Title: Development of a genotyping microarray for studying the role of gene-environment interactions in risk for lung cancer.
Authors: Baldwin, Don A; Sarnowski, Christopher P; Reddy, Sabrina A; Blair, Ian A; Clapper, Margie; Lazarus, Philip; Li, Mingyao; Muscat, Joshua E; Penning, Trevor M; Vachani, Anil; Whitehead, Alexander S
Published In J Biomol Tech, (2013 Dec)
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.
PubMed ID: 24294113
MeSH Terms: Case-Control Studies; Gene-Environment Interaction*; Genotyping Techniques; Humans; Lung Neoplasms/genetics*; Oligonucleotide Array Sequence Analysis/methods*; Polymorphism, Single Nucleotide*