Abstract PO-135: Utility of formalin-fixed, paraffin embedded prostate biospecimens from low-resource international settings for use in next generation sequencing studies in African-descent populations

Abstract

Background: Men of African ancestry experience higher burden from prostate cancer compared to men of other ancestral backgrounds. Limitations in the availability of high-quality biospecimens have hindered the inclusion of this population in genetic studies of prostate cancer. The use of formalin-fixed paraffin-embedded (FFPE) tissues represents a potential rich source of genetic material particularly in some international settings, where fresh frozen tissue is difficult to obtain. Methods: A total of 976 FFPE blocks were collected between 2002 and 2017 from six international sites in Africa and the Caribbean. Genomic DNA was checked for quality and quantity. Differences in mean quality control (QC) for pre and post pathology training were assessed using t-test. Pearson chi-square with trend analysis examined association between time-category and QC success status. Association of continuous DNA quality (Q129/Q41 ratio) and time of specimen collection was estimated with linear regression. Samples with a DNA quantity >0.2µg and a Q129/Q41 ratio >0.00225 were submitted for whole exome sequencing (WES). Findings: Specimens from 2002 to 2010 and 2011 to 2017 had an average total DNA yield of 1.4 μg and 2.4 ug, respectively. There was a statistical positive difference in the quality of DNA samples over time indicating an improvement in quality of specimens. For the samples Insert size, mean mapping quality and alignment error rate significantly (p≤0.05) improved for samples submitted for WES, post pathology training. Interpretation: FFPE samples from low-resource settings could potentially provide sufficient DNA for WES. Improvements in biospecimen collection for research are needed in these settings. Citation Format: Ernest Kaninjing, Damian Francis, Katy Brignole, Keyode Adeniji, William Aiken, Cherif Dial, Mohammed Faruk, Omolara Fatiregun, Andrew Gachii, Denise Gibbs, Serigne Gueye, Maria Jackson, Mohamed Jalloh, Paul Jibrin, B. Karanam, Jyoti Kumar Shravana, Mamadou Ndoye, Ogo Chidiebere Ndukwe, John Obafunwa, Folakemi Odedina, Ademola Popoola, Camile Ragin, Jason White, Clayton Yates, Damali N. Martin. Utility of formalin-fixed, paraffin embedded prostate biospecimens from low-resource international settings for use in next generation sequencing studies in African-descent populations [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-135.