Women’s History Month Q&A with Kate Bogdanova

It is Women’s History Month, which celebrates the contributions of women to events in history and contemporary society. To mark the occasion, we are featuring some of our female employees at Sema4. In the fourth, and final, Q&A of this series, Kate Bogdanova, a Variant Curator on our all-female somatic variant curation team, discusses her innovative work at Sema4 and the influence of her role models. Read the previous installments of this series by clicking here, here, and here

Kate Bogdanova1. What is your role at Sema4?

I am a variant scientist in the oncology curation team. Variants are changes in the DNA, some of which can increase a person’s chance of developing cancer. I act as a liaison between the Knowledge Base (KB) group and the Reporting Laboratory Directors. The KB group provides expertise on specific cancer types and guidance on which treatments may benefit the patient most based on the variants identified in their tumor’s DNA/RNA. My role is to make sure that all the relevant variants are included in the patient’s report, properly annotated and classified. We also ensure that the report itself is cohesive and scientifically correct, and that recommended trials are appropriate based on the patient’s clinical and family history.

2. What motivates you to work at Sema4?

I really appreciate our innovative approach, from the tests we offer, on both the germline and somatic sides, to the tools that we are developing to support those tests. We provide critical information to our patients and physicians and connect them to Pharma to help them get into a trial or the other way around. I take great pride in the role I play in this extensive process. Our reports may help to identify a misdiagnosis or to verify the suspected diagnosis, which will translate into better risk assessment or treatment options for our patients.

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Women’s History Month Q&A with Michelle Ning

It is Women’s History Month, which celebrates the contributions of women to events in history and contemporary society. To mark the occasion, we are featuring some of our female employees at Sema4. In our third Q&A of this series, Michelle Ning, a Genetic Counselor based in our Branford lab, discusses advocating for patients and their families, and why her grandmother inspired her to be a woman of science. Read our previous installments of this series by clicking here and here.

Michelle Ning1. What is your role at Sema4?

As a Lab Genetic Counselor (GC), I wear a lot of different hats, which makes it a particularly rewarding role. I help patients understand the genetic testing process and what it means for them and their families, while also guiding healthcare providers on what our test options are and how the results may impact their patients. I develop comprehensible educational materials, as well as consent forms. In the lab, I review hereditary cancer genetic test orders to ensure they are a good fit for the patient based on their individual and family medical history.

2. What motivates you to work at Sema4?

Sema4 cares about the patient experience. This very much aligns with my philosophy and background. I started my career in the clinic and have always advocated for patients and their families. I am proud to still be able to provide this advocacy as part of my role at Sema4.

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Women’s History Month Q&A with Nefize Sertac Kip

It is Women’s History Month, which celebrates the contributions of women to events in history and contemporary society. To mark the occasion, we are featuring some of our female employees at Sema4. In our second Q&A of this series, Nefize Sertac Kip, Medical Director in our Branford lab, discusses what Women’s History Month means to her and why Turkan Saylan, a prominent female Turkish doctor, has inspired her. Read our first installment of this series by clicking here.

Whitney Jappe1. What is your role at Sema4?

As one of the Oncology Lab Directors, I sign out clinical reports of next generation sequencing of tumor specimens, select appropriate platforms, software, and kits to use in the laboratories and figure out which assays (an investigative procedure in laboratory medicine) to bring on board, or how to validate and apply within New York State. I review the pathology reports and tumor slides to provide the appropriate codes for downstream analysis. I manage the variant curation and annotation team that provides the gene narratives, clinical trial information, and appropriate therapies to explain the roles of the mutant genes in various tumors important in diagnosis, prognosis and therapy. I am also involved in oncology research, fellows’ training and building our histology and AI-driven digital pathology capabilities.

2. What motivates you to work at Sema4?

Sema4 is very futuristic and cutting edge. I am lucky to work with so many knowledgeable and sophisticated lab directors, genetic counselors, bioinformaticians, curators, scientists, software engineers, technicians and administrative staff. We collaborate in a multidisciplinary fashion to deliver the best possible solutions to healthcare providers and their patients.

3. What does Women’s History Month mean to you?

It means a lot. I admire Ataturk, the founder of modern Turkey, whose democratic ideals led him to emancipate women, and encouraged them to receive education in science and join the workforce with equal rights to men. In that spirit, I chose to pursue my medical training. I was following the example of other females in my family who also recognized the importance of education. Many women in my family took on leadership roles. My grandmother, though she did not work, was a very prominent figure at home. My mom, who is an entrepreneur and still working, has been instrumental in my motivation to excel as a human being and as a career-oriented female.

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Women’s History Month Q&A with Whitney Jappe

It is Women’s History Month, which celebrates the contributions of women to events in history and contemporary society. To mark the occasion, we are featuring some of our female employees at Sema4 over the next few weeks. In our first Q&A of this series, Whitney Jappe, Digital Program Manager in our New York City office, discusses what fuels her commitment to helping cancer patients and why she’s thankful to women from previous generations.

Whitney Jappe1. What is your role at Sema4?

I oversee the development and launch of digital oncology tools at Sema4 that enable the exploration of clinical and genomic data in aggregate down to the individual level. They serve to accelerate research and identify opportunities for care improvement using data, and deliver on our mission to advance precision medicine.

2. What motivates you to work at Sema4?

I have a passion for oncology and precision medicine that started when I began my career in oncology 10 years ago at Memorial Sloan Kettering (MSK). I was managing Phase I trials in oncology at a time when immunotherapy and several of the newer EGFR and ALK inhibitors were just entering the treatment landscape, and the results we saw were astonishing. I was blown away that by identifying and targeting proteins and driver mutations, it would have the impact it did, especially in a disease where, at the time, the five-year survival was only around 20%.

So, working at a company like Sema4 that not only performs the sequencing but also delivers the tools and services to further advance precision medicine allows me to continue on this path of improving the lives of cancer patients.

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Digital Health Tools Glean Clinical Intelligence from Patient Records

It has long been a goal in medicine to extract not just data but real intelligence from patient files. In the oncology field, we are finally seeing that goal become reality.

The automated clinical annotation of electronic medical records, together with careful curation of genetic test results, is transforming the type of information available to healthcare providers. For example, big data advances have made it possible for oncologists to visualize a patient’s complete healthcare journey without having to create a mental map based on the many disparate sections of an EMR.

Sema4 Patient Journey
Sema4 Patient Journey – drill-down to visualize an individual patient’s longitudinal journey, including diagnosis, treatments, and outcomes.
Extracting intelligence from each patient’s records is also enabling a better understanding of health at the population level. Oncologists can use sophisticated analytics to see at a glance how any individual patient’s clinical profile maps to a tailored cohort. That same intelligence is making it possible to more precisely match patients to clinical trials, as well as to assess population-level priorities, including quality of care and research.

Today, too many physicians struggle to work with EMR systems that were never designed to provide clinical intelligence that could improve patient care and outcomes. As newer, easier-to-use, and more effective data tools become available, hospital systems and medical practices have the opportunity to support oncologists and help them make the most of patient data.

State of the Data

It is no secret that the process of accessing patient records, entering data, and trying to extract knowledge from EMRs is fraught and painful. The platforms used today for patient data were originally designed for billing purposes, not for clinical care. No wonder, then, that they fail to offer an intuitive user interface for physicians who simply want to understand a patient’s healthcare journey.

Preparing for a clinical interaction with a patient requires oncologists to log into the EMR and then click through many sections, each storing disparate pieces of information. Data that would ideally be readily accessible in a single dashboard — patient demographics, stage and type of cancer, histology data — is instead hidden away in so many silos. Valuable notes from previous visits with other physicians in the same healthcare system are similarly difficult to find, and are not optimized for searching. The platform is designed for physicians to enter and review patients’ data without standardized vocabulary, leading to the burial of information in a mountain of unstructured physician notes. Test or imaging results may be locked away in PDF format, requiring the user to open each file in order to see what’s there. And important data from a patient’s meetings with doctors at other practices or hospital systems will be completely inaccessible unless that patient has taken the time to request the information, which is often shared via obsolete storage devices such as CDs.

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Sema4 Unveils Additional Information on its Biopharma Solutions

Sema4 is proud to be a trusted partner to Biopharma across diverse projects, including our five-year collaborative asthma study with Sanofi. To further showcase our innovative solutions, services, and support for the evolving Biopharma landscape, we have now launched new content on our website.

Sema4 BiopharmaBringing a drug to market is an arduous task; it takes on average at least ten years and close to $3 billion for a drug to move from the lab to the shelf. Sema4 has a proven track record of success in working with Biopharma to deliver comprehensive insights to accelerate the drug discovery, development, and commercialization lifecycle, powered by Centrellis™, our AI-driven health intelligence platform.

We offer an extensive portfolio of health information solutions, providing analytics for actionable insights, pre-clinical and clinical trial support, and advanced sequencing services. As drug development becomes increasingly complex, Sema4 is a partner trusted to deliver innovation and value to the Biopharma industry.

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Multiple Myeloma Study Shows Need for Sophisticated Network Modeling

Predictive network modeling can more accurately stratify multiple myeloma patients by prognosis than conventional methods, according to a recent project led by scientists at Sema4. The publication reporting their results — from lead author Yu Liu, senior author Jun Zhu, and collaborators — recently came out in the journal Cancers.

Building sophisticated network models is a core strength for the Sema4 team, and we were eager to apply it for this important oncology study. We focused on multiple myeloma, which is among the most common hematological cancers and has recently seen rapid growth in the number of treatments available and in the number of gene expression signatures used for establishing a patient’s prognosis. Still, median survival for multiple myeloma patients is only seven years. “While the therapeutic options available are increasing,” Liu et al. point out in the paper, “it remains critical to identify high risk patients early and develop personalized treatment options for them to improve outcomes.”

Multiple Myeloma

As data scientists and biologists, one of the things that struck us about the current landscape of multiple myeloma is that many of the published biomarkers do not overlap each other. Was it really the case that these biomarkers are isolated and acting alone? Or was there a unifying theme that would tie them all together and offer a more cohesive explanation?

To answer those questions, we analyzed more than 300 gene expression profiles, more than 250 copy number variation profiles, and relevant clinical data obtained from a Multiple Myeloma Research Consortium data set. That information allowed us to build a multiple myeloma molecular causal network, which enabled us to distinguish whether gene-gene correlations were driven by biological regulation or genomic co-localization. The resulting multiple myeloma network successfully unified eight previously published prognostic gene signatures that appeared to have few genes in common. The result was a prognostic subnetwork composed of 178 genes, many of them involved in cell cycle activities. Our network also helped to explain different drug responses across patients.

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Sema4 announces scholarship to support trainee genetic counselors

Earlier this month, we celebrated Genetic Counselor Awareness Day, a recognition of the professionals who provide genetic testing support and education to patients, providers, and researchers. With training in both scientific and counseling disciplines, genetic counselors are uniquely placed to help individuals understand genetic testing, guide them through the testing process, and empower them to make informed choices based on the results.

Genetic counselors are part of the backbone of Sema4. We currently employ more than 40 counselors, around half of whom were hired within the last year. We rely on these highly trained professionals to translate genetic testing results into powerful, understandable insights that can shape a patient’s health trajectory.

Recognizing the value of this profession to our field, we also want to ensure that the most capable individuals can enter genetic counseling training programs, regardless of their socioeconomic background. We are therefore proud to announce that we have, for the second year running, provided a tuition scholarship to the Master of Science in Genetic Counseling Program at the Icahn School of Medicine at Mount Sinai (ISMMS).

Madison Maertens
Genetic Counseling scholarship recipient, first year student Madison Maertens

This year’s scholarship has been awarded to Madison Maertens, a first-year student whose undergraduate training in Biology at the University of Washington convinced her that she wanted to pursue a career in genetic counseling. Earlier this year, she was delighted to find out that she had been accepted to ISMMS’s prestigious training program. She was then even happier to find out that she was the deserving recipient of the Sema4 scholarship. “I knew that I wanted to attend Mount Sinai’s program because of its reputation and the mix of academic and clinical training,” said Madison recently between classes. “However, I was concerned about the cost of studying in New York City. So, when I heard that I’d received the scholarship, it was a huge weight off my mind.”

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At AMP 2019, Carrier Screening Session Highlights the Importance of Ethnicity

Carrier screening has undergone major changes in recent years as technology made it possible to cost-effectively scan many genes at once. Where this kind of screening was once limited to just a couple of diseases, it is now feasible to offer much broader testing through options like Sema4’s Expanded Carrier Screen.

But along with this technological shift have come many important clinical and ethical questions. Those were the focus of a carrier screening session at the recent Association for Molecular Pathology Annual Meeting & Expo in Baltimore, where Sema4’s Chief Diagnostics Officer Lisa Edelmann spoke about identifying ethnicity, residual risk, and more.

Dr Lisa Edelmann
Lisa Edelmann, PhD – Chief Diagnostics Officer

Ethnicity matters in carrier screening for a few reasons. First, Edelmann pointed out, many diseases are understudied in certain ethnic groups. This means that guiding people to carrier screening panels developed for a particular ethnic group might miss diseases that are relevant to that group but have not been studied extensively enough within it. Second, patients often misreport their own ethnicity — sometimes because they are not aware of their genetic ancestry and sometimes because the “check-one box” forms fail to provide consumers from admixed populations the chance to fully represent their ethnicity, Edelmann told attendees.

For both of these situations, expanded carrier screening can offer a better option. By testing as many variants as possible, this kind of screening test gives people a greater likelihood of detecting any red flags than a smaller panel focused on a single ethnic population.

Ethnicity also makes a difference for calculating residual risk from negative results in a carrier screen, Edelmann said. This calculation requires understanding carrier frequency within an ethnic population and the detection rate of the screening test. Ethnicity influences both. Historically, residual risk scores were established based on literature searches, Edelmann noted, but now there are better methods. “Currently we can use a data-driven approach for these residual risk calculations [to move] towards a more accurate representation of risk,” she said.

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ASRM 2019: Big Data, Expanded Carrier Screening, and the Patient Journey

Women’s health is a core interest for the Sema4 team, so we were particularly excited to attend the recent annual meeting of the American Society for Reproductive Medicine in Philadelphia. One of the conference highlights was a panel discussion entitled “Transforming the Future of Reproductive Health through Genomics, Big Data, and Patient Engagement.”

Panelists [from left to right]: Kareem Saad, Chief Strategy Officer, Sema4; Jaime M. Shamonki, MD, Chief Medical Officer, California Cryobank Life Sciences; August Calhoun, PhD, EVP and President, Sales & Operations, Change Healthcare; Lisa Edelmann, PhD, Chief Diagnostics Officer, Sema4; and Alan Copperman, MD, Vice-Chairman, Department of Obstetrics, Gynecology, and Reproductive Sciences, Icahn School of Medicine at Mount Sinai, Medical Director, Reproductive Medicine Associates of New York, Chief Medical Officer, Sema4.
At Sema4, transforming healthcare is our primary mission. We believe that more information, deeper analysis, and increased engagement will improve the diagnosis, treatment, and prevention of disease. Our work is based on building dynamic models of human health using Centrellis, our innovative health intelligence platform, to generate a more complete understanding of disease and wellness.

These concepts were central to the ASRM panel discussion, which included Jaime Shamonki, MD, from California Cryobank Life Sciences; August Calhoun, PhD, from Change Healthcare; and Lisa Edelmann, PhD, Alan Copperman, MD, and Kareem Saad from Sema4. The speakers had a lively discussion about big data, variant interpretation, and helping patients all along the reproductive health journey.

Saad, who moderated the panel, set the stage for a conversation about big data in medicine. “There’s a lot of value locked in information that isn’t currently being optimized today,” he said. “Using that information to drive better clinical outcomes — better economic outcomes, even — is clearly the opportunity we have in the industry.”

Big data, said Calhoun, powers new insights that are not obvious without massive amounts of information. “Those insights could be driving early intervention, those insights could be driving understanding risks in pregnancy, those insights could drive better medical decisions,” he told attendees.

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