Acta Dermato-Venereologica 99-13CompleteContent | Page 30

SHORT COMMUNICATION 1303 rs34567942 a Novel Susceptibility Single Nucleotide Polymorphism for Cutaneous Squamous Cell Carcinoma in Organ Transplant Recipients Aleksandar KUZMANOV 1 , Weihong QI 2 , Nadja STENZ 3 , Pierre-Yves BOCHUD 4 , Zoltan KUTALIK 5,6 , Agnieszka WÓJTOWICZ 7 , Gunther HOFBAUER 1 and the Swiss Transplant Cohort Study 1 Department of Dermatology, University Hospital Zurich, Wagistrasse 14, CH-8952 Schlieren, 2 Functional Genomics Centre Zurich, University of Zürich, 3 Medical Faculty, University of Zürich, Zürich, 4 Service of Infectious Diseases, University Hospital and University of Lausanne, 5 Institute of Social and Preventive Medicine, University Hospital Lausanne (CHUV), 6 Swiss Institute of Bioinformatics, and 7 Service of Infectious Diseases, University Hospital and University of Lausanne, Lausanne, Switzerland. E-mail: [email protected] Accepted Sep 25, 2019; E-published Sep 25, 2019 Cutaneous squamous cell carcinoma (cSCC) is the se- cond most common type of solid human tumour and a main cause of cancer-related death in the general popu- lation (1, 2). Typically, it emerges on ultraviolet (UV)- exposed sun-damaged skin from benign intraepithelial lesions called actinic keratosis (AK) (3, 4). High-risk patient groups, such as organ transplant recipients (OTR), display a 65–250-fold increase in cSCC, making cSCC the most frequent cancer in this group (5). However, not all OTR develop cSCC, while some develop a multi­ plicity of sSCC (1). This discrepancy is the major focus of the current study. Specific genetic factors, such as single nucleotide po- lymorphisms (SNPs) determining cSCC susceptibility in OTRs, have been little-studied. Only a few papers have addressed this topic (6–8). Moreover, only one group has performed genome-wide association studies (GWAS), replicating 10 candidate SNPs previously associated with skin cancer in the general population; however, they did not show SNP-significant genome-wide association with cSCC in the OTRs (7). Our GWAS revealed novel OTR- specific SNP associated with cSCC susceptibility in OTR. 42,400,475. Exclusion criteria were: violation of Hardy-Weinberg- principle (p<1 E-6 ), call rate < 0.95, minor allele frequency (MAF) < 0.01, and minor allele count (MAC) < 3. Untyped variants were imputed using a combined reference panel of the 1,000 Genomes Project phase 3 (9) and Genome of the Netherlands v5 (10) total- ling more than 90 million genetic variants across the genome. The software package SHAPEIT (11) was used for phasing and IMPUTE2 (12) for imputation. The info statistic was computed to establish imputation accuracy and markers with info < 0.7 were excluded from further analysis. For the complex MHC region, imputation of SNPs, multi-allelic markers, amino acids, and classical HLA alleles using validated SNP2HLA pipelines were performed. Preliminary results in a subset of samples with HLA serology data showed that accuracy is very high for HLA-A, -B, -DRB1, and DQB1 (> 95%), and high for HLA-C (90%) in Europeans. Manhattan plots were generated using the R package qqman (http://biorxiv.org/content/biorxiv/early/2014/05/14/005165.full. pdf). SNPs were queried against dbSNP (https://www.ncbi.nlm. nih.gov/projects/SNP/) and the ensembl variation database (http:// www.ensembl.org/info/genome/variation/index.html). The results were combined with annotation results obtained with snpEff (13). GWAS identified 1 SNP, rs34567942, to be significantly as- sociated with cSCC in OTRs at the p-value threshold of 5×10 –8 (Fig. 1). Table I shows the characteristics of SNP rs345567942; namely the alternative nucleotide, imputation accuracy and im- METHODS AND RESULTS Patient data and material were collected prospectively from the Swiss Transplant Cohort Study (STCS), from adult solid-organ transplant recipients who received either kidney, liver, lung, heart, pancreas, small bowel or mixed organ transplant between 2008 and 2011. Skin cancer episodes after or during transplantation were reviewed by an independent clinician. All patients had provided written informed consent for participation in the STCS (including genetic analyses). The protocol was approved by the independent ethics committees of each Swiss participating centre (University Hospital of Lausanne; University Hospitals of Geneva; University Hospital Zürich; Cantonal Hospital St Gallen; Inselspital, Bern University Hospital; ClinicaLuganese, Lugano; and University Hospital of Basel and registered at ClinicalTrials.gov Identifier NCT01204944). To identify susceptibility SNPs for cSCC, GWAS were performed on 61 OTR patients with cSCC and 908 skin cancer negative-OTR patients. Genome-wide genotyping was performed on DNA samples extracted from EDTA blood using the Illumina ® Human Omni Express chip Genome Studio software and default parameters were used to call genotypes. GWAS were conducted using frequentist association tests in SNPtest. Asso- ciations meeting the genome-wide threshold p-values of 5 × 10 –8 were considered statistically significant. The raw genotype data-set included 719,665 variants. After ex- clusion, 627,443 remained. The total number of imputed SNPs was Fig. 1. Manhattan plot visualizing genome-wide association of 61 cutaneous squamous cell carcinoma (cSCC)-organ transplant recipients (OTRs) and 908 skin cancer negative-OTRs, showing –log10 p-value of SNPtest along chromosomes. Horizontal red line represents the significant threshold p-value of 5×10 –8 . Arrow indicates single nucleotide polymorphism rs34567942 with the most prominent p-value. This is an open access article under the CC BY-NC license. www.medicaljournals.se/acta Journal Compilation © 2019 Acta Dermato-Venereologica. doi: 10.2340/00015555-3322 Acta Derm Venereol 2019; 99: 1303–1304