Development of a Genotyping Microarray for Studying the Role of Gene-environment Interactions in Risk for Lung Cancer

Overview

Journal J Biomol Tech

Specialties Biotechnology
Molecular Biology

Date 2013 Dec 3

PMID 24294113

Citations 4

Authors

Don A Baldwin

Christopher P Sarnowski

Sabrina A Reddy

Ian A Blair

Margie Clapper

Philip Lazarus

Mingyao Li

Joshua E Muscat

Trevor M Penning

Anil Vachani

Alexander S Whitehead

Affiliations

Soon will be listed here.

Abstract

A microarray (LungCaGxE), based on Illumina BeadChip technology, was developed for high-resolution genotyping of genes that are candidates for involvement in environmentally driven aspects of lung cancer oncogenesis and/or tumor growth. The iterative array design process illustrates techniques for managing large panels of candidate genes and optimizing marker selection, aided by a new bioinformatics pipeline component, Tagger Batch Assistant. The LungCaGxE platform targets 298 genes and the proximal genetic regions in which they are located, using ≈ 13,000 DNA single nucleotide polymorphisms (SNPs), which include haplotype linkage markers with a minimum allele frequency of 1% and additional specifically targeted SNPs, for which published reports have indicated functional consequences or associations with lung cancer or other smoking-related diseases. The overall assay conversion rate was 98.9%; 99.0% of markers with a minimum Illumina design score of 0.6 successfully generated allele calls using genomic DNA from a study population of 1873 lung-cancer patients and controls.

Citing Articles

Quantification of Plasma 8-Isoprostane by High-Performance Liquid Chromatography with Tandem Mass Spectrometry in a Case-Control Study of Lung Cancer.

Ma L, Sun D, Xiu G, Lazarus P, Vachani A, Penning T Int J Environ Res Public Health. 2022; 19(19).

PMID: 36231826 PMC: 9566031. DOI: 10.3390/ijerph191912488.

Environmental exposomics and lung cancer risk assessment in the Philadelphia metropolitan area using ZIP code-level hazard indices.

McKeon T, Hwang W, Ding Z, Tam V, Wileyto P, Glanz K Environ Sci Pollut Res Int. 2021; 28(24):31758-31769.

PMID: 33611735 PMC: 8238722. DOI: 10.1007/s11356-021-12884-z.

On meta- and mega-analyses for gene-environment interactions.

Huang J, Liu Y, Vitale S, Penning T, Whitehead A, Blair I Genet Epidemiol. 2017; 41(8):876-886.

PMID: 29110346 PMC: 5775907. DOI: 10.1002/gepi.22085.

Pretreatment Red Blood Cell Total Folate Concentration Is Associated With Response to Pemetrexed in Stage IV Nonsquamous Non-Small-cell Lung Cancer.

Bagley S, Vitale S, Zhang S, Aggarwal C, Evans T, Alley E Clin Lung Cancer. 2016; 18(2):e143-e149.

PMID: 27863923 PMC: 5346447. DOI: 10.1016/j.cllc.2016.10.010.

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