The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in 2003, with the goal of understanding the DNA grammar of non-coding sequences, which constitutes 98% of the human genome. A new round of funding for five centers was announced on February 2nd to expand this flagship program.
Two of our IHG faculty members, Drs. Nadav Ahituv and Yin Shen, will lead two of the five new “characterization centers” to study how non-coding regulatory elements influence gene expression and, consequently, cell behavior. The Ahituv and Shen labs will be employing novel techniques to study enhancers, which play a critical role in gene expression.
The work of Drs. Ahituv and Shen epitomizes how basic characterization of the human genome and its expression can lead to a fuller understanding of how disease develops and to potential treatment strategies. Hearty congratulations to Nadav and Yin!
The IHG community gathered at the Forest Hill Clubhouse on December 13, 2016 to celebrate the 10th Anniversary of our Organized Research Unit and the year-end holidays.
The evening featured the professional magician-comedian Robert Strong as well as our own talented performers Nadav Ahituv, PhD, who showed off his juggling skills, and Sherman Jia, who gave a viola performance. Those who took advantage of the photo booth donned hats and wigs and shared in some fun with their friends and co-workers.
We wish you all a happy and safe holiday season and we look forward to the next 10 years of genetics advances.
Best wishes for a happy, healthy and prosperous 2017.
U.S. News & World Report has, for the second year in a row, ranked UCSF #3 in Molecular Biology and Human Genetics. In their recent report for 2016, published October 24, 2016, benchmarked against 1000 institutions across 65 countries, UCSF was ranked #16 overall among all institutions (up from #23 from last year). In the area of Molecular Biology and Genetics, UCSF was ranked only behind Harvard and MIT. The evaluation is based primarily on global and regional reputation and publications and citation impact.
Responding to the ranking, IHG Director Neil Risch, PhD said, “Once again, this is an important recognition of the pre-eminence of UCSF in the area of genetics and human genetics as well as molecular biology. It is an exciting and affirming acknowledgment of our sustained major contributions in these areas — and one in which we should all be proud. Hearty congratulations to all of our IHG and UCSF members in Genetics and Molecular Biology.”
For more information about the ranking methodology, please see the article.
UCSF has a longstanding relationship to the American Society of Human Genetics (ASHG), dating back to the arrival of Charlie and Lois Epstein at UCSF in 1967. Three UCSF faculty members have served as ASHG presidents, and many more have received prestigious awards.
This year, we will start a new tradition of highlighting faculty, postdocs, students and staff participating in the ASHG 2016 meeting on October 17-22 in Vancouver, BC. A PDF of the 2016 schedule of UCSF presentations by name and abstract title is here.
Each year, our students and postdocs are among the semifinalists and finalists for the coveted Charles Epstein Trainee Awards. This year, we are proud to report that graduate student Rachel Gate (Ye Lab) was a semifinalist, and postdoc Joshua Hoffman (Witte Lab) is a finalist, for the Epstein Award.
All UCSF faculty, alumni, trainees and staff are warmly invited to attend a reception hosted by IHG and Department of Pediatrics, Division of Medical Genetics on Wednesday, October 19 @ 7:00pm – 11:00pm at Tap & Barrel – Convention Centre at 1055 Canada Place, Vancouver.
For more information, please contact Lynn Duncan at 415.476.1127 | firstname.lastname@example.org
Esteban cultivated an early interest in health disparities, genetics and pulmonary medicine while at Stanford University. As a Harvard medical resident, working with Jeffrey Drazen, MD, Esteban identified a genetic risk factor for asthma severity that was 40% more common in African Americans than European Americans.
Esteban continues to study the genetics, epidemiology and pharmacogenetics of asthma as UCSF’s Harry Wm. and Diana V. Hind Distinguished Professor in Pharmaceutical Sciences. He is best known for the GALA and SAGE studies which analyze the interplay of social, environmental and genetic factors affecting asthma risk and treatment in minority youth. These studies comprise the largest pediatric gene-environment study of asthma in ethnic/racial minority populations in the U.S.
Esteban has consistently advocated for better representation of diverse populations in biomedical research and physicians and scientists from minority and disadvantaged groups, asserting that a better understanding of genetics in minority and underserved populations leads to more targeted therapy for all individuals.
Figure: Lifetime asthma prevalence varies substantially by race/ethnicity, making asthma the most disparate chronic disease in the U.S.
Severe combined immunodeficiency (SCID) is rare, but a founder mutation in the DNA repair enzyme Artemis (DCLRE1C) causes SCID in 1/2000 Navajo Native American infants. SCID infants lack T and B lymphocytes, and untreated SCID patients succumb to viral, bacterial and fungal infections early in life unless treated, usually by bone marrow transplant.
In 2005, Jennifer Puck, MD, developed a newborn screening (NBS) test for SCID based on measuring T-cell receptor excision circles (TRECs) in DNA isolated from infant dried blood spots. This test allows SCID to be detected in pre-symptomatic newborns, making possible optimal treatment. California started universal SCID NBS in 2010.
In a 2014 study of SCID NBS in 11 public health programs, Dr. Puck and her colleagues showed that SCID in the general population is twice as common as previously thought (1/58,000 births); 52 cases were found and none were missed; and the TREC assay also detected other disorders with low lymphocytes. 36 states and the Navajo Nation now have SCID NBS, and UCSF has treated 28 infants, including 5 Navajos referred here for bone marrow transplants. Dr. Puck directs the UCSF Jeffrey Modell Diagnostic Center for Primary Immunodeficiences and with Dr. Mort Cowan is developing gene therapy for Artemis deficient SCID.
U.S. News & World Report has created a new system to rank universities globally. In their recent report for 2015, published in October, benchmarked against 750 institutions across 60 countries, UCSF was ranked #23. However, in the area of Molecular Biology and Genetics, UCSF was ranked #3, following only Harvard and MIT. The evaluation is based primarily on global and regional reputation and publications and citation impact.
Responding to the ranking, IHG Director Neil Risch, PhD said, “This is an important recognition of the prominence of UCSF in the area of genetics and human genetics, as well as molecular biology more generally. Because the ranking is based primarily on the reputation of our faculty members and their published research, it is an exciting and affirming acknowledgment of the major contributions we have made over the past years and currently, and one in which we should all be proud. Hearty congratulations to all of our IHG members and beyond.”
For more information about the ranking methodology, please see the article.
Congratulations to the winners of the IHG Symposium 2015 poster session. The award for Best Poster by a Graduate Student was given to Meena Subramaniam (Ye and Zaitlen labs). Yambazi Banda (Risch lab) and Emilie Barruet (Hsiao lab) shared the award in the Postdoc category.
Meena’s poster outlines a statistical method to leverage Allele Specific Expression in Quantitative Trait Loci (QTL) detection that she is currently developing. Through simulations as well as real data she showed that applying a linear mixed model framework accounting for the noise correlation between the two copies of each gene resulted in more powerful and accurate detection of QTLs.
The work presented in Yambazi’s poster was analyses of mating patterns and genetic ancestry between and within the European, East Asian, Latino, African American, and South Asian participants in the Northern California Kaiser Permanente Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. The very complex nature of structured mating observed suggests a need for its careful consideration when designing and interpreting population-based genetic studies.
Emilie’s poster investigates the role of endothelial cells in abnormal bone formation in Fibrodysplasia Ossificans Progressiva (FOP). She uses human induced Pluripotent Stem Cells to create affected cell types that cannot be directly isolated from FOP patients. She found that FOP iPS-derived endothelial cells show increased cell plasticity as well as a predisposition towards osteogenesis.
The 18 posters printed by students, postdocs, and faculty represented the broad range of research being conducted in the IHG. Congratulations to all who participated.
If it wasn’t clear before, it was by the end of the symposium when Y.W. Kan received a lengthy standing ovation that his work is revered and appreciated by top geneticists around the world.
The IHG was proud to celebrate pioneering geneticist Y.W. Kan in a special research symposium held Monday, November 2. The program included talks by NIDDK Director Griffin Rodgers, Dennis Lo, 2015 Epstein Lecturer Stuart Orkin, Katherine High, James Gusella, and Robert Nussbaum.
Also on hand to deliver special remarks throughout the day were UCSF School of Medicine Dean Talmadge King, UCSF Benioff Children’s Hospital President & CEO Bertram Lubin, and former Dean Lloyd H. Smith. Smith recruited Kan to UCSF in 1972.
During the post-symposium reception, the IHG awarded prizes for the best poster presentations to Meena Subramaniam (graduate student), Yambazi Banda (postdoc), and Emilie Barruet (postdoc).
Also announced were the faculty winners of the IHG Exploratory Grant competition to help seed new research ideas. The two winning proposals were submitted by Jimmie Ye & Yin Shen and Nadav Ahituv.
Y.W. Kan’s pioneering research into the hemoglobinopathies sickle cell anemia and thalassemia has widely impacted genetic research, diagnostics, and treatment of human disease. The Institute for Human Genetics is proud to recognize Y.W. Kan with a symposium honoring his decades-long contributions.
Y.W. Kan arrived at UCSF in the 1970s when he and many others (including Herb Boyer and Bishop & Varmus) helped usher in the era of molecular genetics. With long-time collaborator Andrée Dozy, he discovered the first polymorphism in human DNA by Southern blot analysis in 1978, launching the ability to map genes on human chromosomes.
He and another long-time collaborator, Judy Chang, used those same techniques in 1979 to show how missing genes cause disease. He is the recipient of many national and international awards for his contributions. He continues to investigate the treatment of these diseases using stem cell and iPS cell therapies.
The Symposium will feature presentations from James Gusella, Katherine High, Dennis Lo, Bertram Lubin, Robert Nussbaum, Stuart Orkin, and Griffin Rodgers. Stuart Orkin will be featured as the 2015 Charles J. and Lois B. Epstein Visiting Professor.
Featured topics will include gene mapping, gene therapy, hemoglobinopathies, and non-invasive prenatal testing.
Join us in honoring genetics pioneer Y.W. Kan
The IHG Symposium will be held November 2, 2015 at 1:00-6:30 in Cole Hall on the UCSF Parnassus campus and will include a poster session and awards.
Yin Shen was recruited to the Institute for Human Genetics from Dr. Bing Ren’s lab at Ludwig Institute for Cancer Research at UC San Diego in La Jolla, CA, where she led the genomic functional characterization effort in the mouse ENCODE project. She earned her PhD from UCLA, where she studied epigenetics and gene regulation, utilizing cutting-edge genetics, genomics and stem cell technologies.
Chun (Jimmie) Ye received his PhD in Bioinformatics and Systems Biology at UC San Diego/UCLA, where he developed a number of statistical methods for identifying and interpreting genetic loci associated with gene expression (eQTL). As a postdoc at the Broad Institute under Aviv Regev, Jimmie led a team of computational and experimental biologists to study the role of genetic variation in the response of immune cells to cytokines and/or pathogens.
Yin and Jimmie are settling beautifully into their respective labs on the 9th floor of UCSF Parnassus. Please stop by to say hello, and join us in wishing them great success at UCSF.
The IHG is proud to announce that Louis Ptáček will receive the American Society for Clinical Investigation’s Stanley J. Korsmeyer Award and Ophir Klein will be awarded the E Mead Johnson Award from the Society for Pediatric Research.
Louis Ptáček, MD, PhD is a pioneer in the field of “channelopathies”— episodic and electrical disorders of muscle, heart and brain. He cloned the genes for all the familial periodic paralyses and proposed these rare muscle disorders as a model for pathogenesis of cardiac arrhythmias, epilepsy and migraine. This work has already led to better diagnosis and treatment of patients.
Ophir Klein, MD, PhD has worked at the interface of genetics, development, and evolutionary biology to advance our understanding of stem and progenitor cells. He has used the continuously-growing rodent incisor as a novel system for investigating mammalian stem cells, and his group has also made contributions to the biology of renewal in the intestine, tongue, and other organs.
Louis Ptáček will receive his award at the annual ASCI Meeting in April. Ophir Klein will receive his award at the annual Pediatric Academic Societies meeting in April.
A 1959 graduate of Harvard Medical School, Dr. Epstein moved to San Francisco to join the UCSF Cancer Research Institute, initially as a research physician and later becoming Associate Director. She was a pioneer in the research of interferons, and together with husband Dr. Charles Epstein, developed the first mouse model for Down syndrome. Her many honors included a National Institutes of Health MERIT award, the Lifetime Achievement in Research Award from the International Society for Interferon and Cytokine Research, and an honorary Doctor of Science Degree.
Above all, Dr. Epstein was a warm and loving person who brought a spirit of grace to every aspect of her life. She will be missed. The Epstein Family legacy is honored by The Charles J. and Lois B. Epstein Visiting Professorship, which provides for an annual UC lectureship by a globally renowned human geneticist.
At the recent 2014 annual meeting of the American Society of Human Genetics in San Diego, the ASHG Award for Excellence in Human Genetics Education was given to our own Suzanne Cassidy, MD. The award was established to recognize those who have made significant contributions of exceptional quality and great importance to human genetics education.
Suzanne is well known for her clinical and research leadership in understanding the Prader-Willi syndrome. She has played key roles in the genetics education of medical students, residents, and trainees as well as of patients and their families. She has developed a variety of educational materials, including three editions of the textbook Management of Genetic Syndromes, and clinical genetics training programs around the country. She was also a member of the founding Residency Review Committee for Medical Genetics when the field was first recognized as a medical specialty, and has served on the American Board of Medical Genetics and Genomics. She currently serves as President of the International Prader-Willi Syndrome Organization.
While the IHG has among its members a number of former ASHG award winners, Suzanne holds the unique position as our only recipient of this award.
Knowledge is power. Joseph Shieh MD, PhD and his colleagues are developing new tools to leverage big data for precision medicine. In their recent studies, Dr. Shieh, a genomics physician at UCSF, and colleagues Xiaoyan Ge, PhD and Pui-Yan Kwok MD, PhD teamed up to produce practical tools for healthcare application.
“We’re using smart tools to predict disease by analyzing vast amounts of genetic sequence data,” said Dr. Shieh. Building on a foundation from human genome projects and global population sequencing efforts, the team from UCSF set out to examine thousands of human protein-encoding genes for disease-prediction patterns. Science has deciphered a fraction of the genes that affect health, but with exome technologies advancing, Shieh and his colleagues have developed new predictive tools to analyze variation patterns in thousands of genes. Remarkably, they found genes on the X-chromosome, a sex chromosome, are highly influential in early-onset diseases and harbor many novel disease markers useful for disease prediction. Paper
“The power of informatics and genetics to predict human disease is remarkable,” Ge, a post-doctoral fellow with Dr. Shieh, stated. The team would like to expand the work and use of smart tools to revolutionize care in settings such as the UCSF Genomics Clinic, where Dr. Shieh sees his patients. “There are more than twenty thousand genes in the genome and we can now decode that genetic information, but we need to leverage the knowledge for patients,” Shieh remarked. “These efforts forward care for undiagnosed disease patients, and we should also advance children’s health, preterm birth studies, and preventive care in adults using this collective knowledge.”
Next-generation genomics can be described as the combination of sequencing technologies and big data analytics. The potential impact of this disruptive technology in health care will be primarily realized through extending and enhancing lives through faster disease detection, more precise diagnoses, new drugs, and more tailored disease treatments. The technical challenges inherent in genetic engineering technology are great but may be less formidable than the social, ethical, and regulatory concerns it may generate. Please join us for a discussion of the possibilities and the challenges of next-generation genomics and implications for health care worldwide.
Tuesday, September 16, 2014 @ 6:30 – 8:00 PM
UCSF faculty, staff, and students can attend for FREE if you RSVP HERE using the code: UCSFGENOMICS (ID must be presented at event)
Byers Auditorium, Genentech Hall, UCSF Mission Bay Campus
600 16th Street, San Francisco, CA
Robert Nussbaum — Chief, Department of Medicine & UCSF Institute for Human Genetics, UCSF
Timothy Behrens — Senior Staff Scientist and Director, Human Genetics, Genentech
Francis deSouza — President, Illumina Corporation
Michael Chui — Partner, McKinsey Global Institute
This is a World Affairs Council event and is sponsored by the IHG, UCSF, and BayBio
We are pleased to announce UCSF Informatics Day — Leveraging Clinical Data for Research was a resounding success! Thanks to all who joined for the inaugural UCSF Informatics Day!
With over 400 UCSF Faculty, Students, and Staff in attendance; and a program featuring leadership talks, resource talks, and scientific use cases as well as booths showcasing various campus informatics resources. We will be making many of these talks available on the web, please check the website for updates. Our program featured:
• Plenary Lecture • UCSF Leadership talks • Use-Case talks
• Informatics Resources • Networking Opportunities!
SLIDES OF THE TALKS ARE AVAILABLE on the Informatics Day website
We are pleased to announce the UCSF INFORMATICS DAY — Leveraging Clinical Data for Research. The event will showcase clinical data sources for use in basic, translational, and clinical research. Over the past few years, UCSF has significantly expanded its informatics and IT footprint, providing expanded critical services to support basic, translational, and clinical research. UCSF Informatics Day will give you the opportunity to learn about the systems and tools available to support your research.
The day will feature
- Keynote Speaker addressing the role of informatics in biomedical research
- Short presentations highlighting the available systems and tools
- Scientific presentations by investigators who are utilizing these resources in their own research
- Booths with hands-on demonstrations
Please join us and your UCSF colleagues to see how you can benefit from the investments that we’ve made and continue to make in the informatics infrastructure at UCSF.
Organized by CTSI, Institute for Human Genetics, Institute for Computational Health Sciences, UCSF Office of Research, and UCSF Medical Center
Laurie Stevison, PhD, a Postdoctoral Fellow in the IHG, was recently awarded the John Maynard Smith prize for outstanding young evolutionary biologist from the European Society for Evolutionary Biology (ESEB). Stevison will give the JMS 2014 prize lecture at the ESEB Congress 2015 in Lausanne, Switzerland and has been offered a junior fellowship at the Wissenschaftskolleg Institute in Berlin.
Stevison is an evolutionary geneticist interested in speciation, recombination rate evolution and hybridization. She completed a master’s degree from Rice University working with Michael Kohn on hybridization in macaques. Most recently, she received her PhD from Duke University in 2011, where she studied recombination and speciation in Drosophila with Mohamed Noor.
Stevison is currently an NIH Ruth Kirschstein NRSA Postdoctoral Fellow with IHG Faculty mentor Jeff Wall. She is working on several collaborative research projects, including comparative genomics of recombination rate variation in great apes.
Wylie Burke, PhD, MD, Professor of Bioethics and Humanities at the University of Washington, has been named the 2013-14 UCSF Presidential Chair. The IHG serves as one of Professor Burke’s hosts for this Chair, awarded to encourage new, interdisciplinary program development.
Burke is one of the preeminent scholars examining the ethical, legal, and social implications (ELSI) of advances in human genetics, particularly the translation of novel genomic technologies from the bench to the clinic.
She received a PhD in Genetics and an MD from the University of Washington. Professor Burke is a member of the Institute of Medicine, past President of the American Society of Human Genetics, and former Chair of the Institute of Medicine Roundtable on the Translation of Genome-based Research for Health. She is also the founding director of the University of Washington’s Center for Genomics and Healthcare Equality, funded by the National Human Genome Research Institute.
While at UCSF, Professor Burke will give a series of lectures (the PRESIDENTIAL CHAIR LECTURE SERIES) MAY 5-9, 2014, teach an inter-disciplinary course “Challenges in ‘Precision’ Genomic Medicine and Public Health,” in the Spring Quarter 2014, and participate in seminars and working groups sponsored by the Kaiser Permanente / UCSF Center for Transdiciplinary ELSI Research in Translational Genomics (CT2G) and the Institute for Human Genetics (IHG).
Two long-term genetics faculty retired on June 30, 2013. We would be remiss if we didn’t acknowledge their long term contributions to the field of human genetics both locally and nationally/internationally.
Jane Gitscher, PhD, Professor of Medicine and Pediatrics and Associate Director of the IHG, and Seymour “Sy” Packman, MD, PhD, Professor of Pediatrics have devoted upwards of 60 years (combined) to UCSF. Both have a strong history of training students and seeking answers to genetic questions — Sy on the clinical side and Jane at the bench and in the classroom. They also collaborated on a research project to study disorders of copper transport caused by gene mutations. Both are internationally recognized for their long and productive careers, numerous important findings, and service to human genetics organizationally.
Human Genetics at UCSF owes its prominence today to faculty like Sy and Jane who energetically pushed for greater Genetics presence in the curriculum and in the clinics. We are grateful for their participation and contributions to the Institute for Human Genetics and look forward to seeing them at future IHG events as emeritus/emerita faculty!