Single nucleotide polymorphism (SNP) analysis of mouse pulmonary adenoma susceptibility loci 1–4 for identification of candidate genes
- Division of Human Cancer Genetics, Ohio State University Comprehensive Cancer Center, 420 West 12th Avenue, Columbus, Ohio 43210, USA
- Correspondence to: Dr M You, Manuel Tzagournis Medical Research Facility, Room 514, 420 West 12th Avenue, Columbus, Ohio 43210, USA;
- Pas, pulmonary adenoma susceptibility
- PCR, polymerase chain reaction
- QTL, quantitative trait loci
- RT-PCR, reverse transcriptase PCR
- SNPs, single nucleotide polymorphisms
- Scc1, susceptibility to colon cancer 1
Lung cancer is the leading cause of mortality from cancer in both men and women in developed countries. There is evidence that, although incidence is almost always associated with environmental factors such as smoking or occupational exposure, susceptibility has a genetic component with early onset lung cancer following Mendelian inheritance.1,2 Moreover, susceptibility is largely intrinsic to the lung itself as shown by the classical experiments involving lung explants from sensitive and resistant mice.3 Identification of the genes predisposing to cancer could yield targets for treatment or chemoprevention. In humans, the wide variety of carcinogens and varying degrees of exposure make identifying the predisposing genes difficult, but in a mouse model, such confounding variables can be controlled.
Past studies have mapped four susceptibility loci (Pas1–4) for pulmonary adenoma in which A/J and C57BL/6J (B6) mice have different alleles that affect incidence and multiplicity of tumours. With the release of a genome wide SNPs database, it has become feasible to analyse these genetically determined QTLs for genes polymorphic in these strains.
Celera’s discovery database (CDS 3.6, SNP 1.0) was scanned for SNPs in the Pas1–4 QTLs. SNPs were first screened according to the following criteria: (1) A/J and B6 were polymorphic for the SNP; (2) SNPs appeared in the coding region, the 5′ regulatory region, or the 3′ untranslated region; (3) SNPs appeared in known genes; (4) B6 and DBA/2J, phenotypically similar to B6, shared the same allele.
Genes for which associations or other plausible links with cancer have been published were deemed as final candidates. All 11 selected SNPs within candidate genes were verified by polymerase chain reaction (PCR) sequencing. We have also attempted to verify a series of differentially expressed candidate susceptibility genes to lung tumours in our previous microarray analysis with semiquantitative reverse transcriptase …