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J Biomol Tech. 2013 Dec;24(4):198-217. doi: 10.7171/jbt.13-2404-004.

Development of a genotyping microarray for studying the role of gene-environment interactions in risk for lung cancer.

Author information

1
Pathonomics LLC, Philadelphia, Pennsylvania 19104, USA; ; Center of Excellence in Environmental Toxicology.

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.

KEYWORDS:

LungCaGxE; Tagger Batch Assistant; environmental exposures; genetic association

PMID:
24294113
PMCID:
PMC3792704
DOI:
10.7171/jbt.13-2404-004
[Indexed for MEDLINE]
Free PMC Article

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