Genetic Changes that Cause Autism Are More Diverse Than Previously Thought

Researchers find that the genetic causes of autism consist of a wide variety of genetic changes —

The types of gene mutations that contribute to autism are more diverse than previously thought, report researchers at University of California, San Diego School of Medicine in the March 24 online issue of The American Journal of Human Genetics. The findings, they say, represent a significant advance in efforts to unravel the genetic basis of autism spectrum disorder (ASD). …Read the Full Story from the UC San Diego Newsroom


Keith Vaux, MDDr. Keith Vaux, Professor of Clinical Medicine in the Division of Medical Genetics and Professor of Neurosciences, is a coauthor of the study report.

He conducts neurodevelopmental research with particular interest in rare diseases, epilepsy and autism.

Dr. Vaux did his internship and received his pediatrics residency training at the Naval Medical Center, San Diego. In his fellowship work in dysmorphology and medical genetics, Dr. Kenneth Lyons Jones was his mentor.

Dr. Vaux is Clinical Chief of Medical Genetics for UC San Diego Health.

Altman Clinical and Translational Research Building Makes Its Debut

New structure will be campus hub for advancing basic science to clinical applications —

Rising above Interstate 5 on the east campus of UC San Diego, the Altman Clinical and Translational Research Institute Building (ACTRI) officially opened its doors Friday in a ribbon-cutting ceremony under blue skies.

The new seven-story building of steel, glass and grooved concrete is home to the Clinical and Translational Research Institute (CTRI) at UC San Diego, established in 2010 as part of a national consortium of 60 medical research institutions created to energize bench-to-bedside efforts. … Read the Full Story from the UC San Diego Newsroom

Countdown To Twin Astronaut’s Return – UC San Diego Readies Next Steps in Landmark Study

Study of identical twin astronauts advances NASA’s preparations for mission to Mars —

When astronaut Scott Kelly returns to Earth on March 1, half of NASA’s first-of-its-kind study of twin astronauts and long duration space flight, researchers at University of California, San Diego School of Medicine and elsewhere will launch the mission’s next phase.

UC San Diego School of Medicine researchers are part of a national collaboration between NASA’s Human Research Program, the National Space Biomedical Research Institute and 10 investigative teams around the country, all seeking to better understand the effects of extended space travel by analyzing blood, urine and other samples from identical twin astronauts, Scott and Mark Kelly. … Read the Full Story from the UC San Diego Newsroom


Kumar Sharma, MD, FAHA

Kumar Sharma, MD, FAHA

Kumar Sharma, MD, Professor of Medicine in the Division of Nephrology and Hypertension, is a collaborator in the NASA twins study.

Dr. Sharma is Director of the Institute of Metabolomic Medicine at UC San Diego School of Medicine.

Identical Twin Astronauts Mark and Scott Kelly. Credit: NASA.

Identical Twin Astronauts Mark and Scott Kelly.
Credit: NASA.

Melissa Gymrek, PhD, Speaks This Friday, Feb. 26: “Dissecting the Contribution of Complex Genetic Variation to Human Traits”

Computer Science and Engineering Colloquium Talk / Winter 2016

Melissa Gymrek, PhD
Massachusetts General Hospital and the Broad Institute

Friday, February 26, 2016
12 – 1 p.m.

Computer Science and Engineering Building EBU-3B, Room CSE 1202

Title: Dissecting the Contribution of Complex Genetic Variation to Human Traits

Abstract:
Recent studies have made substantial progress in identifying genetic variants associated with disease and molecular phenotypes in humans. However, these studies have primarily focused on single nucleotide polymorphisms (SNPs), ignoring more complex variants that have been shown to play important functional roles. Here, I focus on short tandem repeats (STRs), one of the most polymorphic and abundant classes of genetic variation. I will first present lobSTR, a novel algorithm for genotyping STRs from whole-genome sequencing datasets. Next, I will describe insights into population-wide trends of STR variation revealed by applying lobSTR to thousands of sequencing datasets to generate the largest and highest-quality STR catalog to date. I will then show how we used this catalog to conduct a genome-wide analysis of the contribution of STRs to gene expression in humans. This survey revealed that STRs explain 10-15% of the heritability of expression mediated by all common cis variants and potentially play an important role in clinically relevant conditions. Finally, I will discuss preliminary analyses incorporating functional genomics data with high-quality complex variant genotypes to predict and validate the function of non-coding variants driving common human diseases. Altogether, these results highlight the putative phenotypic contribution of complex variants and the opportunity for a wealth of genetic discoveries to be gained by expanding analyses to less-understood regions of the genome.

Bio:
I am currently a post-doctoral fellow at Massachusetts General Hospital and the Broad Institute. I recently received my PhD in Bioinformatics and Integrative Genomics from the Harvard/MIT Division of Health Sciences and Technology under the supervision of Yaniv Erlich and Mark Daly. Prior to my PhD, I received my B.S. in Computer Science and Mathematics at MIT.

My major research interest is to understand complex genetic variants that underlie phenotypic changes, ultimately leading to human disease. My recent work focuses on repetitive DNA variants known as short tandem repeats (STRs) as a model for complex variation. I develop computational methods for analyzing and visualizing complex variation from large-scale sequencing data. These tools allow us for the first time to answer many questions regarding STRs and other variant types, including their contribution to complex human phenotypes. In future work, I aim to build on my experience dissecting challenging regions of the genome to develop and test predictive models of the regulatory effects of complex sequence variation.

Faculty Host:
Vineet Bafna, PhD
Professor of Computer Science and Engineering
Jacobs School of Engineering
UC San Diego
vbafna@ucsd.edu

What Makes A Bacterial Species Able to Cause Human Disease?

Global effort produces first cross-species genomic analysis of Leptospira, a bacterium that can cause disease – and death – in targeted mammals, including humans —

An international team of scientists, led by researchers at University of California, San Diego School of Medicine and the J. Craig Venter Institute (JCVI), have created the first comprehensive, cross-species genomic comparison of all 20 known species of Leptospira, a bacterial genus that can cause disease and death in livestock and other domesticated mammals, wildlife and humans. … Read the Full Story from the UC San Diego Newsroom


Dr. Joseph Vinetz

Dr. Joseph Vinetz

Joseph M. Vinetz, MD, senior author of the study, is Professor of Medicine in the Division of Infectious Diseases and Director of the UC San Diego Center for Tropical Medicine and Travelers Health.

Fellow UC San Diego Division of Infectious Diseases faculty members Michael A. Matthias, PhD, and Douglas E. Berg, PhD, are the other Department of Medicine investigators in the international multi-center leptospirosis project. Dr. Berg is Professor of Medicine and Professor of Genetics, and Dr. Matthias is Assistant Professor of Medicine.

Dr. Vinetz conducts his research in tropical infectious disease in laboratories at UC San Diego and at Instituto de Medicina “Alexander von Humboldt,” Universidad Peruana Cayetano Heredia in Lima, Peru.  He focuses his work on malaria and leptospirosis.

Read the article in PLOS Neglected Tropical Diseases (Open Access)

Four Department of Medicine Faculty Members Are on 2015 Thomson Reuters Highly Cited Researchers List

Dr. William Sandborn

William Sandborn, MD

Four UC San Diego Department of Medicine researchers are among the most influential researchers in the world, according to the 2015 Thomson Reuters Highly Cited Researchers list.

They are , William Sandborn, MDDon W. Cleveland, PhD, Lewis J. Rubin, MD, and Sergei L. Kosakovsky Pond, PhD.

Dr. Don W. Cleveland

Don W. Cleveland, PhD

Dr. Sandborn is Professor and Chief of the Division of Gastroenterology & Hepatology.

Dr. Cleveland is Chair of the Department of Cellular and Molecular Medicine and Distinguished Professor of Medicine, Cellular and Molecular Medicine, and Neurosciences.

Sergei L. Kosakovsky Pond, PhD

Sergei L. Kosakovsky Pond, PhD

Dr. Pond, Associate Professor of Medicine, is a specialist in infectious disease with a focus on developing software models of evolving pathogens such as HIV and hepatitis C virus.

Dr. Rubin, whose research addresses pulmonary vascular disease and pulmonary arterial hypertension, is Professor of Medicine, Emeritus, in the Division of Pulmonary, Critical Care & Sleep Medicine.

Lewis Rubin, MD

Lewis Rubin, MD

With 165 faculty members on the latest edition of the list, the UC System ranks first in the world on the list of highly cited researchers.

Each year, Thomson Reuters uses citation analysis to identify the world’s most influential contemporary scientists. The 2015 list, encompassing publications from 2003 to 2013, contains more than 3,100 names.

More on the UC System’s achievement from the UC Office of the President

See the names of all UC System faculty members on the list

More about the list and the methodology from Thomson Reuters

View a searchable database of the researchers

GenomeSpace “Recipes” Help Biologists Interpret Genomic Data

Data analysis platform will enlist the user community to streamline use of multiple bioinformatics tools —

Many biomedical researchers are striving to make sense of the flood of data that has followed recent advances in genomic sequencing technologies. In particular, researchers are often limited by the challenge of getting multiple bioinformatics tools to “talk” to one another. To help address this need, researchers at University of California, San Diego School of Medicine, in collaboration with labs at the Broad Institute of MIT and Harvard, Stanford University, Weizmann Institute and Pennsylvania State University, developed GenomeSpace, a cloud-based, biologist-friendly platform that connects more than 20 bioinformatics software packages and resources for genomic data analysis.

The team is now developing and crowdsourcing “recipes” — step-by-step workflows — to better enable non-programming researchers to interpret their genomic data … Read the full story from the UC San Diego Newsroom


Dr. Jill Mesirov

Dr. Jill Mesirov

Jill Mesirov, PhD, is senior investigator on the GenomeSpace project. Dr. Mesirov joined UC San Diego in 2015 as Associate Vice Chancellor for Computational Health Sciences and Professor of Medicine in the Division of Medical Genetics.

Trey Ideker, PhD, Professor of Medicine, is a coauthor.

The article citation: Qu K, Garamszegi S, Wu F, et al. Nature Methods. 2016 Jan 18. doi: 10.1038/nmeth.3732.

Newly Evolved, Uniquely Human Gene Variants Protect Older Adults from Cognitive Decline

December 1, 2015

Humans evolved unique gene variants that protect older adults from neurodegenerative disease, thus preserving their valuable contributions and delaying dependency —

Many human gene variants have evolved specifically to protect older adults against neurodegenerative and cardiovascular diseases, thus preserving their contributions to society, report University of California, San Diego School of Medicine researchers in the November 30 issue of Proceedings of the National Academy of Sciences. …Read the full story from the UC San Diego Newsroom


Ajit Varki, MD, and Pascal Gagneux, PhD, led the study. Dr. Varki is Distinguished Professor of Medicine and Cellular and Molecular Medicine at UC San Diego School of Medicine, adjunct professor at the Salk Institute for Biological Studies and co-director of the UC San Diego/Salk Center for Academic Research and Training in Anthropogeny (CARTA).

Dr. Gagneux is associate professor of pathology and associate director of CARTA.

Forty-One Department of Medicine Physicians Named on San Diego’s 2015 “Top Doctors” List

This year’s San Diego Magazine/San Diego County Medical Society Top Doctors list includes 41 Department of Medicine faculty clinicians. View photo gallery

Jill P. Mesirov Appointed Associate Vice Chancellor for Computational Health Sciences

UC San Diego School of Medicine recruits world leader in computational biology —

Leading computational biologist Jill P. Mesirov, PhD, has been appointed associate vice chancellor for computational health sciences and professor of medicine at University of California, San Diego School of Medicine and Moores Cancer Center. Mesirov most recently served as associate director and chief informatics officer at the Broad Institute of MIT and Harvard, where she directed the Computational Biology and Bioinformatics Program. … Read the full story from the UC San Diego Newsroom


Dr. Mesirov joins the Department of Medicine as a professor in the Division of Medical Genetics.