Characterization of copy number alterations in Pakistani patients with colorectal cancer

Abstract PurposeIncidence and mortality rates of colorectal cancer (CRC) in South Asia are expected to rise by 70% between 2020 and 2040. Despite recent advances in the understanding of molecular alterations in CRC, the representation of South Asians in published genomic datasets is very limited. To address this gap, we performed a pilot study based on a transnational collaboration between academic centers in the US and Pakistan to characterize copy number alterations in a Pakistani cohort with CRC. MethodsWe obtained archived formalin-fixed paraffin-embedded (FFPE) tissue samples from 43 CRC patients treated at Aga Khan University (AKU) Hospital. DNA was extracted and evaluated for quality at AKU, and whole genome sequencing library preparation and shallow whole genome sequencing was performed at University of Wisconsin–Madison. Sequencing data was aligned to the human genome, and we used ichorCNA and GISTIC2 to determine relative copy number alterations. ResultsAfter removing 13 samples with insufficient DNA quality or quantity, tumor sequencing data was analyzed from 30 patients. The cohort consisted of 19 (63.3%) males with a mean age of 50.1 years and standard deviation (SD) of 17.8 years. Twenty-one (70.0%) patients had tumor stage T3 or T4, and 15 (50.0%) had tumors of the colon. A mean of 265 ng (SD, 29 ng) of DNA was extracted from each FFPE tumor sample, and each sample was sequenced to a mean depth of 0.22× (0.21×). Analysis of copy number alterations revealed recurrent gains in regions 8q and 13q, as well as losses in region 8p. ConclusionsThis transnational pilot study helped identify the challenges related to FFPE sample quality that can impede similar efforts in the future. Our results revealed similarities in the most common copy number alterations in CRC identified in native Pakistani patients and published datasets.