Page 309 - Personalised medicine of fluoropyrimidines using DPYD pharmacogenetics Carin Lunenburg

Manhattan plot is shown in Figure 2. The corresponding QQ-plot of p-values is shown in Figure 3. The inflation factor is 1.04. Table 2 shows the list of the top 30 identified markers. No variants were identified to be statistically significant associated with severe fluoropyrimidine-induced toxicity at the genome-wide level. However, six SNPs were found to be suggestive. None of these SNPs have previously been reported in publications or in the ClinVar database of the National Center for Biotechnology Information (NCBI).32 The variants are reported in the SNP database of the NCBI.33 Three variants are stated on the website as having ‘no gene consequence’, two were listed as an intron variant in RNA gene LOC101927414 (rs114105116) and protein coding gene COL6A3 (rs12622722), and one was listed as an 2KB upstream variant in LOC107984256 (rs10786179).
Genotyping and quality control
A set of 692,367 markers was genotyped. After several QC steps, 186,920 markers were excluded. Of these, 18,114 markers (2.6%) were excluded based on a deviation from Hardy- Weinberg equilibrium (HWE). Filtering for allele frequencies (threshold 0.5%) resulted in the exclusion of 147,607 markers (21.3%). The missingness cut-off was set at 10%, 23,835 markers (3.4%) were excluded based on the missing data analysis. Of the abovementioned excluded markers, 2,636 had multiple QC failures. In total, 505,447 markers met the QC for statistical analyses. These markers were imputed using the 1000 Genomes dataset as a reference panel. In total, 4,650,899 variants were available for statistical analyses. In the integrative QC, individuals and markers from the marginal QC steps were excluded. An MDS was executed in order to detect population stratification. No individuals were excluded. IBD/ IBS clustering was executed to assess duplicates. No individuals were excluded.
Polygenic risk score
To calculate the PRS all SNPs with a p-value <0.01 for their association with severe fluoropyrimidine-induced toxicity were selected. To reduce linkage disequilibrium, SNPs were pruned for a minimum distance of 105 bps. This resulted in a set of 5,055 SNPs. Finally, an elastic net regression (R package glmnet, α=0.5) was performed and evaluated by cross- validation. The receiver operating characteristic (ROC) curve is shown in Figure 4, where it is compared to the model containing only clinical covariates. The two corresponding areas under the curve (AUCs) were 96% and 62%, respectively.
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Genome-wide association study
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