Gene Mutation “Hotspots” Linked to Better Breast Cancer Outcomes

Genetic phenomenon associated with low tumor invasiveness and longer patient survival could inform prognosis and help identify patients who would best respond to immunotherapy and other treatments —

Kataegis is a recently discovered phenomenon in which multiple mutations cluster in a few hotspots in a genome. The anomaly was previously found in some cancers, but it has been unclear what role kataegis plays in tumor development and patient outcomes. Using a database of human tumor genomic data, researchers at the University of California San Diego School of Medicine and Moores Cancer Center have discovered that kataegis is actually a positive marker in breast cancer — patients with these mutation hotspots have less invasive tumors and better prognoses. … Read the Full Story from the UC San Diego News Center


Dr. Jill Mesirov

Dr. Jill Mesirov

The study coauthors included Department of Medicine faculty researchers Pablo Tamayo, PhD, and Jill P. Mesirov, PhD. Both are Professors of Medicine in the Division of Genetics.

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Hannah Carter Receives NIH Early Independence Award

CTRI Helps Launch Career of Bioengineer Hannah Carter

November 22, 2013 – With support from UC San Diego’s Clinical and Translational Research Institute (CTRI), bioengineer Hannah Carter, PhD, received the highly prestigious NIH Early Independence Award and recently began began her transition to a junior faculty position at UC San Diego.

Presently she is acquiring a research team and computational resources to delve into her project: Network approaches to identify cancer drivers from high-dimensional tumor data. … Read the full story from CTRI News & Events


Hannah Carter, PhDHannah Carter, PhD, is assistant professor of medicine in the Division of Medical Genetics. Her project is Network Approaches to Identify Cancer Drivers from High-Dimensional Tumor Data.

She is now recruiting postdoctoral fellows for her project, which is funded for five years.

Carter Laboratory website

 

UC San Diego-Human Longevity Inc. Agreement Seeks to Accelerate Medical Science

Thousands of patient genomes expected to fuel diverse medical research, beginning with cancer

The new collaborative research agreement between Human Longevity Inc. (HLI) and the University of California, San Diego, announced today, represents a significant and necessary step in efforts to research and translate the potential of the human genome into novel and real treatments and therapies able to change and improve the human condition.

“This agreement brings together the resources of two entities that, in combination, may ultimately help improve countless lives,” said David A. Brenner, MD, vice chancellor of health sciences at UC San Diego and dean of the UC San Diego School of Medicine. “HLI aims to bring leading-edge thinking in genomics technologies. UC San Diego boasts some of the world’s finest researchers and physicians working at places like the Moores Cancer Center. Together, we will collaborate to marshal the people, the tools and the resources to really make a difference in human health.” … Read the full story from the UC San Diego News Center

The Role of “Master Regulators” in Gene Mutations and Disease

Researchers identify key proteins that help establish cell function

Researchers at the University of California, San Diego School of Medicine have developed a new way to parse and understand how special proteins called “master regulators” read the genome, and consequently turn genes on and off. … Read the full story from the UC San Diego News Center


Christopher K. Glass, MD, PhDThe principal investigator of the reported study is Christopher K. Glass, MD, PhD, professor of medicine in the Division of Endocrinology & Metabolism and professor of cellular and molecular medicine at UC San Diego.

He is on the faculty of the UC San Diego Institute for Genomic Medicine.

Visit the Glass Laboratory website.

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Toward a New Model of the Cell

Everything You Always Wanted to Know About Genes

Turning vast amounts of genomic data into meaningful information about the cell is the great challenge of bioinformatics, with major implications for human biology and medicine. Researchers at the University of California, San Diego School of Medicine and colleagues have proposed a new method that creates a computational model of the cell from large networks of gene and protein interactions, discovering how genes and proteins connect to form higher-level cellular machinery. …Read the full story from the UCSD Newsroom


Trey Ideker, PhDThe new approach comes from the medical genetics laboratory of Trey Ideker, PhD, in the departments of bioengineering and medicine. Postdoctoral fellow Janusz Dutkowski, PhD, is lead author and Michael Kramer, PhD, a coauthor of the study report in Nature Biotechnology.

Ideker, senior author, is professor of bioengineering and medicine and chief of the Division of Medical Genetics in the Department of Medicine.

Citation for the report:  Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nature Biotechnology (2012) doi:10.1038/nbt.2463. Published online 16 December 2012  Read the abstract

Discovery Provides Blueprint for New Drugs That Can Inhibit Hepatitis C Virus

Finding Could Pave Way for Drugs Against Virus That Kills More In US Than HIV

Chemists at the University of California, San Diego have produced the first high resolution structure of a molecule that when attached to the genetic material of the hepatitis C virus prevents it from reproducing . …. Read the full story from the UCSD Newsroom

Laboratory test tubes
David L. Wyles, MD, is a coauthor of the study report. He is associate professor of clinical medicine in the Division of Infectious Diseases and a researcher in the UC San Diego Antiviral Research Center.

Read the study report in the Proceedings of the National Academy of Sciences

Related story:
UC San Diego School of Medicine Launches Hepatitis C Clinical Trials

Searching for the Soul of the Genome

The discovery that a “gene desert” on chromosome 9 was a hotspot for coronary artery disease (CAD) risk was among the highlights of findings produced recently by genome-wide association studies, which compare the genomes of many people for genetic variations and have been broadly used in the past few years to study hundreds of diseases and complex traits. Gene deserts are large genomic segments devoid of genes. … Read the full story from the UCSD Newsroom

One of the co-authors of the study report is M. Geoffrey Rosenfeld, M.D., pictured at left. Dr. Rosenfeld is Professor of Medicine in the Division of Endocrinology and Metabolism and Professor of the Howard Hughes Medical Institute.