UCSF Offers Free Genome Sequencing to Enhance Precision Medicine

August 26, 2020 - UC San Francisco (UCSF) has launched a precision medicine initiative to offer free genome sequencing to all UCSF Health patients, creating a genomic database of diverse populations.

The initiative, called the UCSF 3D Health Study (for Data, Discovery, and Diversity) is the most comprehensive program of its kind in the US. The project will aim to broaden scientists’ understanding of the genomic variations underlying health and disease, and will help ensure that precision medicine at UCSF serves all individuals.

“We need to be able to identify and respond to diseases much earlier than we are now using preventive therapies based on deep understanding of disease biology,” said UCSF Chief Genomics Officer Aleks Rajkovic, MD, PhD, medical director of the UCSF Health Center for Clinical Genetics and Genomics, who is leading the new initiative.

“Central to that is having genetic data on a diverse spectrum of patient populations that can teach us how to keep everyone well rather than responding in crisis when they become ill.”

Other US health centers offer genotyping screenings that look for specific known markers of genetic variation, or sequence panels of specific genes associated with particular diseases. In contrast, the UCSF Health initiative will sequence the entire genome of any patient who signs up for the study, which can be done at the initiative’s website, 3dHealthStudy.org.

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“We’re strong believers that if you’re going to do genetic research using patient data, patients should benefit by getting results on valuable insights from the data,” said Elad Ziv, MD, a professor of medicine at UCSF and a lead primary care physician of the project.

“To begin with, we are focusing on a very specific list of actionable risk factors, but hope that as we expand this initiative we can add reports on genetic variants in drug response, polygenic risk scores for certain diseases, and other information that will be useful for patients and their medical teams.”

Participants in the initiative will receive reports on their genetic ancestry, as well as actionable genetic risk factors for selected diseases including cancer, cardiovascular disease, and neurological disease.

The initiative will only report findings for which there are clear clinical guidelines and management options that will allow UCSF Health providers to work with patients to reduce their health risks in a meaningful way.

“Importantly, not only will clinically relevant results be returned to individual patients, but the data will also serve as a unique and invaluable resource to the research community as a whole,” said Keith Yamamoto, PhD, director of UCSF Precision Medicine and UCSF Vice Chancellor for Science Policy and Strategy.

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“The 3D Health whole genome data will be de-identified and integrated into a secure biorepository that includes de-identified clinical, social and behavioral information, and analyzed in our precision medicine knowledge network, SPOKE, an AI-powered computational tool that will enable researchers and clinicians to define the underpinnings of health and the genetic and environmental determinants of disease across our diverse patient population.”

To adapt to the current climate surrounding the COVID-19 pandemic, the study is completely contactless. Researchers will inform participants about the study, obtain consent, ship DNA-collection kits to their homes, and process the tests without requiring any in-person interaction.

This approach will also help to diversify genomic samples, enabling a wide range of patients to participate in the study.

“One of the greatest challenges facing genomic precision medicine is that the vast majority of genetic and genomic studies have focused on a very small slice of the population: mostly male, white, and high socioeconomic status. As a result, our genomic data is the worst for the most medically underserved populations,” said Sawona Biswas, MS, LCGC, the director of the 3D Health project and scientific and clinical lead for genomics administration at UCSF.

“This is what we want to change with this study, in particular, we hope our contactless approach can improve our ability to benefit a more diverse group of people who we might not reach through our clinics alone.”

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Additionally, the initiative will work to overcome structural biases in the health research system by partnering with the Special Populations for Health Equity in Research and Education (SPHERE) Committee. This committee consists of diverse community leaders and a UCSF team with experience with diverse research participants.

“We are building a partnership with the 3D Health Study Team to help with recruitment of diverse patients and to learn how to address issues like mistrust, structural racism, and unequal access in research,” said Paula Fleisher, MA, program manager of SPHERE, senior staff of the UCSF Clinical & Translational Science Institute (CTSI) Community Engagement and Health Policy Program and associate director of the UCSF Center for Community Engagement. 

As diversity in clinical trials and genomics research is a longstanding issue in the healthcare industry, the UCSF team will work to remove barriers to participation and improve precision medicine for all patient populations.

“It’s a unique collaborative learning process that we hope will ultimately lead to equity in health and healthcare through precision medicine for our diverse communities,” said Monique LeSarre, PsyD, executive director of the Rafiki Coalition for Health and Wellness and a member of the SPHERE Committee representing the African American Community Health Equity Council. 

Through the UCSF 3D Health Study, researchers will aim to broaden representation of diverse populations in healthcare studies.

“Diversity is essential to the fabric of UCSF. Ultimately, underrepresentation of any group compromises the delivery of healthcare,” said Rajkovic.