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

Baldwin, Don A, Sarnowski, Christopher P, Reddy, Sabrina A et al. (2013). Development of a genotyping microarray for studying the role of gene-environment interactions in risk for lung cancer. . 24(4), 198-217. 10.7171/jbt.13-2404-004

cited 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

fiu authors

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.

publication date

  • December 1, 2013

keywords

  • Case-Control Studies
  • Gene-Environment Interaction
  • Genotyping Techniques
  • Humans
  • Lung Neoplasms
  • Oligonucleotide Array Sequence Analysis
  • Polymorphism, Single Nucleotide

Digital Object Identifier (DOI)

Medium

  • Print

start page

  • 198

end page

  • 217

volume

  • 24

issue

  • 4