Lung eQTL Dataset: Molecular Insights

The description of the lung eQTL dataset and subject demographics have been published previously [54] (link)–[56] (link). Briefly, non-tumor lung tissues were collected from patients who underwent lung resection surgery at three participating sites: Laval University (Quebec City, Canada), University of Groningen (Groningen, The Netherlands), and University of British Columbia (Vancouver, Canada). Whole-genome gene expression and genotyping data were obtained from these specimens. Gene expression profiling was performed using an Affymetrix custom array (GPL10379) testing 51,627 non-control probe sets and normalized using RMA [57] (link). Genotyping was performed using the Illumina Human1M-Duo BeadChip array. Genotype imputation was undertaken using the 1000G reference panel. Following standard microarray and genotyping quality controls, 1111 patients were available including 409 from Laval, 363 from Groningen, and 339 from UBC. Lung eQTLs were identified to associate with mRNA expression in either cis (within 1 Mb of transcript start site) or in trans (all other eQTLs) and meeting the 10% false discovery rate (FDR) genome-wide significant threshold.

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Wain L.V., Sayers I., Soler Artigas M., Portelli M.A., Zeggini E., Obeidat M., Sin D.D., Bossé Y., Nickle D., Brandsma C.A., Malarstig A., Vangjeli C., Jelinsky S.A., John S., Kilty I., McKeever T., Shrine N.R., Cook J.P., Patel S., Spector T.D., Hollox E.J., Hall I.P, & Tobin M.D. (2014). Whole Exome Re-Sequencing Implicates CCDC38 and Cilia Structure and Function in Resistance to Smoking Related Airflow Obstruction. PLoS Genetics, 10(5), e1004314.

Publication 2014

Human1M-Duo BeadChip array

Gene expression Genome Lung Microarray Mrna Patients Surgery lung Tissues Tumor

Corresponding Organization : NIHR Leicester Respiratory Biomedical Research Unit

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Variable analysis

independent variables

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Whole-genome gene expression data

dependent variables

MRNA expression

control variables

Non-tumor lung tissues from patients who underwent lung resection surgery at three participating sites: Laval University (Quebec City, Canada), University of Groningen (Groningen, The Netherlands), and University of British Columbia (Vancouver, Canada)
Gene expression profiling using an Affymetrix custom array (GPL10379) testing 51,627 non-control probe sets and normalized using RMA
Genotyping using the Illumina Human1M-Duo BeadChip array
Genotype imputation using the 1000G reference panel

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