Journal article
Development of a Genotyping Microarray for Studying the Role of Gene-Environment Interactions in Risk for Lung Cancer
Journal of biomolecular techniques, Vol.24(4), pp.198-217
12/2013
Handle:
https://hdl.handle.net/2376/110068
PMCID: PMC3792704
PMID: 24294113
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.
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Details
- Title
- Development of a Genotyping Microarray for Studying the Role of Gene-Environment Interactions in Risk for Lung Cancer
- Creators
- Don A Baldwin - Pathonomics LLC, Philadelphia, Pennsylvania 19104, USAChristopher P Sarnowski - Penn Molecular Profiling FacilitySabrina A Reddy - Penn Molecular Profiling FacilityIan A Blair - Center of Excellence in Environmental ToxicologyMargie Clapper - Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USAPhilip Lazarus - Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210, USA; andMingyao Li - Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USAJoshua E Muscat - Department of Public Health Sciences, Pennsylvania State University, Hershey, Pennsylvania 17033, USATrevor M Penning - Center of Excellence in Environmental ToxicologyAnil Vachani - Center of Excellence in Environmental ToxicologyAlexander S Whitehead - Center of Excellence in Environmental Toxicology
- Publication Details
- Journal of biomolecular techniques, Vol.24(4), pp.198-217
- Academic Unit
- Pharmaceutical Sciences, Department of
- Publisher
- Association of Biomolecular Resource Facilities; Bethesda, MD
- Identifiers
- 99900547154301842
- Language
- English
- Resource Type
- Journal article