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 types4-7. 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 :
Ngoi NYL, Tan DSP. ESMO Open 2021;6(3):100144.
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
Robson ME, Tung N, Conte P, et al. Ann Oncol 2019;30(4):558–66.
González-Martín A, Pothuri B, Vergote I, et al. N Engl J Med 2019;381(25):2391–402.
de Bono J, Mateo J, Fizazi K, et al. N Engl J Med 2020;382(22):2091–102.
Mekonnen N, Yang H and Shin YK. Front Oncol. 202212:880643.
Li, S., Wang, L., Wang, Y. et al. The synthetic lethality of targeting cell cycle checkpoints and PARPs in cancer treatment. J Hematol Oncol15, 147 (2022). https://doi.org/10.1186/s13045-022-01360-x
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
This February 28th, we at SOPHiA GENETICS can't help but feel a profound sense of connection with those living with rare diseases. Rare Disease Day isn't just about raising awareness - it's about celebrating the incredible individuals who have touched our lives in ways we could never have imagined. Despite facing immense challenges, these real-life superheroes have shown us the true meaning of strength and resilience. By sharing their stories, we hope to inspire others to join us in supporting and celebrating their lives.
Today, we're honored to share the story of one of our own at SOPHiA GENETICS. One of our colleagues, Ragen, has a dear family friend, Brooklynn, who lives with a rare CDKL5 deficiency disorder. Brooklynn is a beacon of positivity, touching the lives of all who know her. At just 8 years old, she's a true superhero who inspires those around her with her infectious smile and unwavering spirit. Supported by a loving network of family and friends, Brooklynn lives life to the fullest, bringing joy and happiness to all who cross her path.
“I am part of #BrooklynnsCrew – we have matching t-shirts and support Brooklynn to live a happy life with a rare disease.”
Brooklynn’s rare disease story started when she had her first seizure at 2 months old. The doctors at the ER and the family pediatrician weren’t concerned and said that she had myoclonic jerks that she would soon grow out of. Not satisfied with this assessment, her family managed to record a few seconds of one of Brooklynn’s seizures for another opinion from a neurologist.
The neurologist ordered EEGs, a pH probe procedure, x-rays with barium, a semi-MRI, and an overnight EEG to try and get to the root of the problem. The overnight EEG indeed detected a seizure, and so Brooklynn was started on levetiracetam to manage the seizures. She was seizure free for a month, before another seizure sparked a dose increase, and the same happened after another and another month. Brooklynn ended up receiving the highest possible dose of levetiracetam before an epilepsy specialist switched her to oxcarbazepine.
At this point in their patient journey, Brooklynn’s family saw a geneticist who recommended that when her seizures could no longer be controlled by medication, that they could do genetic testing. Not wanting to wait until the seizures got increasingly worse, Brooklynn’s family requested genetic testing be done straight away. Brooklynn’s exome was sequenced and at 9 months old, she received a diagnosis of CDKL5 Deficiency Disorder.
“Brooklynn’s sister, Madison, is a volleyball player, whose team wears #BrooklynnsCrew shirts for warmups at local and out of state tournaments to show support and help spread awareness.”
Brooklynn’s family discovered that her CDKL5 mutation is extremely rare and were motivated to raise awareness in any way they could. The family began the Believe in Brooklynn Facebook page to share their story, and all Brooklynn’s family and friends are part of #BrooklynnsCrew with matching t-shirts! Brooklynn is now 8 years old and although her seizures, neurodevelopmental delay, and low muscle tone affect her cognitive, motor, speech, and visual function, she leads a happy life and is doted on by her family and friends. She has a great upbeat personality and although she cannot communicate in the typical way, she has no hesitation in letting you know her likes and dislikes. Brooklynn’s sister is a volleyball player, whose team wears #BrooklynnsCrew shirts for warmups at local and out of state tournaments to show support and help spread awareness.
Brooklynn loves riding in the ranger (off-road vehicle) around the ranch and dirt roads - the faster the better! Swinging is also another favorite activity of hers, the higher the better. She is quite the thrill seeker and loves motion! “Sunshine time” is her favorite time of day and sometimes she just lays out with her family for 20 minutes or they go for walks in her wagon with her puppy Coco. Brooklynn also loves being in the water. She will spend hours playing, splashing and floating in the bath or in her swim spa that she received from Make A Wish, San Diego. Traveling is another favorite of hers - she goes out of state with her family multiple times a year for sister Madison’s volleyball tournaments. She loves flying on the plane and always gets a window seat! The craziness at the tournaments with all the whistles, kids screaming, and commotion actually has a calming effect on her, and she seems to take the best naps there.
We sincerely thank Ragen and Brooklynn’s family for sharing her story to raise awareness of CDKL5 Deficiency Disorder on this Rare Disease Day. If you want to follow Brooklynn’s story or donate to her medical fund, check out her Facebook page.
If you would like to learn more about CDKL5, you can visit the International Foundation for CDKL5 Research (IFCR) website for a range of resources, clinical trial information, support information and groups, and to learn how to get involved or donate.
About Childhood Cancer
According to the World Health Organization, over 400,000 children and adolescents (0-19 years old) are diagnosed with cancer (1), while every 3 minutes, a child loses the battle with the disease. Although childhood cancer incidence is rare, it is the leading cause of disease-derived deaths past infancy (children and adolescents 0-19 years old) in the US and other developed countries (2). The most common types of cancer in children and adolescents are leukemias, lymphomas, central nervous system (CNS) and brain tumors (3).
This year, the focus of theInternational Childhood Cancer Day (ICDD), is to pay tribute to the groundbreaking impact that families and caregivers are having on children and adolescents with cancer. Additionally, the day is focused on raising awareness around the World Health Organization (WHO) Global Initiative for Childhood Cancer, an initiative aiming to achieve at least 60% global survival and reduce suffering of all children with cancer, by 2030 (3).
Why raising awareness on childhood cancer matters?
Raising awareness about childhood cancer requires a multi-faceted approach, as the impact of childhood cancer goes far beyond physical health. The emotional and financial toll on families and on survivors can also be overwhelming. Children and adolescents who survived cancer, often deal with treatment-derived comorbidities, cognitive impairment, heart disease, high risk for secondary tumors and others(4).
Despite the significant progress made in the field of childhood cancer, contributing to the decrease of cancer deaths, there is still work to be done. The overall incidence of childhood cancer has an average increase rate of 1% per year from 1997(4). In developed countries, approximately 80% of the childhood cancer incidents are treated, whereas low and middle-income countries (LMICs)the survival rates dramatically drop to 30% due to the lack of awareness, tools for timely and accurate diagnosis, inaccessibility to care, and relapse(5,6,7).
Do you want to know more about the Childhood Cancer survival rates in your country? Click here.
As childhood cancer prevention is not generally feasible, a comprehensive strategy is urgently needed to reduce the burden of cancer in children and improve patient outcomes . Coordinated efforts are needed from global governments, industry experts, Non-Governmental Organisations (NGOs) and civil society to build prompt and accurate diagnosis pathways, accompanied with personalized and evidence-based treatment decisions, as well as tailored long-term supportive care for cancer survivors.
SOPHiA GENETICS: Our knowledge at Clinician Researchers’ fingertips to fight cancer, together
Everyone touched by cancer needs a prompt and clear path to the right care. We, at SOPHiA GENETICS, simplify complex data and reveal what matters most.
Genomic-powered precision medicine is at the forefront of innovation in cancer research. Advancements in next-generation sequencing (NGS) technology have brought a new era in cancer care, expanding our understanding of pathogenic variants triggering oncogenesis and therapeutic targets.
Genomic research is playing a critical role in the battle against childhood cancer through identifying new targets and personalizing treatment options, developing new diagnostic tools, improving risk stratification as well as advancing immunotherapy solutions(8).
By providing biologically actionable in the underlying biology of childhood tumors, we can provide information and access to relevant clinical trials, effective existing treatment schemes and improved outcomes for children with cancer worldwide. Our CE-IVD bundle solutions empower data-driven decisions at all stages of the cancer research journey through a combination of accurate healthcare data analysis, intuitive interpretation functionalities, and secure knowledge sharing.
Our commitment is to provide clinician researchers and caregivers with evidence-based clinical decision tools, to establish research collaborations to unravel the pathophysiology of various cancers and unleash the power of precision medicine, leveraging our AI-based platform and solutions.
By continuing to invest in cancer research, we aim to actively contribute to the elimination of cancer-related deaths. Fighting childhood cancer is essential for building a healthier, equitable and prosperous future for all. Working together, we can make a significant progress in the battle against childhood cancer and bring a positive impact in the lives of children with cancer and their families.
How can you help? Advocate for change!
Every effort matters, and every voice is necessary. Global advocacy raises awareness and can therefore bring a change and hope to childhood cancer. By using social media to support and participate in relevant events and organizations, educating yourself and others you can help make a difference in the fight against childhood cancer.
References:
Steliarova-Foucher E, Colombet M, Ries LAG, et al. International incidence of childhood cancer, 2001-10: a population-based registry study. Lancet Oncol. 2017;18(6):719-731.
World Health Organization. (2023). CureAll framework: WHO global initiative for childhood cancer: increasing access, advancing quality, saving lives. World Health Organization. https://apps.who.int/iris/handle/10665/347370
CAC2 Coalition Against Childhood Cancer. (2021). Childhood Cancer Fact Library. [Online]. . Available at: https://cac2.org/interest-groups/awareness/childhood-cancer-fact-library/
World Health Organisation - International Agency for Research on Cancer. (2021). WHO Global Initiative for Childhood Cancer. [Online]. . Available at:https://www.iarc.who.int/featured-news/iccd-2022/
World Health Organization. (2021). CureAll framework: WHO global initiative for childhood cancer: increasing access, advancing quality, saving lives. World Health Organization. https://apps.who.int/iris/handle/10665/347370
Lam CG, Howard SC, Bouffet E, Pritchard-Jones K. Science and health for all children with cancer. Science. 2019 Mar 15;363(6432):1182-1186. doi: 10.1126/science.aaw4892. PMID: 30872518.
Berger MF, Mardis ER. The emerging clinical relevance of genomics in cancer medicine. Nat Rev Clin Oncol. 2018 Jun;15(6):353-365. doi: 10.1038/s41571-018-0002-6. PMID: 29599476; PMCID: PMC6658089.
Breast cancer patients are faced with varying challenges including genetic makeup, financial circumstances, and health care access. For this reason, researchers and technology developers are working hard to evolve options, to give patients around the world equal access to enhanced cancer detection and more personalized treatment.
Advanced medical imaging technology aids in breast cancer research
After initial concerns are raised by a patient, undergoing medical examination and imaging are usually the first steps of the diagnostic journey. Oftentimes, breast cancer patients do not exhibit symptoms, so multiple tests are done to diagnose breast cancer including mammograms, breast X-rays, ultrasounds, and magnetic resonance imaging (MRIs).
Imaging tests are helpful in detecting cell abnormalities, but as of now, a biopsy is still the only definitive way to prove a patient does in fact have breast cancer. During a biopsy, healthcare practitioners take a sample of breast tissue to perform further lab testing. Laboratory technicians can then check for the presence of biomarkers in the sample collected and confirm a patient’s cancer diagnosis.
The future of breast cancer research involves AI and data-driven medicine
Radiomics is a process of extracting large volumes of quantitative data from digital medical images and amalgamating these together with general clinical and personal patient data into searchable shared databases. By analyzing multiple sources of data (multimodal) the researcher can start to visualize a much larger picture of an individual’s overall health.
These recent advancements in technology enable researchers worldwide to collaborate and continually find new therapies through the ongoing globalization of clinical trials. SOPHiA GENETICS helps accelerate this process by providing a solution to optimize clinical trial site performance and find additional centres for ongoing trials not meeting recruitment goals. SOPHiA DDM™ Trial Match has been designed to connect individual cases with the appropriate clinical trial site where medical researchers run feasibility analyses for a patient’s enrollment process. This results in a growing network of research communities that allow for enhanced patient profiling for key genomic markers relevant to oncology. Ultimately, cancer centres are expected to offer more affordable and more precise treatment options to their patients.
SOPHiA DDM™ Trial Match is for research use only - not for use in diagnostic procedures
The first World Gynecologic Oncology (GO) Day was launched on September 20th, 2019 by the European Society of Gynaecological Oncology (ESGO) and the European Network of Gynaecological Cancer Advocacy Groups (ENGAGe). Their mission is to raise awareness of ovarian, uterine, cervical, vulvar, and vaginal cancers. The collective term for these five types of cancer is gynaecological cancer.
With over 1.3 million women worldwide diagnosed with gynaecological cancers in 2020, it’s more important now than ever to equip them with tools and resources to promote prevention and early detection of potential cancers. Increased public awareness of gynaecological cancer prevention can ultimately lead to improved quality of life and increased survival rate of affected women. Although there are warning signs, women can learn ways to reduce their risks in ways that make sense for their personal health, as signs and symptoms are not the same for everyone. It’s important to consult your doctor to discuss your unique situation and to schedule preventative screenings.
Over the years, World GO Day has been a joint effort by various advocacy groups around the world with both in-person and virtual events including interactive activities on the World GO Day website, scientific workshops, information sessions, and sporting events involving healthcare providers, cancer survivors, and supporters.
On September 20th you may see people wearing purple ribbons or clothing to show their support. It’s the color meant to combine awareness for all gynaecological cancers in one. In the first year of the awareness day, 33 patient advocacy groups from 22 countries in Europe and Asia joined to raise awareness with sporting events and games. This also helped to create a stronger network of people and organizations who still work together year after year to provide resources to the community.
ENGAGe says their priorities and objectives are to:
Facilitate the development of national gynaecological cancer patient groups in Europe and to facilitate networking and collaboration between them.
Disseminate information and share best practices to empower patient groups and improve the quality of care across Europe.
Increase patient representation in ESGO activities through education on current research and health policy.
Advocate patient care policies practices and access to appropriate care at both national and international levels.
Educate patient groups, health professionals, the general public, and health decision makers.
SOPHiA GENETICS is proud to support the efforts of World Go Day. You can choose to join this movement by educating yourself, sharing information with others, and showing your support. For the latest World Go Day updates, follow them on Facebook, Twitter, Instagram, and YouTube.
SOPHiA GENETICS is proud to announce the launch of SOPHiA DDM™ Dispatch. It represents an expansion of the SOPHiA GENTICS Integrated Solutions business area, which is a well-established model for working with partner labs to democratize data driven medicine by increasing access to next-generation sequencing and accompanying analysis. SOPHiA DDM™ Dispatch makes it even easier for partner labs to come online and operate independently.
With SOPHiA DDM™ Dispatch, our partner labs can handle orders directly with the clients, streamlining operations and improving efficiency. Dispatch enables labs to take advantage of any unused capacity and creates an additional source of samples. For clients looking for sequencing services, SOPHiA DDM™ Dispatch offers increased data visibility, data ownership and simplifies the ordering process.
With SOPHiA DDM™ Dispatch and SOPHiA GENETICS Integrated Access, client institutions can get access to powerful insights without the setup costs. Clients send their samples to partner labs for sequencing, then the sequencing data is delivered to the institutions in their SOPHiA DDM™ account. This gives growing institutions better access to accurate analysis and allows them to retain ownership of their sequencing data. SOPHiA DDM™ Dispatch and SOPHiA GENETICS Integrated Access offer institutions more than just a report, by combining raw data ownership and ongoing access to powerful tertiary analysis.
Partner labs can easily begin offering service through either Integrated Solutions model, offering an opportunity to gain an additional revenue stream. Partner labs control the testing menu they offer and do not have to do data interpretation, since clients are enabled to do interpretation through SOPHiA DDM™. Furthermore, new tests can be seamlessly incorporated into your existing workflow.
Clinical Trials Day, May 20th, brings awareness to clinical trials, but most importantly it celebrates and recognizes the people who run clinical trials and their contribution towards improving health. May 20th marks the anniversary of what is considered to be the first randomized clinical trial, performed in 1747 by James Lind1. He conducted a controlled clinical trial that compared six treatments for scurvy in 12 sailors with scurvy who all lived in the same quarters and had the same diet. He was able to identify that the two men who were treated with fresh citrus had the most positive results, however he never concretely recommended this treatments as a cure for scurvy and continued to find other remedies since fresh citrus was in limited supply. Lind is recognized for his experimental methods when conducting this study, attempting to compare similar subjects, thus reducing confounding variables2. You can learn more about James Lind and his achievements here.
Clinical Trials Today: impacting lives in the precision medicine era
Clinical trials today have obviously advanced way beyond this approach; however, we can still see how trials are rooted in Lind’s work, analyzing different treatments to identify their effects on a disease. Clinical trial work today is not only more advanced but being conducted on a much larger scale and across the world. Since 1999 over 671,000 clinical trials have been registered with the World Health Organization, with just under 60,000 being registered in 2021 alone. These trials increase access and knowledge of experimental treatments.
Currently, there are around 4,000 active trials that are using targeted biomarkers associations for oncology. To truly test the efficacy and effectiveness of these drugs, it is imperative to find patients with compatible biomarker signatures for the treatment. As diagnostic testing advances, these biomarker signatures can become more and more specific.
Running these clinical trials would not be possible without the clinical research professionals that support them. These individuals work across a variety of functions and to maintain the integrity of the research through a wide range of duties including data collection, recruitment, development of documentation, education and so much more. We at SOPHiA GENETICS are happy to take time to recognize these individuals and we thank them for all they do to advance research, medicine, and care.
SOPHiA GENETICS Helps Sites Gather and Analyze Multimodal Data in their Population of Interest
In one of our ongoing clinical studies in lung cancer, the DEEP-Lung-IV study, we aim to leverage deep learning-enabled analysis to aggregate multimodal data (e.g., 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.
This international and multicentric project addresses an important translational research question in a pragmatic way.Our collective intelligence receives many negative or positive predictive signals (clinical, imaging and molecular signals) in this area, yet it is currently unable to integrate them in an intelligible way.The goal of the DEEP-Lung-IV project is to integrate all these individual, discrete predictive signals into an artificial intelligence-based framework to enable us to make this information intelligible and thus allow us to intelligently choose the first line of treatment for our patients.
Pr. Jacques Cadranel, Sorbonne Université and AP-HP Hôpital Tenon – Paris, France
Accelerate biomarker-driven participant recruitment, even in rare biomarker cohorts with SOPHiA DDM Trial Match. This real-time site and patient identification analytical solution enables you to optimize clinical trial site selection ahead of clinical trial set up and supports your trial rescue strategy by finding additional centers for ongoing trials not meeting recruitment goals. Learn more about how SOPHiA DDM Trial Match can support identifying your targeted trial population.
Milne, Iain. “Who Was James Lind, and What Exactly Did He Achieve.” Journal of the Royal Society of Medicine, vol. 105, no. 12, 2012, pp. 503–508., https://doi.org/10.1258/jrsm.2012.12k090.
It’s not easy even for experts to pull useful insights from complex datasets. It’s even harder when the machine learning tools they’re using are only trained to work within a single nation, region, or more specifically, racial population.
Consider the recent popular Netflix documentary Coded Bias. MIT Media Lab researcher Joy Buolamwini discovered that facial recognition does not see dark-skinned faces accurately. She’s pushed for legislation in the US to govern against bias in algorithms. It’s a real problem that many in healthcare are now facing as the use of artificial intelligence in health data analysis becomes more and more prevalent and clinically useful. But the same push for diversity in machine learning reference for health data has been lacking throughout the industry. For this reason, and for the reasons you’ll learn from just one case study below, SOPHiA GENETICS has taken a decentralized and global approach for more than a decade.
A family without answers
A Moroccan couple living in Spain had suffered one of the worst human experiences, not just once, but twice. As they began to expand their new family, they had three pregnancies throughout the span of about one decade. Only one of their children, a healthy baby girl born in 2012, survived. One boy lived for 43 days, and one girl lived only for 20. The immense grief that this brings to parents is immeasurable, and the only thing nearly as horrible than the actual experience of loss is having a lack of answers – never knowing why.
After the death of their infant boy in 2019, the couple worked with regional medical experts in Spain to try and discover the root cause of what seemed to be neurodevelopmental disorders at birth. Researchers started by performing clinical exome sequencing and targeted gene analysis including a Microarray-based Comparative Genomic Hybridization test to look for any abnormalities that would possibly provide more clues. Much to their dismay, the results were inconclusive. The standard of care and testing used at the time were letting them down.
In 2022, they were able to perform more advanced testing after the death of their second daughter. This included TRIO analysis with the SOPHiA DDM platform. TRIO analysis takes clinical exome testing to a deeper level by analyzing data from the infants as well as both parents, giving researchers a better picture of familial, inherited genomic traits. The results finally confirmed that both parents carried a heterozygous frameshift variant. It was inherited by their infants as a homozygous pathogenic variant in the SMPD4 gene, causing neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies in the children. While identifying causative variants in recessive genes is challenging through conventional clinical testing, the SOPHiA DDM™ platform’s TRIO analysis enabled the researchers to overcome this limitation.
This family is now better informed about their risk of potential complications in future pregnancies. They’re able to work with genetic counselors to seek guidance regarding family planning that takes the anxiety out of the unknown.
Why diversity matters
In this case, it wasn’t just the type of testing that resulted in a successful discovery. Because SOPHiA GENETICS has worked on a global scale since inception (unlike more common approaches), the SOPHiA DDM platform’s machine learning algorithms have been better trained to analyze the health data of more diverse populations. Meaning, no matter where in the world this family had been trying to seek answers, their clinical researchers would have benefited from more accurate analysis of data that reflected who they are at the core of their genomes.
Every person is unique. We can clearly see this within the more than one million genomic profiles analyzed by our technology. This is why since day one SOPHiA GENETICS has adopted a global approach and placed it at the core of our company’s DNA. We strive to enable better research and health data analytics for all, no matter where they live or where they come from.
If you’d like to learn more about the SOPHiA DDM platform, contact us for a demo or learn more by exploring the many resources of our website.
Using a third-party sequencing service is an attractive option to institutions for whom the up-front capital investment of starting up a sequencing lab is an obstacle. There are many benefits to having access to a sequencing service, such as having predictable expenses and turn-around-times. However, in most cases there are significant challenges that remain in terms of data access and interpretation. Third party sequencing services often provide either a report for each sample, or just raw data. If a report is the only deliverable, institutions do not get access to the raw data and won’t be able to share it, archive it, or reanalyze it later. If raw data alone is delivered by the sequencing service, then institutions are on their own to find and test suitable secondary and tertiary analysis tools.
Gaining access to the raw data enables labs to perform data analysis in-house, for further analysis or to be aggregated with other samples for cohort-level investigation. Doing the analysis in house also gives the institution visibility into all variants present and detected within the sample, rather than just the reported variants. This visibility can lead to greater genomic discovery and increase knowledge of potentially relevant variants.
Doing data analysis in house can also help to support better decision making. Integrating the analysis platform into your institution’s existing health data management systems will allow decision makers to take a more comprehensive view of all the individual’s data which could help them consider more variants that might otherwise not be reported. Keeping interpretation in house will also allow institutions to consider the individual’s history. Breaking these data silos through integrations with native systems and bringing genomic analysis in house can support better decision making by focusing on the most relevant variants.
There are also cost benefits to doing the genomic analysis in house. Many sequencing services charge for the sequencing and the interpretation of the data. Doing the interpretation in house removed the associated costs, requiring expenses only for sequencing.
Decentralizing the analysis of genomic sequencing data can help institutions further adopt data driven medicine through ownership of their data. SOPHiA Integrated Solutions can help institutions bring genomic data analysis in house. With SOPHiA Integrated Solutions, samples are sent to one of our partner sequencing labs and the raw data is transferred back to your SOPHiA DDM account for analysis. This allows you to harness the analytical power of SOPHiA DDM to identify and report the relevant variants.
Since 2011, we’ve taken a unique, decentralized approach, operating in many regions to ensure that our machine learning algorithms provide accurate detection of rare and challenging cases, analyzing data in a way that reflects many diverse populations around the world. In turn, one million genomic profiles analyzed allows researchers globally to benefit from more precise, real-world data analysis, furthering the capabilities of data-driven medicine.
To mark the occasion, our coworkers celebrated on multiple continents from our various offices and headquarters including Switzerland, France and Boston, MA and more joined remotely through video chats. We asked our peers what this accomplishment means to them and here’s what some of them had to say:
When I started six years ago, SOPHiA GENETICS was just starting to be known in the market, and now we are a key player in it.
The community is growing and with more analyses, SOPHiA GENETICS AI becomes more robust and smarter. We are now unlocking new ways to help researchers.
(St. Sulpice, Switzerland HQ)
It is incredible that we have impacted so many people, bringing them solutions to their real problems. Clients needed results, experts needed support and we have been there, close to them, doing our best!
This is what we come to work for every day, no matter which department or role.
(Boston, MA US Headquarters)
It brings purpose to my job, being able to say that our efforts have now touched the lives of so many.
I don’t know how many companies that have had the pleasure of achieving such a huge goal.
Looking forward to celebrate the two million!
Check out the photos of our celebrations below and contact us if you’d like to learn more about the SOPHiA DDM™ Platform.
SOPHiA GENETICS products are for Research Use Only and not for use in diagnostic procedures unless specified otherwise.
SOPHiA DDM™ Dx Hereditary Cancer Solution, SOPHiA DDM™ Dx RNAtarget Oncology Solution and SOPHiA DDM™ Dx Homologous Recombination Deficiency Solution are available as CE-IVD products for In Vitro Diagnostic Use in the European Economic Area (EEA), the United Kingdom and Switzerland. SOPHiA DDM™ Dx Myeloid Solution and SOPHiA DDM™ Dx Solid Tumor Solution are available as CE-IVD products for In Vitro Diagnostic Use in the EEA, the United Kingdom, Switzerland, and Israel. Information about products that 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 indications for use. Please contact us at [email protected] to obtain the appropriate product information for your country of residence.
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