Abstract
The Translational Genomics Core (TGC) at Partners Personalized Medicine (PPM) serves as a fee-for-service core laboratory for Partners Healthcare researchers, providing access to technology platforms and analysis pipelines for genomic, transcriptomic, and epigenomic research projects. The interaction of the TGC with various components of PPM provides it with a unique infrastructure that allows for greater IT and bioinformatics opportunities, such as sample tracking and data analysis. The following article describes some of the unique opportunities available to an academic research core operating within PPM, such the ability to develop analysis pipelines with a dedicated bioinformatics team and maintain a flexible Laboratory Information Management System (LIMS) with the support of an internal IT team, as well as the operational challenges encountered to respond to emerging technologies, diverse investigator needs, and high staff turnover. In addition, the implementation and operational role of the TGC in the Partners Biobank genotyping project of over 25,000 samples is presented as an example of core activities working with other components of PPM.
Highlights
Technological and analytical advancements in genomics and decreasing cost of sequencing and array-based platforms in recent years are a key catalyst in the exponential growth of translational research initiatives and broader integration of clinical genetic testing
Our operational experiences highlight common considerations encountered at academic research core such as evolving with the advancement of genomic and transcriptomic technologies and assays, and responding to the diverse needs of investigators at an academic and clinical research institution
As highlighted in this article, several key components have allowed us to thrive in this environment, including: (1) building a core set of genomics and bioinformatics services developed through partnerships and collaborations with a clinical lab or researchers within the institution, (2) having a broad and flexible Laboratory Information Management System (LIMS) system that can handle the tracking and management of variety of sample and library types and can adapt and integrate new technologies, and (3) cross training of junior staff across multiple platforms and techniques to engage current staff and limit the impact of staff turnover on productivity
Summary
Technological and analytical advancements in genomics and decreasing cost of sequencing and array-based platforms in recent years are a key catalyst in the exponential growth of translational research initiatives and broader integration of clinical genetic testing. More recently developed technologies, such as NGS, as well as established platforms, such as array-based technologies, require significant laboratory infrastructure and operational expertise to maximize their utility, and are often aggregated in core facilities at academic medical institutions. Healthcare Personalized Medicine (PPM) established the Translational Genomics Core (TGC) as part of its center to provide access and expertise of leading technologies to academic clinical and translational researchers at Partners Healthcare. Alongside its role as a core facility to researchers, the TGC is integrated into the initiatives and operations of other components within Partners Personalized. Targeted gene panel sequencing (hybrid capture method or amplicon enrichment method)
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