Combinations of genetic data in a study of oral cancer
Erling Mellerup1, Gert Lykke Moeller2, Pinaki Mondal3, Susanta Roychoudhury4
1 Laboratory of Neuropsychiatry, Department of Neuroscience and Pharmacology, Faculty of Health, University of Copenhagen, Denmark
2 Genokey ApS, ScionDTU, Technical University of Denmark, Hoersholm, Denmark
3 National Brain Research Centre, Gurgaon, India
4 Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
Correspondence:
Erling Mellerup, email:
Keywords: combinations, genetic data, oral cancer, leukoplakia, genetic subgroups
Received: September 23, 2015 Accepted: September 29, 2015 Published: October 03, 2015
Abstract
In the single locus strategy a number of genetic variants are analyzed, in order to find variants that are distributed significantly different between controls and patients. A supplementary strategy is to analyze combinations of genetic variants. A combination that is the genetic basis for a polygenic disorder will not occur in in control persons genetically unrelated to patients, so the strategy is to analyze combinations of genetic variants present exclusively in patients. In a previous study of oral cancer and leukoplakia 325 SNPs were analyzed. This study has been supplemented with an analysis of combinations of two SNP genotypes from among the 325 SNPs. Two clusters of combinations containing 95 patient specific combinations were significantly associated with oral cancer or leukoplakia. Of 373 patients with oral cancer 205 patients had a number of these 95 combinations in their genome, whereas none of 535 control persons had any of these combinations in their genome.
