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New Pittsburgh Genome Center Plans Sequencing Trial for Cancer Patients Receiving Immunotherapy

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SAN FRANCISCO (GenomeWeb) – The University of Pittsburgh and its medical center, UPMC, have launched a genome center that will initially focus on whole-genome sequencing and RNA sequencing.

The new center was born out of the Immune Transplant and Therapy Center, founded earlier this year by UPMC and the University of Pittsburgh with a $200 million investment. It will initially support ITTC's work but will also collaborate with the Institute of Precision Medicine, researchers at the University of Pittsburgh, physicians at UPMC, as well as external customers.

The center is housed in a new building near the planned ITTC and is equipped with five Illumina NovaSeq 6000 instruments. It also plans to acquire 10x Genomics' Chromium system and is evaluating long-read sequencing technology from Pacific Biosciences and Oxford Nanopore Technologies.

As one of its initial projects, researchers plan to sequence the tumor genomes of all 600 cancer patients who are receiving immunotherapy at the UPMC Hillman Cancer Center, according to Adrian Lee, director of the Institute for Precision Medicine. The goal is to identify markers of response and resistance. Lee said that the researchers plan to begin sequencing patient samples retrospectively soon, with the aim of discovering new biomarkers. After that, the goal is to use sequencing prospectively to stratify patients based on biomarkers.

Another early project will be to study how whole-genome sequencing can be used to diagnose infants admitted to the Children's Hospital of Pittsburgh, Lee said. For that project, one major goal will be to turn whole-genome sequencing into a rapid diagnostic and study both the clinical and economic utility of a sequencing-based diagnostic for those infants. "We think that's how we move toward clinical testing and demonstrating value for the payor," he said. The team is currently developing the neonatal intensive care unit sequencing protocol, but Lee said he hopes that it will be up and running within six months.

While the center's ultimate focus is on clinical testing and clinical research aimed at demonstrating the value of genomic testing, it is also planning population-based genetic and genomic research studies aimed at finding novel disease-associated variants.

The UPMC has a large biobank containing over 800,000 samples from its network of 35 hospitals, which it plans to tap into for research projects. It also has rapid autopsy programs for breast and lung cancer that enable tumor samples to be collected immediately after death so that the tissue can be kept alive for further testing.

The University of Pittsburgh and UPMC are also partners in the NIH's All of Us research program that aims to sequence the genomes of 1 million individuals.

Eventually, the center aims to collaborate with industry partners, pharmaceutical companies, and other academic researchers to offer clinical sequencing services for translational research and, ultimately, for diagnostics.

Whole-genome sequencing for disease risk prediction is a "long-term vision," Lee said. In order to reach that goal, he said, the team plans to first focus on disease risk prediction in populations that are already known to be at higher risk for certain types of cancer, for instance, where there is a screening paradigm in place. The goal would be to test whether genomics could serve as a better, more cost-effective screening tool.

Annerose Berndt, vice president of clinical genomics at UPMC, said that although the ITTC will provide the genome center's initial customers, because it has such large sequencing capacity, it will also offer its services to outside organizations and customers.

Berndt said that the center has also invested heavily in automation, including liquid handling systems for sample prep. The sequencers are also connected to DNAnexus' cloud-based platform for analysis. DNAnexus' platform does all of the raw data processing, converting the sequence data into VCFs, she said. For annotation, interpretation, and clinical reporting, the center has partnered with WuXi NextCode, Berndt said.

For clinical testing, Berndt said, physicians will have access to the clinical reports that are generated by WuXi NextCode and "in the future, we anticipate bringing back more granular information into the electronic medical record and building a clinical decision support engine for physicians," she said.

In addition, she noted, the center will look to expand on technology. It currently has access to a 10x Genomics Chromium system housed at the University of Pittsburgh but plans to install its own system soon that it will use for single-cell sequencing. It is analyzing PacBio's Sequel and Oxford Nanopore's MinIon for structural variant analysis as well as microbiome analysis.

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