Characterization of copy number alterations in Pakistani patients with colorectal cancer

Purpose Incidence 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. Methods We 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. Results After 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. Conclusions This 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. ### Competing Interest Statement M.M. has consulted for AstraZeneca, Bristol Myers Squibb, and Castle Biosciences; now consults for TGen; and serves on the scientific advisory board of and holds stock options for PetDx. ### Funding Statement This study was funded by grant 5 T32 HG002760 from the National Human Genome Research Institute (to C. Marcinak), grant 3 P30 CA014520-48S4 from the National Cancer Institute Early-Stage Surgeon Scientist Program (to S. N. Zafar), and grants 5 R01 CA223481 and 5 U01 CA243078 from the National Cancer Institute (to M. Murtaza). Data generation in this study was supported by the Ebrahim Endowment Fund. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Ethical Review Committee at The Aga Khan University and the National Bioethics Committee of Pakistan gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.