In January 2013, New York-Presbyterian Hospital and Weill Cornell Medical College created the Institute for Precision Medicine (IPM), a translational research hub to promote molecular diagnostics and therapeutics. Dr Mark Rubin was named as the Institute’s first Director. Relevant to ProMis, patients with metastatic prostate cancer are referred to the Precision Medicine Clinic, led by A/Prof Beltran, MD.r
After informed consent through an IRB approved protocol, metastatic tumour biopsy is performed and both tumour and germline sequencing are performed. Through an integrative sequencing strategy, clinically relevant targets for treatment are identified and reviewed by a multi-disciplinary Precision Medicine Tumour Board.
Clinically relevant results are disclosed to the patient and referring clinician, patients are followed prospectively for response to therapy and clinical outcomes, and data is captured in a clinical database. The state-of-the art IPM Biobank uses novel techniques developed at Weill Cornell to expertly prepare tissue samples, and it provides qualified investigators access to well-annotated human biospecimens in a regulatory compliant manner. Annually, approximately 800 prostate cancer patients are diagnosed and treated at Weill Cornell, and within the past four years, more than 2,000 prostate samples have been collected and stored.
Protocols for collection and processing of metastatic samples, particularly sclerotic metastasis, have been developed to ensure that high quality samples are obtained and processed with consideration of patient safety, time to sample preparation, and maximised tumour density. This is an iterative process, and genomic results are monitored and benchmarked to ensure that the processing pipeline is optimal for this activity.
IPM sequencing core equipment includes Illumina 2500 and MiSeq sequencers, Agilent 2100 Bioanalyzer, Nanodrop, Qubit fluorometer, Taqman 7900HT real-time PCR machine, Affymetrix GeneChip platform, GenePix 4000B array reader, Covaris S2 High Performance Ultrasonicator, and Ion Torrent Personal Genome Machine (PGM). Notable assets include several large-memory, multi-CPU systems (including several 32 core nodes with 384 GB of memory and Infiniband networking) and over 2 TFlops and nearly 600 processor cores of cluster computing power, much of it backed by a high-speed, low latency fiberoptic interconnect. This computational power is backed by a large, 1 Petabyte pool of managed storage. Users’ home directories and most systems are backed-up daily.
Additionally, local mirrors of commonly used biological datasets (such as sequence databases, COSMIC, and the Protein Data Bank) are maintained and continuously updated. The IPM computational data analysis pipeline is built on many years of experience in the area of cancer genomics and includes applications for mathematical and statistical modeling, graphics and data visualisation, molecular and systems modeling packages, and many others. The Institute has also implemented visualization tools including a customised cBIO cancer genomics portal from Memorial Sloan Kettering for use by laboratory-based investigators, which will facilitate data sharing with other team members as part of this application.