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Baldwin DA , Sarnowski CP , Reddy SA , Blair IA , Clapper M , Lazarus P , Li M , Muscat JE , Penning TM , Vachani A , Whitehead AS
Development of a genotyping microarray for studying the role of gene-environment interactions in risk for lung cancer
J Biomol Tech. 2013 Dec;24(4) :198-217
PMID: 24294113    PMCID: PMC3792704   
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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 approximately 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.
Notes
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 United States J Biomol Tech. 2013 Dec;24(4):198-217. doi: 10.7171/jbt.13-2404-004.