How Safe is it to Go Back to School?

As schools start to reopen across the country, parents have some new concerns to contend with, alongside the usual anxieties about new teachers, classmates, and choosing the right backpack. Could their child catch COVID-19 at school and fall ill? Might they bring the infection home and pass it to vulnerable family members? Will further outbreaks lead to school shutdowns and more missed learning opportunities?

The most recent research indicates that while children can contract COVID-19, their symptoms are, fortunately, usually mild. However, even mildly affected children can spread SARS-CoV-2, the virus that causes COVID-19. A study published in JAMA Pediatrics found that infected children shed (release from their body) at least as much SARS-CoV-2 virus as adults. Children also shed SARS-CoV-2 for a prolonged period, according to research published in the Journal of Pediatrics, and can simultaneously have the virus and antibodies against it (often seen as an indicator of immunity) in their system. Furthermore, an in-depth contact tracing study in South Korea concluded that school-aged children were slightly more likely to transmit the virus to family members in the home than adults.

Since fever is a common symptom of COVID-19, many workplaces and other communal spaces have attempted to minimize the spread of infection by measuring the temperatures of everyone entering their premises. Could this approach help keep COVID-19 out of our schools? Unfortunately, this kind of screening could miss many infected students since not all children with COVID-19 experience fever and infected individuals can spread the virus for days before they feel ill.

The best way to detect COVID-19 is through viral testing, as it does not rely on the identification of symptoms. However, schools currently face two significant obstacles to implementing such a strategy: speed and detection.

Continue reading “How Safe is it to Go Back to School?”

Sema4 Chief Medical Officer Discusses COVID-19 and Telehealth

The COVID-19 pandemic has impacted how medical practices conduct their business as they have been forced to adopt innovative telehealth programs and processes to fulfill patients’ urgent needs. Though telehealth was already an existing method of delivering care to patients, COVID-19 has shifted many more practices towards implementing telehealth tools to continue their care of patients and become more innovative in the long run. In the video below, Sema4’s Chief Medical Officer, Dr. Alan Copperman, provides some insights on the importance of medical practices catching up to innovative solutions and how telehealth has changed healthcare for the better.  

How Sema4 Expanded Carrier Screening Brought A Family Relief — and Reliable Results

For two years, Elizabeth and Michael* lived with their daughter’s diagnosis of Gaucher disease, a genetic disorder that impacts many of the body’s organs and tissues. They anxiously watched Sophie’s development through infancy into toddlerhood for early signs and symptoms. They engaged with disease advocacy organizations and patient communities, found specialists they trusted, and prepared as best they could for the financial crush of biweekly intravenous infusions that Sophie would eventually need to cope with her illness.

However, Sophie never had Gaucher disease. Her diagnosis was the result of a false positive on a lab test, caused by a nonfunctional piece of DNA called a pseudogene.

medRxiv articleUncovering the unexpected

When Elizabeth was pregnant with Sophie, she found out through a targeted carrier screen for people of Ashkenazi Jewish descent that she was a carrier of a relatively mild version of Gaucher disease. Carriers themselves are unaffected; it’s only when someone inherits the disease-causing variant from both parents that he or she will develop the disease. Gaucher disease affects the spleen, liver, and bone marrow and is a variable onset disease, which means symptoms may appear anytime during childhood or even early adulthood. While treatable, treatment for most people means intravenous infusions every two weeks for life. On top of the emotional and physical stress of this disease, treatment is very expensive, running into hundreds of thousands of dollars per year for a single patient – a heavy financial burden that many people cannot afford.

Continue reading “How Sema4 Expanded Carrier Screening Brought A Family Relief — and Reliable Results”

Outcomes Data Published from Large, Diverse COVID-19 Patient Study in NYC

Today, Sema4 scientists released results from an analysis of patients tested for SARS-CoV-2 at five hospitals in the Mount Sinai Health System. Spanning more than 28,000 patients, this is one of the largest and most racially diverse COVID-19 studies performed in the U.S. to date. The study findings were posted as a preprint on medRxiv.

medRxiv articleOur team analyzed de-identified electronic medical records from 28,336 patients tested for SARS-CoV-2 at Mount Sinai Health System hospitals in Manhattan, Brooklyn, and Queens between February 24 and April 15. Of those patients, 6,158 tested positive for the coronavirus and 3,273 were admitted to the hospital.

Consistent with other reports, this study confirmed that COVID-19 prevalence in African Americans and Hispanics is disproportionately high in New York City. However, for patients admitted to the hospital, our analysis found no differences in mortality rates based on ethnicity, indicating that in-patient care helps to address this healthcare disparity.

Continue reading “Outcomes Data Published from Large, Diverse COVID-19 Patient Study in NYC”

Sema4 Study Underscores the Importance of Expanded Carrier Screening for Individuals of Jewish Descent

Expanded carrier screening provides maximal carrier identification for individuals of all Jewish backgrounds, according to a recent study, by researchers from Sema4 and the Icahn School of Medicine at Mount Sinai. Our results, published in Molecular Genetics & Genomic Medicine, showed that the majority of variants detected using an expanded panel would be missed by following subgroup-specific guidelines.

Jewish Migration MapScreening for genetic disease in Jewish populations

Some genetic diseases are more common in individuals of Jewish ancestry than in the general population. There are also differences in disease frequency between Jewish subgroups. These disparities have led to subgroup-specific recommendations for what should be tested and the labeling of conditions as Ashkenazi Jewish (AJ)- or Sephardi/Mizrahi Jewish (SMJ)-specific.

Sema4’s core mission is to improve health outcomes through increased data and information. The study’s authors, headed by our Chief Diagnostics Officer, Dr. Lisa Edelmann, therefore questioned whether a subgroup-specific approach is an optimal way to detect carriers, or whether a broader approach is better. To answer this question, we set out to design a next-generation sequencing (NGS)-based targeted panel that included not only AJ and SMJ diseases but also pan-Jewish and pan-ethnic conditions.

Continue reading “Sema4 Study Underscores the Importance of Expanded Carrier Screening for Individuals of Jewish Descent”

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.

Continue reading “Women’s History Month Q&A with Kate Bogdanova”

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.

Continue reading “Women’s History Month Q&A with Michelle Ning”

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.

Continue reading “Women’s History Month Q&A with Nefize Sertac Kip”

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.

Continue reading “Women’s History Month Q&A with Whitney Jappe”

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.

Continue reading “Digital Health Tools Glean Clinical Intelligence from Patient Records”