SNPs/Pools: A methodology for the identification of relevant SNPs in breast cancer epidemiology

The identification of allelic variants of human genes is of great importancewhen assessing genetic susceptibility. The emerging role of genetic polymorphismsin association studies has created the need for high throughput genotyping methodologiesthat allow a more rapid identification of relevant polymorphisms related to individualcancer risk enabling the extension to large-scale association studies. DNA poolingmethodology may be of great importance considering the cost, time and labor thatare involved in large-scale genotyping analysis carried out on individual samples.Alternatively, when using pooled samples which are made up of DNA from many individualstreated as a single sample, these factors are decrease drastically. In this way,the use of DNA pooling methodology, as a pre-selection tool, allows the identificationof the most relevant polymorphisms to be studied, facilitating the estimationof the allelic frequency of each SNP in different populations. The present studyinitially aimed to validate the DNA pooling approach for the identification ofgenetic polymorphisms potentially associated with individual cancer risk generatingpools with known allelic frequencies and using studies ongoing in the laboratory.Finally, our main aim was to test the accuracy of the pooled DNA analysis comparingthe results of the allelic frequencies determined using pooled samples with theallelic frequency previously estimated by individual genotyping and previouslypublished. In order to analyze the possibility of establishing differences betweenpopulations, we created DNA pools using a Portuguese control population, a breastcancer population and a Xavante Indian population characterized by a total absenceof breast cancer cases. The pools were firstly created with known allelic frequencies,previously determined by individual genotyping, and, latter, randomly incrementedin sample size to 200 patients and controls. Our results showed that the DNA poolingapproach was a useful tool for the analysis of allelic distribution in the differentpopulations studied. Ιn conclusion, our results showed that this methodology canbe applied as an effective approach to identify SNPs of importance in geneticsusceptibility to disease which may be used in association studies conducted subsequentlyby individual genotyping.