Investigating Lead SCC Variants and mRNA Expression

To investigate the association between lead SCC variants and mRNA expression, we used three lung eQTL data sets from the Microarray eQTL study. In the Microarray eQTL study[57 (link)], lung tissues for eQTL analysis were obtained from patients who underwent lung surgery at three academic sites: Laval University, the University of British Columbia (UBC) and the University of Groningen. Whole-genome gene expression profiling in the lung was performed on a custom Affymetrix array and is available through GEO (https://www.ncbi.nlm.nih.gov/geo/) accession number GSE23546. Genotyping was carried out on the Illumina Human 1M-Duo BeadChip array, data is accessible in dbGaP (phs001745.v1.p1). Genotypes and gene expression levels were available for 408 (Laval University), 342 (Groningen) and 287 (UBC) patients. Microarray and genotypes preprocessing, quality control and eQTL mapping have been described previously[58 (link)]. We also investigated top aerodigestive SqCC associations in the public GTEx catalog (V8)[26 (link)] for lung and esophageal tissue eQTLs and sQTLs, summary statistics based on RNAseq and genotypes analyses obtained via the GTEx data portal (https://www.gtexportal.org).

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Lesseur C., Ferreiro-Iglesias A., McKay J.D., Bossé Y., Johansson M., Gaborieau V., Landi M.T., Christiani D.C., Caporaso N.C., Bojesen S.E., Amos C.I., Shete S., Liu G., Rennert G., Albanes D., Aldrich M.C., Tardon A., Chen C., Triantafillos L., Field J.K., Teare M.D., Kiemeney L.A., Diergaarde B., Ferris R.L., Zienolddiny S., Lam S., Olshan A.F., Weissler M.C., Lacko M., Risch A., Bickeböller H., Ness A.R., Thomas S., Le Marchand L., Schabath M.B., Wünsch-Filho V., Tajara E.H., Andrew A.S., Clifford G.M., Lazarus P., Grankvist K., Johansson M., Arnold S., Melander O., Brunnström H., Boccia S., Cadoni G., Timens W., Obeidat M., Xiao X., Houlston R.S., Hung R.J, & Brennan P. (2021). Genome-wide association meta-analysis identifies pleiotropic risk loci for aerodigestive squamous cell cancers. PLoS Genetics, 17(3), e1009254.

Publication 2021

Human 1M-Duo BeadChip array

Gene expression Genome Genotypes Human Lung Lung surgery Microarray Mrna Patients Tissue

Corresponding Organization : Institute of Cancer Research

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Variable analysis

independent variables

Lead SCC variants

dependent variables

MRNA expression

control variables

Lung tissues for eQTL analysis obtained from patients who underwent lung surgery at three academic sites: Laval University, the University of British Columbia (UBC) and the University of Groningen
Whole-genome gene expression profiling in the lung performed on a custom Affymetrix array
Genotyping carried out on the Illumina Human 1M-Duo BeadChip array
Microarray and genotypes preprocessing, quality control and eQTL mapping have been described previously

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