Abstract C23: Improved methods for collection of germline DNA in community settings

Abstract

Abstract Introduction: The Ponce School of Medicine and Health Sciences (PSMHS), in Ponce, Puerto Rico (PR), has established a partnership with the Moffitt Cancer Center (MCC) in Tampa, Florida with the primary goal of fostering high quality basic, clinical and community outreach research in cancer-related health disparities. Central to this research collaboration has been the development of the Puerto Rico Biobank (PRBB), which was created to collect richly annotated, high quality tissue and blood samples from PR patients with cancer and healthy individuals. These biospecimens are collected from patients who have signed an informed consent providing permission for the PRBB to collect any excess tissue not needed for their medical care that would otherwise be discarded. Leveraging on MCC's significant biobanking experience and PSMHS's ability to consent Puerto Rican patients, a tremendous resource has been developed to facilitate basic science research on cancers with high incidence in Puerto Ricans. Since 2009, over 450 solid tumors samples and 110 blood samples have been collected in PR. Methods: The development of biobanking standard operating procedures (SOPs) based on those at MCC were modified to meet constraints posed by the lack of a biobanking infrastructure in PR and the geographical locations of PSMHS's biospecimens collection facilities (previously described in Flores et al, Biopreservation and Biobanking (2011) 9: 363). The PRBB, based in PR, has the capacity to collect high quality snap frozen tumor tissue and paraffin blocks. After the implementation of solid tumor collection, the PRBB next examined how to effectively collect and bank peripheral blood from patients to yield high quality germline DNA. In the initial phase, blood draws were collected in 10ml K2EDTA Vacutainer tubes (BD), and tubes were frozen until shipped to MCC for DNA extraction using the Qiagen AutoPure DNA platform. In a second phase, whole blood was collected in PAXgene DNA tubes (Qiagen), and yield and DNA quality compared. Results: DNA yields from K2EDTA tubes generated an average DNA yield of 140 μg per 10 mL tube, which is significantly less than the typical yields of up to 250 to 400 μg of DNA (based on MCC's experience). Even more concerning was the failure of 27% of the tubes to yield any measurable amount of DNA. A review of the blood collection procedure identified a lack of consistent post blood draw handling conditions in the community settings due to variations in the time the tubes were held at room temperature or at 4°C. The PRBB team identified the availability of PAXgene DNA tubes, specifically designed for collection of blood at remote sites and most important the ability to stabilize whole blood at room temperature. Utilization of these tubes resulted in significantly improved (by over 107%) DNA yields from blood collected in PR. The average yield is nearly 300 μg per tube of high quality germline DNA as evidence by an A260/280 ratio of 1.86. Based on these results, the blood collection SOP was revised to utilize PAXgene DNA tubes. Conclusions: This experience is an example of the flexibility needed to develop and establish biobanking activities in a community setting without an established biobanking infrastructure. In addition, it also provides an invaluable lesson learned for future remote site blood biobanking studies that can utilize the minimal resource requirements of PAXgene DNA tubes and can conceivably allow extension of blood collection efforts across the entire island without compromising sample yield and quality. Citation Format: Edward Seijo, Sonnian Oliver, Sylvia Gutierrez, Domenico Coppola, Teresita Munoz-Antonia, Idhaliz Flores. Improved methods for collection of germline DNA in community settings. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr C23. doi:10.1158/1538-7755.DISP13-C23