TY - JOUR
T1 - Development of a genotyping microarray for studying the role of gene-environment interactions in risk for lung cancer
AU - Baldwin, Don A.
AU - Sarnowski, Christopher P.
AU - Reddy, Sabrina A.
AU - Blair, Ian A.
AU - Clapper, Margie
AU - Lazarus, Philip
AU - Li, Mingyao
AU - Muscat, Joshua E.
AU - Penning, Revor M.
AU - Vachani, Anil
AU - Whitehead, Alexander S.
PY - 2013/12
Y1 - 2013/12
N2 - A microarray (LungCaGxE), based on Illumina Bead Chip 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.
AB - A microarray (LungCaGxE), based on Illumina Bead Chip 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.
KW - Case-Control Studies
KW - Gene-Environment Interaction
KW - Genotyping Techniques
KW - Humans
KW - Lung Neoplasms/genetics
KW - Oligonucleotide Array Sequence Analysis/methods
KW - Polymorphism, Single Nucleotide
UR - http://www.scopus.com/inward/record.url?scp=84891517708&partnerID=8YFLogxK
U2 - 10.7171/jbt.13-2404-004
DO - 10.7171/jbt.13-2404-004
M3 - Article
C2 - 24294113
AN - SCOPUS:84891517708
SN - 1524-0215
VL - 24
SP - 198
EP - 217
JO - Journal of Biomolecular Techniques
JF - Journal of Biomolecular Techniques
IS - 4
ER -
