Fig 1.
Analysis of TCF4 TGC repeat polymorphism in homozygous FECD cases and controls.
PCR was performed on genomic DNA from cases and controls carrying the shortest or the longest TCF4 TGC repeat length. Data from two representative cases (F-31 and F-137 with 12 and 83 repeats, respectively) and controls (C-62 and C-05, with 12 and 18 repeats, respectively) are shown. A. Agarose gel electrophoresis of the PCR amplified repeat region from homozygous FECD cases and controls. Sizes of the products are shown on the right and correspond with the expected sizes (F-31 and C-62, 265 bp each; F-137, 478 bp; C-05, 283 bp). Sizes of DNA markers are indicated on the left. B. Sequencing chromatograms of FECD-affected (F-31 and F-137) and control (C-62 and C-05) individuals homozygous for the shortest (B.I and B.II) and the longest (B.III and B.IV) repeat alleles are shown. TGC repeat length in each individual was calculated by substracting 230 bps, corresponding to the DNA region flanking the repeat region amplified during PCR, from the detected PCR product size and dividing the difference by 3 (number of nucleotides of the repeat). C-F. Electropherograms showing the sizes of TGC repeat alleles in FECD cases F-31 (C) and F-137 (E) and in two control individuals C-62 (D) and C-05 (F) detected by STR assay. The peaks representing the TCF4 TGC repeat fragments are indicated by arrows. Multiple peaks seen in panel E are due to variation in product size when large repeats are amplified. X-axis, fragment sizes in base pairs; Y-axis, relative fluorescence units; orange peaks, sizes of internal standards; red line across the electropherograms, slope threshold for peak start/end.
Table 1.
Characteristics of the FECD case and control cohorts, and dichotomised distribution of the TCF4 TGC repeat alleles in cases and controls.
The age and sex between cases and controls were compared using the Student’s t-test and chi-square test, respectively. Expanded allele counts between cases and controls were compared using chi-square test.
Fig 2.
Distribution of TGC repeat lengths in the TCF4 gene in FECD cases and controls.
Median repeat length in cases = 53; range: 11–115, and median repeat length in controls = 18; range: 11–83. The box represents the second and third quartiles and the line in the middle indicates median. The lower and upper wiskers represent the limits of the first and fourth quartiles, respectively. The dots represent individual data points for controls (n = 183) and cases (n = 189).
Fig 3.
Distribution of genotypes of the TCF4 TGC repeat alleles in FECD cases and controls.
The numbers of individuals with each of the three possible genotypes of the dichotomised repeat alleles are shown. S represents short (<40 repeats; non-expanded) and L long (≥40 repeats; expanded) allele. SS represents homozygous non-expanded, LL homozygous expanded, and SL heterozygous with one non-expanded and one expanded allele.
Table 2.
Association between common haplotypes of genotyped polymorphisms (TGC repeat locus, L/S, and rs613872, G/T) in the TCF4 gene and FECD.
f = frequency; OR = Odds ratio; CI = Confidence Interval; L = long repeat allele; S = short repeat allele.