Figure 3. Allelic variants in CIPN-susceptibility associated CMT genes.
A. PRX singleton SNV. Of the CIPN-susceptible patients, 8 carried a non-synonymous SNV in PRX. The protein encoded by PRX is shown with the positions of SNV found in CIPN susceptible patients (blue) and sites of known CMT mutations42 (grey).
B. Validation by Sanger sequencing. Individual SNV in PRX were confirmed by Sanger sequencing. Shown are stacks of next generation sequencing reads from the present study and confirmatory electrophoretic tracings obtained by capillary sequencing for the heterozygous variant at chr19:40909664 in a CIPN-susceptible patient and the reference genotype (in another patient).
C. AHRGEF10 recurrent SNV. Three recurrent non-synonymous SNV were detected. The observed MAF was similar to the MAF reported in the 1000 Genomes Project and NHLBI_6500 exome sequencing reference datasets. The three SNV were not correlated (occur independently) in reference cohorts as shown in a linkage disequilibrium (LD) plot generated from 1000 Genomes Project data.
D. Observed frequency of hetero- and homozygous genotypes and validation by TaqMan PCR. For each SNV the relative frequencies of the three possible genotypes observed in the study (homozygous for the major allele, or heterozygous, or homozygous for the minor allele) were consistent with the Hardy Weinberg equilibrium. The accuracy of SNV was confirmed by orthogonal laboratory techniques.
E. AHRGEF10 alleles in CIPN-susceptible patients and controls. The association of ARHGEF10 alleles with CIPN-susceptibility was dominated by rs9657362. Absence of its minor allele was strongly associated with CIPN-susceptibility with an OR=4.8; the same result can also be expressed as the inverse, i.e., OR=0.21, to mean that the minor allele was associated with control group status, i.e. it was protective. The association of rs9657362 was statistically highly significant with p=4×10−4.
The SNV rs17683288 and rs2294039 showed a trend toward a protective and a risk-effect respectively.
A Venn diagram shows the frequency of all possible AHRGEF10 genotypes (all 8 possible combinations of carrying a minor allele at rs9657362, rs17683288 and rs2294039) among CIPN-susceptible and control patients.