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UPDATE: Penn Genome Frontiers Institute to Launch Personalized Genomics Centers

This article has been updated with more information about the new centers and comments from a PGFI official.

By Alex Philippidis

NEW YORK (GenomeWeb News) – The University of Pennsylvania's Penn Genome Frontiers Institute plans to invest $5 million in establishing two internal centers for large-scale projects focused on translational and personalized genomics as well as funding five pilot projects.

Over the next three years, PGFI said today, it will spend $2 million on next-generation sequencing equipment, and $3 million on projects focusing on applications of next-gen sequencing to health and disease. As part of the effort, the Institute has established two internal centers: the Center for Translational and Personalized Genomics of NSAIDs, whose principal investigator is Garret FitzGerald, and the Center for Translational and Personalized Genomics of Inherited Retinal Degenerations, whose PI is Eric Pierce.

The centers are needed "to facilitate and participate in" processing the torrents of data being generated through next-gen sequencing, PGFI said in a statement.

The new centers will use $2 million in next-generation sequencing equipment PGFI has recently purchased. The equipment consists of two Illumina HiSeq machines, and one ABI SOLiD 4.0 machine. The SOLiD machine will be upgraded in December, PGFI Co-Director Jim Eberwine told GenomeWeb Daily News.

The Institute added that the two centers were selected by an external peer review process from an open proposal solicitation to the Penn community. The solicitation also revealed a "great need" for access to next-gen sequencing technology. As a result, PGFI said that it will provide a total of $200,000 in pilot funding over three years for projects targeting atherosclerotic cardiovascular disease; African integrative genomics; ocular cancers, autism spectrum disorders; and cancer genomics.

The Center for Translational and Personalized Genomics of NSAIDs also goes by the name TRAPGEN. It will specialize in studying individual variability in response to inhibitors of the cyclooxygenase, or COX, enzymes, specifically aspirin and nonsteroidal anti-inflammatory drugs or NSAIDs.

An existing NIH-funded study has identified a population of patients with a specific phenotype of aspirin resis¬tance that is stable over time. According to the institute, TRAPGEN will profile that patient population for genomic variations that might explain why aspirin fails to inhibit the formation of platelet-derived COX-1-dependent thromboxane formation—the mechanism by which aspirin prevents heart attacks and strokes.

Another TRAPGEN initiative will focus on predicting the risk of heart attack and stroke in individual patients from NSAIDs. The center will combine high-throughput screening data with metabolomic, epi¬genetic, proteomic and imaging responses to NSAIDs — both unbiased and biased through means such as prostaglandin inhibition — using similar experimental paradigms in yeast, mammalian cells, zebrafish, mice and humans.

The Center for Translational and Personalized Genomics of Inherited Retinal Degenerations will study the set of diseases that lead to blindness through a progressive dysfunction and death of the rod and cone photoreceptor cells of the retina.

It will use next-gen sequencing to carry out both selective exon capture and whole exome capture, with the goal of identifying disease genes for IRDs in several patient cohorts. The center will also employ NGS transcriptome analyses to test its hypothesis that mutations in RNA splicing factors cause disease by generating aberrant transcripts in the retina and/or retinal pigment epithelium. Also to be employed are three gene-targeted mouse models of the RNA splicing factor forms of retinitis pigmentosa, as well as induced pluripotent stem cell-derived RPE cells from patients with these disorders for these studies.

The next-gen sequencing machines are being housed in a new high-throughput screening facility created by the institute at the Carolyn Lynch Laboratory. The facility will contain bioanalyzers, an Illumina cBot workflow automation system for construction of the facility’s library, and upgraded computer equipment.

"With the next-generation sequencers, what you also have to do is improve your computational infrastructure. We're bolstering our server and all of this in anticipation of data that's being generated," Eberwine said in an interview. "We are in the process of doubling our capacity right now."

Eberwine said that the new high-throughput screening facility will also be used by the five PIs whom PGFI has each awarded $200,000 over three years — for a total of $1 million — for the pilot research programs. Those programs include atherosclerotic cardiovascular disease, African integrative genomics, autism spectrum disorder, cancer genomics, and ocular cancers.

Eberwine told GWDN that PGFI may create additional translational and personalized medicine centers, but timing and other details have yet to be decided.

Until the new equipment began operation earlier this fall, PGFI carried out next-gen sequencing at core facilities that housed older-model Illumina GA IIx machines and also a Roche 454 Life Sciences machine.

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