Faster Genome Sequencing May Provide New Therapies for Cancer, Genetic Disease, and Other Challenges

In 2003, scientists made a significant breakthrough in the study of genome sequencing. For the first time, researchers were able to unravel a human being’s DNA and read the more than 3 billion bases (or letters) of which it is made. Variations in these bases contribute to the diversity and disease conditions in humans. This effort, known as the Human Genome Project, cost one billion dollars and took 13 years to complete.

Today, new automated sequencing equipment and robotic handling systems have reduced the time it takes to complete this feat to just two days, at a cost of just a few thousand dollars. At UPMC and other medical centers around the world, this breakthrough is changing medicine.

Case in point: In June 2018, UPMC and the University of Pittsburgh launched the UPMC Genome Center. Established with funding from the new UPMC Immune Transplant and Therapy Center and the Institute for Precision Medicine at UPMC and Pitt, the UMPC Genome Project is a $20 million initiative. Here, some of the nation’s top gene scientists and doctors are investigating whether rapid, low-cost whole-genome sequencing can help find new ways to support clinical diagnostics and research initiatives in immunotherapy and precision medicine, tailoring treatments to an individual’s unique genetic makeup.

Sequencing a Newborn and Her Family for Faster Diagnosis

One of the Center’s first research applications is to examine whether whole-genome sequencing can be used to diagnose a critically ill infant admitted to UPMC Children’s Hospital of Pittsburgh. Sequencing the DNA of the newborn female, and her entire family, to identify a genetic disease could potentially lead to an earlier diagnosis and could also be less expensive and more effective than a conventional diagnosis.

Researchers at the UPMC Genome Center are also targeting cancer. As part of this effort, UPMC experts will sequence the genomes of approximately 600 patients who are currently undergoing immunotherapy at UPMC Hillman Cancer Center to determine the impact of their genetic makeup on treatment response. This response will help guide doctors in determining the appropriate cancer therapy for their patients.

World-Class Genomics Infrastructure

“The UPMC Genome Center provides researchers and physicians with access to a world-class genomics infrastructure that they previously had to outsource to other companies or institutions outside of this region,” says Annerose Berndt, PhD, the center’s director.

“We now can sequence a complete genome in less than two days and analyze it in less than two hours — a remarkable advance that not only increases the pace of basic research, but also provides a crucial advantage in the clinical setting where doctors are looking for tools to help them diagnose and treat sick patients quickly,” she says.

Providing this advanced genetic information in days instead of months takes a significant investment in technology. The UPMC Genome Center uses five next-generation NovaSeq 6000 Systems along with robots to automate the preparation and processing of blood, tissue, and saliva samples. The laboratory is also tightly integrated with fully cloud-based, cutting-edge bioinformatics capabilities that allow researchers to monitor and access data from anywhere.

CLIA Certification and Biobanking

The UPMC Genome Center has undergone rigorous validation testing and has obtained Clinical Laboratory Improvement Amendments (CLIA) certification, required to conduct clinical research and diagnostics. It is the largest and only CLIA-certified, high-throughput whole-genome sequencing center in Pennsylvania.

In the future, the center also will leverage the University’s extensive bio-banking effort, which has more than a half million biological samples, and hopes to work with industry partners to advance drug discovery and develop new therapies.

Research generated by physicians and scientists at the UPMC Genome Center promises to play an important role in accelerating our understanding of disease and of our ability to precisely deliver next-generation therapies for some of the world’s most complex health challenges.