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Core Facility Helping Scientists Unlock the Human Genome

Lifang Hou

Lifang Hou

Nearly every human ailment has some basis in our genes.

Using data from human DNA, scientists and clinicians have many more powerful ways to study the role genetic factors play in complex illnesses, such as cancer, diabetes and heart disease. Genomics can be used to solve many problems, and the genomic research at Northwestern just keeps getting better.

Northwestern’s state-of-the-art Genomics Core Facilityoriginally resided inside two spaces on the Chicago campus—one in the Montgomery Ward Building and the other in the Tarry Building. Last year both spaces came together into a single laboratory in Tarry specifically designed to support genomics research. That space is sectioned into compartments to separate experiments.

“Before, we had two open floor plan labs in two different buildings and the experiments were done in two different locations,” said Nadereh Jafari, MD, research associate professor at the Center for Genetic Medicine and director of the core facility. “Now, most of our experiments and protocols are performed in separated areas in one large laboratory. This format minimizes the potential for impurities and increases quality. Having all of our core equipment in one location has increased staff cross-training and communications.”

The quality is so high, in fact, that the core’s DNA extraction service recently received accreditation from the College of American Pathologists. With this accreditation, Genomics Core Facility joined an elite group of internationally recognized facilities that meet the highest standards in laboratory practices.

The Genomics Core at the Center for Genetic Medicine is a shared resource facility that provides genomic services to investigators at the Lurie Cancer Center, Feinberg, across Northwestern University and outside institutions.

“Being located right on campus allows investigators to drop their samples at any time and easily discuss their projects during working hours,” Jafari said. “We offer the Northwestern investigators our experience, recommendations and access to new technologies.”

The Genomics Core has played a critical role in supporting a number of large studies. One example is the Hyperglycemia and Adverse Pregnancy Outcomes (HAPO) study led by Boyd Metzger, MD, professor emeritus of Medicine-Endocrinology and William Lowe, MD, Vice Dean Academic Affairs and a professor of Medicine-Endocrinology. As part of the HAPO Study, the Genomics core extracted DNA from 25,000 samples recruited from 15 different field centers around the world. These DNA samples have provided critical infrastructure for a number of NIH grants examining genetic variants that impact maternal metabolism during pregnancy and fetal growth and adiposity. Currently, the Genomics Core is preparing DNA from 14,000 HAPO mothers and their HAPO children in a new NIH-funded follow-up study.

Another ongoing collaboration at the core is a large methylation analysis on thousands of samples for

Lifang Hou, MD, PhD, associate professor of Preventive Medicine-Cancer Epidemiology and Prevention and a member of the Lurie Cancer Center. This large study includes samples from different cohorts like the Women’s Health Initiative clinical trial and MOBILIZE Boston, a cohort that studies the associations between particulate matter air pollution, DNA methylation and cardiovascular disease.

The core has worked closely with different departments in Evanston as well, including the Physical Sciences- Oncology Center and Proteomics Center for Excellence.

The Genomics Core has also worked with Northwestern student groups, including the award-winning International Genetically Engineered Machines synthetic biology team. In the past two years the team has won a gold and a silver medal at the iGEM Jamboree.

The core can provide services for high, medium and low throughput genome sequencing, genotyping, methylation and expression profiling, Ampliseq technology and custom and fixed cancer panels.

In the next few months it will roll out a new application to be used for Sanger sequencing. The core will begin using a GeneSifter Lab Edition system for traditional sequencing. This replaces the Corefac and will simplify the sample-submission process.

“The genomics-related technologies and industry moves very fast, but we work hard to stay on top of new advances in this field and provide the related services to our research community,” Jafari said. “Our goal is to provide our investigators access to new instrumentation and technologies so that they can excel in their research.”

Learn more about the Genomics Core Facility