The Center for Translational and Public Health Genomics has several core infrastructure components that provide a solid foundation and take advantage of well-characterized patient cohorts, an established patient recruitment infrastructure, extensive epidemiologic and clinical databases, a rich repository of biospecimens, and diverse faculty expertise.
Blood Specimen Research Resource
The major initiative within the CTPHG will be the establishment of the Blood Specimen Research Resource (BSRR). The BSRR will systematically collect and bank residual blood samples from all newly diagnosed patients seen at MD Anderson. The future goal is to enhance the blood sample banking activities through the collection of an additional tube of blood to enable banking of plasma/serum suitable for research purposes.
Patient History Database
The Department of Epidemiology established the Patient History Database (PHDB) to systematically collect core risk and exposure epidemiology data from patients coming to MD Anderson for their cancer care. The data collection includes information regarding family history, medical history, smoking behavior, occupational exposures, and other important epidemiology variables. The data collected by this initiative is now integrated into the medical record and readily available for clinician use. We are actively working on an electronic version of the PHDB to collect additional information that will also allow for the implementation of cancer-site specific modules.
MD Anderson Cancer Patient Cohort
Together, these components form the MD Anderson Cancer Patient Cohort (MDACPC) – an exciting and high-impact initiative within the CTPHG that will couple the extensive BSRR biobank to multiple patient data resources, such as the PHDB, our electronic medical record, and other databases and genomics expertise. The ability to link inherited genetic variations, circulating biomarkers, epidemiological variables, behavioral characteristics, clinical data, and somatic molecular data (e.g., mutation, DNA copy number, mRNA and miRNA expression arrays, methylation array, and tissue microarray) of tumor tissues would make the MDACPC a unique resource for research of functional genomics and systems biology. The MDACPC is poised to become a tremendous resource and make MD Anderson a leader in translational epidemiology.
The CTPHG has a fully-functioning Genotyping Facility equipped with the most advanced genotyping technology, including a 384-well ABI TaqMan system, Illumina’s iScan and BeadXpress, and the Ion Torrent next generation sequencing platform. These instruments allow us to use a comprehensive candidate SNP-based, whole genome scanning, and targeted sequencing approaches. These platforms also enable molecular profiling of patient specimens, such as chromosomal aberrations through array CGH, global methylation, gene expression, and microRNA and other non-coding RNA expression.
The CTPHG is also integrated with and collaborates closely with two other programs within the Department of Epidemiology and supported, in part, by the Duncan Family Institute for Cancer Prevention Risk & Assessment. These programs provide research resources and complementary expertise to fully interrogate the factors influencing the entire cancer continuum.
Personalized Risk Prediction Program (PRPP)
The PRPP focuses on the development of tools and approaches to understand an individual’s risk of cancer development. Through this program, biospecimens and demographic, clinical and risk factor data are collected from healthy controls and individuals at high risk (i.e., smokers) to facilitate the building risk models to identify, quantitate, and stratify individuals most at risk for cancer.
Premalignant Genome Atlas (PGA)
The detection and elimination of precancerous lesions is the best strategy to prevent cancer. The goal is to identify the earliest molecular defects that cause cancer, thus gaining the ability to identify patients at high risk of malignant transformation. Toward this, we will integrate clinical, molecular, and epidemiological risk factors to a) create a personalized risk profile, b) detect cancer early, c) identify potential drug targets, and d) predict response to prevention measures. The PGA is actively collecting blood and tissue from patients undergoing colonoscopy screening at MD Anderson; this includes normal and polyp tissue specimens. Patients with polyps will be followed up to determine whether or not they develop colorectal cancer – creating a cohort to investigate the factors influencing colorectal cancer development.