Identification of susceptibility genes for complex diseases using pooling-based genome-wide association scans

Abstract

The success of genome-wide association studies (GWAS) to identify risk loci of complex diseases is now well-established. One persistent major hurdle is the cost of those studies, which make them beyond the reach of most research groups. Performing GWAS on pools of DNA samples may be an effective strategy to reduce the costs of these studies. In this study, we performed pooling-based GWAS with more than 550,000 SNPs in two case-control cohorts consisting of patients with Type II diabetes (T2DM) and with chronic rhinosinusitis (CRS). In the T2DM study, the results of the pooling experiment were compared to individual genotypes obtained from a previously published GWAS. TCF7L2 and HHEX SNPs associated with T2DM by the traditional GWAS were among the top ranked SNPs in the pooling experiment. This dataset was also used to refine the best strategy to correctly identify SNPs that will remain significant based on individual genotyping. In the CRS study, the top hits from the pooling-based GWAS located within ten kilobases of known genes were validated by individual genotyping of 1,536 SNPs. Forty-one percent (598 out of the 1,457 SNPs that passed quality control) were associated with CRS at a nominal P value of 0.05, confirming the potential of pooling-based GWAS to identify SNPs that differ in allele frequencies between two groups of subjects. Overall, our results demonstrate that a pooling experiment on high-density genotyping arrays can accurately determine the minor allelic frequency as compared to individual genotyping and produce a list of top ranked SNPs that captures genuine allelic differences between a group of cases and controls. The low cost associated with a pooling-based GWAS clearly justifies its use in screening for genetic determinants of complex diseases.

Copy number variation analysis reveals additional variants contributing to endometriosis development

“…DNA pooling has been originally used as an economic and alternative tool for genotyping and GWAS; therefore, it can be applied to discover common CNVs in certain studies [30,31]. However, the copy number estimation represents a challenge in terms of false-positive rates, so it has been suggested that CNVs identified from SNP genotyping data must always be validated with an alternative method to avoid erroneous calls [31,32].…”

“…However, the copy number estimation represents a challenge in terms of false-positive rates, so it has been suggested that CNVs identified from SNP genotyping data must always be validated with an alternative method to avoid erroneous calls [31,32]. A past study with schizophrenia in Brazilian samples also used pooling strategy to evaluate the CNVs and the possible role in the disease.…”

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

“…However, the results obtained with this type of stratification may reflect only the allelic distribution for each pool, which is of importance to determine whether any significant differences exist between the populations under study. However, pooling methodology does not exclude the use of individual genotyping to develop association studies (30,31).…”

“…This approach is also a very useful tool for genome-wide association studies (GWAS), as it allows allelic frequency estimation, rather than specific genotypes, allowing for analysis and the classification of the likelihood of association with a disease. The development of this technique in GWAS studies allows cost savings which are essential in studies of this size (31).…”

Genome-wide association studies - A summary for theclinical gastroenterologist

“…An even cheaper approach is to employ DNA-pooling [34] . This means that the DNA samples from several individuals are pooled together and subsequently used for genotyping.…”