Gene and SNP | SNP alleles | CRPS discovery cohort allele frequency (n=34) | 1000 Genomes χ2 p value (FDR corrected) | EVS χ2 p value (FDR corrected) | CRPS discovery and replication cohorts allele frequency (n=84) | CRPS combined cohort data uncorrected p value against EVS | CRPS combined cohort data uncorrected p value against UK Biobank | Chronic pain cohort allele frequency (n=39) |
ANO10 rs41289586 | p.Arg263His | 0.088 (6/68) | 1.52×10–6 | 0.018 | 0.065 (11/168) | 0.0016 | 0.0029 | 0 (0/39) |
P2RX7 rs28360457 | p.Arg307Gln | 0.059 (4/68) | 1.47×10–6 | 0.04 | 0.030 (5/166) | 0.0869 | 0.236 | 0 (0/39) |
PRKAG1 rs1126930 | p.Thr57Ser | 0.103 (7/68) | 7.5×10–7 | 0.05 | 0.054 (11/168) | 0.0267 | 0.0221 | 0 (0/39) |
SLC12A9 rs80308281 | p.Ile350Thr | 0.044 (3/68) | 6.91×10–11 | 8.53×10–5 | 0.029 (5/168) | 0.0001 | 0.0001 | 0 (0/39) |
The SNP names with the gene they occur in, and common and rare alleles are shown in the first two columns. In each cohort, ‘n’ refers to the number of people in a cohort. The study results are given for each SNP rare allele for the discovery CRPS-1 discovery cohort and combined CRPS-1 cohorts, and the chronic pain cohort (CPC). Published SNP allele frequencies for 1000 Genomes GBR cohort (most like our cohorts), the Exome Variant Server (EVS) European American cohort (predominantly northern European) and the UK Biobank are shown in table 3. We include population cohort allele frequencies in a more complete version of table 2 (see online supplemental table 5). Cohort study results are given for each SNP as allele frequency uppermost, and then in brackets are the number of rare alleles over total alleles. For each SNP in the CRPS-1 discovery cohort, the statistical difference of a false discover rate (FDR) corrected (against the total number of SNPs, see text) χ2 without Yate’s correction two-tailed p value is given. This is shown against 1000 Genomes reference data and EVS data separately. For the combined CRPS-1 cohort (discovery and replication cohorts) results we conducted a χ2 (without Yates correction) two tailed test against EVS and UK Biobank SNP allele frequencies. The final column shows the results of an fSNPd discovery analysis for our chronic pain cohort (CPC) with all four SNPs with genotypes and coverage confirmed; statistics are not given as no individuals of the cohort had any of the CRPS-1 SNP rare alleles.