching the early signs of cancer that their physician could help discover from screening.

During the COVID-19 global pandemic, a Harvard Gazette report showed that there was a sharp decline in routine cancer screening. Some projections showed that in the next five years, the death rate related to cancer could be 4-17% higher because of the limitations brought on by the pandemic. Reports showed decreases of 85-90% and more than 9.5 million missed cancer screenings in the United States, according to facts released from the White House in early February. President Biden said during Wednesday’s press conference that this tide must be turned and that proper cancer screening of Americans must be prioritized.

New approaches

While the American Cancer Moonshot was originally launched in 2016, this new commitment to advancing American healthcare comes with more federal support for research and development through emerging technologies. The idea is that more progress can be achieved through data-sharing initiatives, breaking through traditional silos between medical institutions.

Many advancements in research have allowed for genomic biomarkers to play a larger role in identifying early signs of certain cancers. Those advancements can lead to earlier detection rates and the development of better cancer therapies and treatments. The President acknowledged that the US still has much further to come in advancing data-driven initiatives and that many Americans sadly do not realize the struggle of seeking answers during the cancer diagnostic journey until it’s too late. A proposal was also announced for the creation of an Advanced Research Projects Agency for Health (ARPA-H)  that would focus on the U.S. government’s capabilities “to speed research that can improve the health of all Americans”.

Data-Driven Solutions

SOPHiA GENETICS is committed to enhancing clinical research through advanced analysis of medical data through the SOPHiA DDM^TM Platform. By enabling faster, more cost effective, and highly accurate data analysis, we continue to make the greatest impact for users who must comb through extremely large sets of clinical data to derive impactful insights that will aid their research.

If you’d like to learn more about how our technology can help improve clinical research, click here.

2021 has been quite a year for us at SOPHiA GENETICS. We’re rounding out a full decade of significant growth since we began at EPFL with just a handful of people in a 10 square meter room back in 2011. Now, we’re opening expanded office and R&D capabilities around the world for hundreds of employees who work hard every day to bring our mission and values to life. These are a few of the most notable moments from this substantial year for our company…

Expanding the portfolio

We kicked off 2021 with the announcement of three blood cancer solutions, greatly expanding the coverage we can offer by targeting DNA or RNA to detect any molecular biomarkers. Our blood cancer portfolio gives more in-house options to labs of all sizes based on their needs.

In the spring, we released SOPHiA DDM^TM for TSO500, designed to maximize the utility of the Illumina TSO500 assay. Early adopters said that this solution helps them to easily see the variant filter and rapidly evaluate the significance of specific mutations.

SOPHiA GENETICS launched a new Clinical Exome Solution in October, which allows us to elevate the statistical power of the data. Rare and inherited disorder analyses benefit from enhanced detection capabilities within the entire mitochondrial genome.

Our latest product launch stems from our partnership with Agilent, extending SOPHiA DDM™ Universal Whole Exome analytical capabilities to include SureSelect Human All Exon v8 by Agilent. This solution optimizes for Agilent-specific sample data to be further analyzed and studied within the universal SOPHiA DDM^TM platform.

IPO & collaborations

In early July, we announced our plans for an initial public offering (IPO), officially listing as SOPH on the NASDAQ by the end of that month. We successfully raised $234 million to help us further democratize Data-Driven Medicine globally. This was a major step forward for our company’s growth.

Before that great accomplishment, we were already in discussions with some of the largest biotechnology firms in the world to create lasting partnerships. These partnerships will help drive shared success and evolve the use of multimodality. Multimodality combines multiple sources of medical data that can be enhanced with AI, generating more actionable insights for clinicians and medical researchers.

Our partnerships included teaming up with the Spanish Lung Cancer Group in February to explore predictive potential of multimodal health data in resectable stage IIIA non-small lung cancer. In March, we announced our long-term collaboration agreement with Hitachi to unlock the potential of multimodal health data.

Since our IPO, we’ve reported how we’re working with more than 780 medical institutions around the world. This included a recently expanded partnership with Dasa for the first decentralized cancer biomarker detection solution in Latin America.

We announced an agreement with Agilent to expand co-marketing of our new end-to-end solution, which automates NGS library preparation and analytics processes for cancer research.

In early July we signed a letter of intent with GE Healthcare to match multimodal patient data and cancer types. We officially announced the collaboration recently at RSNA where we co-hosted a comprehensive symposium about the role of the Radiologist and their use of emerging clinical technology as part of the healthcare revolution.

On the horizon

As I’ve mentioned earlier this year, we continue to invest heavily in research and development. This includes the recent launch of our DEEP-Lung-IV multimodal clinical study. It will leverage deep learning-enabled analysis of the aggregation of multimodal clinical, biological, genomic, and radiomics data to identify and validate predictive signatures associated with response to immunotherapy and prognosis of patients with metastatic non-small cell lung cancer. Our goal is to enroll 4,000 patients from approximately 30 sites across North America, Europe, and Latin America.

SOPHiA GENETICS will continue to enhance medical research capabilities around the world as we enter a new year with great momentum and determination. If you’d like to learn more about our progress, I invite you to join our journey by following our social media pages and signing up for our monthly newsletter below.

The new building offers additional office space for the growing workforce of our Swiss HQ, as well as a brand-new R&D lab, replacing our former lab in Geneva. The layout and infrastructure of these new facilities is specially designed to accommodate various requirements including Experimental Quality Check to Supply Chain and more, offering a tailor-made environment to meet our company's R&D activities.

Led by none other than our CEO, Jurgi Camblong, a special tour of the new office was offered to representatives of the State of Vaud where the building is located. Celebrations continued with speeches by State Counsellor Philippe Leuba and our CEO, who cut the inaugural ribbon together.

"These last 10 years have been quite incredible; we’d never have thought we’d be filling up a location this big when we started in 2011 in a 530 square foot space with a handful of people. Today, we’re opening an office and lab that is 100 times bigger – almost 54,000 square feet! SOPHiA GENETICS is growing, and with it, our growing social responsibility to continuously make the best use of our resources and talent to help create new paths for medical research worldwide. We call it democratizing data-driven medicine, together.”

Jurgi Camblong, CEO and Founder

News coverage of the expansion:

24 Heures, Sept 1^st

https://www.24heures.ch/nee-a-lepfl-sophia-genetics-va-amener-350-emplois-a-rolle-845679550550

L’Agefi, Sept 1^st

https://agefi.com/actualites/entreprises/venir-a-rolle-nous-permettra-de-grandir-confortablement

Our team at SOPHiA GENETICS continues to work to help advance the efforts of SARS-CoV-2 surveillance and research. During the first stages of the pandemic, we leveraged our experience in NGS and developed a robust solution for full-genome analysis of SARS-CoV-2 to identify circulating and emerging strains. Recently, our genomic experts have worked with international partners to offer new guidelines in amplicon-based SARS-CoV-2 genotyping, overall improving data quality and confidence.

Going beyond the detection and surveillance of emerging strains, including the B.1.1.7 “UK variant” or the B.1.167.2 “Indian variant”, the SOPHiA DDM™ platform enables the analyses of individual mutations.

As we continue to advance the analyses of SARS-CoV-2, our research experts have identified an important and novel mutational hotspot.

Our researchers recently reported a striking increase in the frequency of recruitment of diverse substitutions at a critical residue, W152, positioned in the N-terminal domain (NTD) of the Spike protein. The NTD is the most rapidly mutating part of the Spike protein, and these substitutions at position W152 have been observed repeatedly across independent phylogenetic and geographical contexts.

W152 is an important interaction point for neutralizing antibodies, and these frequent mutation recruitment events were reported with a clear increase in intensity since the end of 2020 (week 55 of the pandemic). Notably, researchers have reported this specific mutation has spurred >150 clusters that directly or indirectly contributed to contaminating over 15,000 patients.

As vaccination efforts improve around the globe, this research SOPHiA DDM™ platform enables continues to be fundamental to better understand the variants that “escape” immunity.

Read the full publication here

On World Cancer Day, we have an opportunity to celebrate the medical advances that have been made in Oncology and how they are enabling patients to access pioneering care.  The most significant advances of the last decades were made in the field of personalized medicine.

One of the main promises of the Human Genome Project (HGP) - personalized medicine - originates from pioneering, passionate, genomic research. The study of the changes that occur in the genes of tumor cells has uncovered important insights into the characteristics of tumors. For example, which genes support their functions, growth, sensitivity to treatment - what makes each of them uniquely suited to survive. This information has enabled researchers to conceive targeted therapies; drugs that are designed to pinpoint the uniqueness of each tumor - commonly known as biomarkers. Through the analysis of these biomarkers, healthcare professionals can now refine cancer classifications, staging and prognosis, providing doctors with a novel type of tailored care for their patient.

Non–small cell lung cancer (NSCLC) has become a prominent example of personalized medicine among solid tumor malignancies. Many fields of medicine contributed to forge the novel tools of the medical arsenals and advance NSCLC research. Indeed, the study of various genes involved in lung carcinoma (ALK, RET, MET, ROS1, NTRK, PIK3, AKT, EGFR etc.) was used as a foundation to develop drugs that take advantage of the consequences of their mutations.

In parallel, the demand for molecular testing increased and solutions were developed to help laboratories navigate the abundance of information to assess a tumor’s biomarkers and carefully, prioritize, and report molecular findings.

Since lung carcinomas exhibit strong differences that can be visualized by medical imaging, another ally in the fight against cancer appeared in 2012: Radiomics. This concept can be defined as the comprehensive quantification of tumor phenotypes by applying a large number of quantitative image features. In other terms – images are more than pictures, they are data. Data that can also be measured to assess tumor evolution.

Along with biological data, both radiomics and genomics have become permanent staples of the cancer care toolbox.

What’s next then?
Advanced analytics able to generate insight based on the sum of genomics, radiomics and biological data brings a concept known as multimodality. A limited but rapidly increasing body of literature suggests that, thanks to novel computing capacities, multimodality holds the potential to increase precision in diagnosis, prognosis and treatment decision.

While NSCLC appears to be shifting toward multi-markers, it is likely that exciting innovations will come from multimodal approaches. These approaches could represent transformative progress for patients around the world: discovery of novel biomarkers to develop new therapies, further capacity to match the right treatment to the right patients in clinical trials as well as in routine clinical care, and the ability to follow patients longitudinally through a multimodal approach. This could refine the prediction of disease evolution and consolidate drug development, further personalizing patients’ care.

For more information on how multimodal approaches can advance precision medicine development: click here to book a non-promotional virtual meeting with one of our experts.