By Matt Jones
NEW YORK (GenomeWeb News) – The Penn State Milton S. Hershey Medical Center and the Penn State College of Medicine have launched a new institute that will focus on personalized medicine and engage in interdisciplinary research with other institutes at the campus.
The Penn State Hershey Institute for Personalized Medicine will connect faculty, resources, and programs currently at the school to advance research areas that could translate into clinical applications, Penn State Hershey said late last week.
The institute will collaborate with departments and institutes around the Penn State Hershey campus, including the Penn State Clinical and Translational Science Institute, to translate research findings into clinical applications.
The institute, which will move into its permanent lab space in the College of Medicine in June, will obtain blood and other biosamples from consenting patients at the Medical Center which will then be stored in a biorepository, also housed on campus.
Along with the samples, information about the patients' treatments and outcomes stored on electronic medical records will be deposited in a database for use in correlation studies, James Broach, who chairs the department of biochemistry and molecular biology at Penn State College of Medicine and who will be the inaugural director of the institute, told GenomeWeb Daily News on Monday.
"This has the potential to expand to the nearly a million people who come through the hospital and the associated clinics under the umbrella of the Hershey Medical Center," he said.
Depending on the disease interest, the samples can be pulled from the repository and analyzed in any number of ways, including conducting SNP analyses using Illumina's SNP arrays, and in-house deep sequencing studies with the Illumina HiSeq and other next-generation sequencing platforms, Broach said.
The large volumes of data the institute expects to generate will be analyzed by researchers at Penn State's University Park campus using the Galaxy software package to identify relevant SNPs for each individual patient. Developed by Penn State and Emory University, Galaxy is an open source system for data integration and analysis that was developed for genomics research and now is used as a general bioinformatics workflow management system.
The institute will then seek to compare the genomic information with the outcome and treatment data found in the EMRs.
Establishing correlations between genotype and outcomes is the hard part, Broach explained, because of the large number of patients that are required to identify parts of the genome that are correlated to diseases with any statistical significance.
"Our approach will be much in the way that people are beginning to think about doing clinical trials with limited a number of patients – where you keep redirecting the cohort as the information comes in," Broach said.
The early phases of research will focus on this type of study, with the longer aim of generating knowledge linking genes and variants with outcomes in ways that could be used in treatment.
"Ultimately, the goal will be that when the patient comes in, we take their blood samples, we do the sequence, we get the SNPs, and on the basis of our previous correlations, you can make the prediction that this person would respond to one treatment versus another treatment," he said.