The Institute for Human Genetics Fall/Winter Newsletter 2023

IHG Fall/Winter

Newsletter 2023

Message from the Director:

Dear IHG Community,

As we approach the end of the year, I want to extend warm wishes to each and every one of you for a happy, healthy, and safe holiday season. This time of reflection prompts mixed emotions as we consider the events both within our Institute and in the wider world. While we remain dedicated to our crucial work in research and patient care, it is impossible to ignore the ongoing conflicts in the Middle East and Ukraine. The sadness that these situations bring weighs on our hearts, and our thoughts are with those affected.

Despite the ongoing challenges, the Institute for Human Genetics is looking toward the future with optimism. In the midst of these unusual times, there have been noteworthy highlights and exciting developments within our community. As we pause to reflect, let's take a moment to acknowledge and celebrate some of the positive events that have occurred this past year.

First and foremost, we extend our heartfelt congratulations to our very own Neil Risch, Ph.D., the former Director of this Institute, for being honored with the prestigious title of Lifetime Achievement Award by the ASHG. This esteemed award is a testament to Neil's outstanding contributions to the field of human genetics and genomics throughout his career. We applaud Neil for his lifetime of achievements and acknowledge the pivotal role he played in founding this Institute.

In the ever-evolving field of genetics and genomics, staying at the forefront of advancements is crucial. We had a very successful second Genotech Symposium. Our goal when establishing this event was to provide a consistent platform that effectively bridges the gap between industry and academia. The event this past October exceeded all expectations, drawing over 400 registered participants. It featured 19 speakers from diverse backgrounds, engaging panel discussions and corporate sponsorships, and provided invaluable networking opportunities. By fostering collaboration, sharing insights, and facilitating meaningful connections, we aspire to contribute significantly to the continued growth and progress of our dynamic field. The success of this year's symposium is a testament to the dedication and enthusiasm of our community. We eagerly anticipate building on this momentum, creating an even more impactful and enriching experience in the years to come. A heartfelt thank you to everyone who contributed to the success of the IHG Genotech Symposium. We look forward to many more fruitful collaborations and advancements on the horizon.

I am also pleased to report on the success of our ongoing community events, particularly the Technology Seminar Series held alongside CAT & Co-Labs. Over the past year, we have hosted ten events featuring highlights from various partners in the industry. The attendance at these seminars has been impressive, underscoring the community's interest and engagement in staying informed about the latest technological advancements.

Additionally, our IHG Seminar Series has continued to thrive, with thirteen events since January. I want to express my sincere gratitude to Laurie Weiss, PhD and Elliott Sherr, MD, PhD for their dedicated efforts in organizing these seminars. Their commitment has been instrumental in the success of the series, allowing us to showcase the outstanding work of faculty members and present remarkable studies conducted by our trainees. These events not only contribute to the dissemination of knowledge but also foster a sense of community and collaboration within our Institute. Looking ahead, we are committed to maintaining the momentum of these events and providing valuable platforms for learning, networking, and showcasing the exceptional talent within our community.

I am delighted to share the thriving success of our Genetic Counseling Master Program, a testament to the exceptional leadership of Cindy Morgan, MS. Under her guidance, the program has flourished, recently welcoming its third cohort to campus in late September. As the fall quarter comes to a close, we can proudly acknowledge the hard work and dedication of all students. It brings us great joy to witness the achievements of our alumni, particularly those from the inaugural cohort, who are actively contributing to the larger genetics community. Two alumni had the honor of presenting their capstone research projects as podium presentations at the annual Genetics Exchange conference in September in Madera, CA. Additionally, six alumni showcased their capstone research through poster presentations at the annual Genetic Counseling Conference in October in Chicago. These accomplishments reflect the quality of education and training provided by our program, and we are immensely proud of the impact our graduates are making in the field. A heartfelt thank you to Cindy Morgan for her outstanding leadership and to all those who contribute to the success and growth of our Genetic Counseling Master Program. We look forward to seeing continued excellence and innovation from our students and alumni in the future.

I'm pleased to inform you that our faculty search is well underway, and we've received an overwhelming response with over 125 applications. The search committees are diligently reviewing the submissions, and we anticipate making some exciting updates regarding this recruitment in the coming months. The high level of interest and the caliber of applicants are truly promising, reflecting the continued growth and excellence of our Institute. We are enthusiastic about the potential contributions that new faculty members will bring to our dynamic community. If you have any questions or would like more information about the ongoing faculty search, please feel free to contact me. Your input and engagement are valued as we work to strengthen and expand our team.

Thank you all for your continued dedication, hard work, and resilience. Together, we look forward to a brighter future and contributing to positive change in the world.

We are wishing you and your loved ones a peaceful holiday season.

Sincerely,

Nadav

Faculty Profile: Neil Risch, PhD

Neil Risch, PhD, the Lamond Family Foundation Distinguished Professor in Human Genetics and founding director of the IHG, is the 2023 recipient of the Lifetime Achievement Award from the American Society of Human Genetics (ASHG). The award recognizes substantial and far-reaching scientific contributions to human genetics, and it comes with a $25,000 prize.

Risch feels humbled and honored to receive the award, he said. When he started reflecting on his five-decade career and all the people he wanted to thank for their contributions along the way, he recorded an acceptance speech that turned out to be 67 minutes.

“All my teachers, mentors, colleagues, collaborators, students, clinical fellows, trainees, postdocs, grad students — there are so many people to acknowledge and thank,” he said. “However far I've gone, it has been because of all the people around me who supported the work.”

Collaboration is what Risch has enjoyed most about his career so far, he said. It was the spirit he brought to his role as founding director of the IHG.

“We partnered with various departments to create a community,” he said. “It includes a broad spectrum of people, and I feel that is so important, because all of us in our different disciplines have something important to contribute to the problems that we are studying in genetics.”

Risch is currently studying common diseases such as cardiovascular disease, as well as rare Mendelian disorders.

“The most rewarding part of what I do is mentoring my trainees,” he added. “When I see their success, nothing means more to me than that.”

Researcher Profile: Kiruthika Sivaraman, MCS

Kiruthika Sivaraman, MCS is bringing together more than a decade of computer science experience and her passion for genetics in the effort to learn more about the genes responsible for autism.

Sivaraman is a researcher in the lab of Dr. Lauren A. Weiss, a professor in the IHG, Department of Psychiatry and Behavioral Sciences, and Weill Institute for Neurosciences. The Weiss Lab’s goals are to use genetic tools to improve the understanding, prevention, diagnosis, and treatment of autism and related traits. Sivaraman’s efforts are focused on analyzing autism data to understand the genes responsible for sex differences in the prevalence of autism. Approximately four males are diagnosed with autism for every one female diagnosed.

“Currently, neurological diseases like autism are very hard to understand,” Sivaraman said. “I am driven every day by knowing I am playing a small role in improving our knowledge of autism.”

Sivaraman holds bachelor’s and master’s degrees in computer science, and she leads the effort to parse big data for the Weiss Lab, with datasets that can reach 10 million records. She writes code that automates processes and reduces the manual intervention needed to analyze massive amounts of data. She is continually finding new ways to improve her coding, too, including modifying one code so it went from a one-day running time to just four minutes.

“Because I come from a tech background, it is really easy for me to pick up new software, tools, and operating systems like Unix, then start making progress quickly with analyzing data,” she said.

Sivaraman is applying for doctorate programs and plans to focus on genetics and bioinformatics.

Staff Profile: Suzanne Mackey, JD

Suzanne Mackey, JD has worked across the full spectrum of administrative support roles at UCSF over the years, earning deep insights into university policies and systems along the way.

She has learned the process for both submitting and reviewing reports in university systems including MyExpense for expenses and BearBuy for procurements.

“I am really highly skilled at noticing what is allowable or what is not allowable, then making sure that people have all the information they need to process expenses or move along procurement,” she said.

In her current role as an administrative officer with the IHG, Mackey has a wide variety of duties. She provides administrative assistance to several of the IHG committees, including the executive committee. She also provides executive level support for several faculty and supports four principal investigators. Her duties include processing expense requests, arranging travel, and managing calendars. She works with the human resources team to help with all aspects of onboarding when new lab members are hired, too.

Recently, Mackey has been supporting recruitments for two faculty openings at IHG. She reviewed applications to make sure they were complete and organized the applicant information for the search committee.

“I am fortunate to work in a very positive environment and to work with a lot of wonderful faculty and staff,” she said. “It is a joy to work with such diverse and talented individuals. Everyone here is bright, fun, and collaborative. I really enjoy interacting with them on a daily basis.”

Meet Our New IHG Faculty Members

Ryan Corces, PhD

Assistant Professor of Neurology

The Corces lab melds epigenomics, computational biology, large-scale screens, and single-cell technologies to study neurodegeneration. We make heavy use of primary patient tissue to form hypotheses that can be tested in cellular and organismal model systems. Our long-term research interest is to use insights from the epigenome to inform our understanding of neurological disease with the goal of identifying novel avenues for therapeutic intervention. More specifically, we are interested in how the genome and epigenome intersect and how inherited genetic variation interfaces with lived experiences and environmental factors to produce durable and functional epigenetic alterations that lead to Alzheimer’s and Parkinson’s disease.

Hani Goodarzi, PhD

Associate Professor of Biochemistry and Biophysics

Cancer, fundamentally, is a disease of disordered gene expression. Cancer cells rely on deregulated expression of oncogenic and tumor suppressive pathways to initiate and maintain the transformation process. Thus, delineating how cancer cells achieve such pathologic gene expression states is a crucial step towards understanding and ultimately treating cancer as a disease. Towards achieving this goal, The Goodarzi Lab employs a systems biological and multidisciplinary approach that integrates computational and experimental strategies to identify and characterize key regulatory programs that underlie cancer progression. The systems-level frameworks implemented in our lab ensure a truly unbiased and systematic approach to studying this key biological challenge.

Karla Lindquist, PhD

Head of Data Science, UCSF Library

Dr. Lindquist has worked on a variety of projects as a statistician and bioinformatician at UCSF since 2001. Her interest in genetics and genomics began while working on the Human Genome Project prior to joining UCSF. Her equal passion for analytics led her to UCLA for a master's degree in Biostatistics, followed by a PhD in Biological and Medical Informatics from UCSF, where she studied the genomic landscape of urologic cancers and other complex diseases. Since 2017, she has also been involved in various education efforts at UCSF as the Head of Data Science in the UCSF Library and as the Co-Chair of the IHG Education Committee.

Vasilis Ntranos, PhD

Assistant Professor, Diabetes Center

Vasilis Ntranos obtained his PhD in Electrical Engineering from USC in 2015, working on network information theory problems and their applications in data storage and wireless communications. After his graduate studies, Vasilis moved his focus to computational biology and machine learning, completing his postdoctoral training in EECS and Biological Engineering, working with Lior Pachter and David Tse at UC Berkeley, Stanford, and Caltech.

Arun Padmanabhan, MD, PhD

Assistant Professor of Medicine

Dr. Padmanabhan is a cardiologist specializing in general cardiology. His specific interests include preventive cardiology, lamin A/C gene (LMNA) associated cardiomyopathies, and right heart disease in athletes.

Dr. Padmanabhan’s research focuses on understanding the gene-regulatory and epigenetic pathways that govern cell fate decisions during early cardiac development and cell state transitions in the pathophysiology of heart failure.

Vasanth Vedantham, MD, PhD

Associate Professor of Medicine

Dr. Vedantham is a physician scientist and clinical cardiac electrophysiologist with a special interest in treating patients with inherited arrhythmias and cardiomyopathies. The Vedantham Lab is focused on the intersection of the basic biology of heart rhythm with human genetics. They use both hiPSC-derived cardiomyocytes and mouse models to explore the regulatory networks that guide formation and function of the cardiac conduction system, and to define the impact of rare and common genetic variation on heart rhythm phenotypes including heart rate regulation and atrial fibrillation. Ultimately, the lab hopes to leverage their discoveries to define new therapeutic targets and treatments for patients with heart rhythm disorders.

Honors & Awards

ASHG Honors Neil Risch, PhD with the 2023 ASHG Lifetime Achievement Award

The American Society of Human Genetics (ASHG) has named Neil Risch, PhD, Lamond Family Foundation Distinguished Professor in Human Genetics and Founding Director of the Institute for Human Genetics, at the University of California, San Francisco (UCSF), as the 2023 recipient of the annual ASHG Lifetime Achievement Award.

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Yusuph Mavura, MS - Awarded F99 Grant

Mr. Mavura's F99 application titled “Assessing the Clinical Utility of Polygenic Risk Scores in Ancestrally Diverse Real-World Cohorts" was deemed overall an exceptional application in nearly every way by the the GNOM-G review panel.

"The PI is well positioned to take maximum advantage of the F99 training mechanism. A great deal of enthusiasm was expressed for the application and candidate."

Akinyemi Oni-Orisan, PharmD, PhD - Awarded R01 Grant

Dr. Oni-Orisan's R01 application titled “Genetic and social determinants of pharmacological health outcomes in ancestrally diverse populations” was awarded as exceptional.

"This is an outstanding investigator who has assembled a superb team to study genetic and social determinants of drug outcomes in diverse populations. The SEP expressed enthusiasm for the application."

Over 30 UCSF Scientists Honored for Highest Impact in Their Fields

Thirty-two UC San Francisco scientists are among the most influential individuals in their respective fields, according to the most recent analysis of research citations by the science and intellectual property company, Clarivate.

Researchers were chosen according to authorship of highly-cited journal articles – those that ranked in the top 1% by citations for their field(s) and publication year over the past decade. This citation-based list was then refined by expert judgment at Clarivate to produce a final slate representing the top 0.1% of all scientists.

IHG Faculty Include: