Genome-wide association studies (GWAS) benefit from large sample sizes, and FFPE tissue represents a valuable but challenging resource for genotyping. Our study demonstrated high genotyping concordance between FFPE- and blood-derived DNA, with microarray technology outperforming lcWGS in recall and precision while also being more cost-effective. Despite this, lcWGS remains a promising alternative for comprehensive genetic analyses in future studies.
Objective The power of genome-wide association studies (GWAS) to identify common disease variants depends primarily on the number of included samples. The availability of formalin-fixed paraffin-embedded (FFPE) samples in pathology institutes provides a valuable resource for GWAS, but the use of this material poses significant challenges. To explore the suitability of FFPE tissue for GWAS, we analysed the genotyping concordance between FFPE-derived DNA and blood-derived DNA. We evaluated both microarray technology and low-coverage whole-genome sequencing (lcWGS) to determine whether there were differences between genotyping methods. Results In our concordance study, FFPE tissue showed high recall and precision values across both genotyping methods when compared to matched blood samples for single nucleotide polymorphisms. This demonstrates that FFPE samples are suitable for GWAS and that both methods are viable options for genotyping. However, microarray technology outperformed lcWGS, as evidenced by significantly higher recall (p = 0.005) and precision (p = 0.003) values. This, together with the lower cost of genotyping and computational efficiency, makes microarray technology currently the superior method for GWAS using FFPE tissue. Nevertheless, lcWGS has shown reliable results and holds the potential to provide more comprehensive and unbiased genetic variant analysis across diverse populations in the future. Combined with the right genotyping method, the large number of FFPE samples stored in pathology institutes can significantly increase the power of future GWAS.