Table 1.
Characteristics of patient samples.
Table 2.
Primer sequences for RT-PCR.
Table 3.
Differential splicing events.
Fig 1.
Validation of RNA Sequencing identified mis-splicing events.
(A) RT-PCR amplified products derived from specific primers (Table 2) that flanked selected exons in the ADD3, INF2, and CADM1 genes. Amplification of a larger DNA fragment in ADD3 and CADM1 (exon inclusion) and a smaller DNA fragment in INF2 (exon exclusion) are shown in samples obtained from two independent FECD patients that have a TCF4 trinucleotide repeat expansion (denoted with a plus sign). In contrast, these bands are either lacking or in reduced amounts in a sample from a FECD patient that does not contain a TCF4 trinucleotide repeat expansion (denoted with a minus sign) or a non-FECD patient sample (labeled with a C). (B) Numbers in boxes represent percentage of PCR products containing inclusion/exclusion of exons for each sample in (A). Numbers in parentheses are percent spliced in values obtained from RNASeq on the same samples from which PCR was performed. These results confirm exon inclusion and exclusion as identified by RNA sequence and PCR analysis.
Table 4.
Differential gene expression between RE+ and RE- corneal endothelial sample.
Fig 2.
Identification of a rare LAMC1 variant in RNA79 (from patient 2011–291).
RNASeq (top panel) and exome sequencing data (bottom panel) from the same individual are shown. The location of a C->T variant which leads to the R490W substitution in the LAMC1 protein is highlighted in both panels. Images were obtained from the Integrative Genomics Viewer.
Fig 3.
Identification of a rare TSPOAP1 variant in RNA142 (from patient 2011–395).
RNASeq data (top panel) and a Sanger sequencing trace from patient 2011–395 DNA (bottom panel) are shown. Top panel image obtained from the Integrative Genomics Viewer.
Fig 4.
TSPOAP1 variants in FECD patients.
The locations of two substitution variants in the primary sequence of TSPOAP1 are shown in bold red (positions 1058 and 1738) under a diagram of the structure of the TSPOAP1 gene. The exon that is preferentially excluded from RE+ samples by alternative splicing is shown in red, and the location of this sequence in the TSPOAP1 protein is also shown in red (position 1298–1577). The vertical black arrow designates the start of the region of the TSPOAP1 protein that is thought to interact with TSPO.
Fig 5.
Identification of TSPOAP1 variants in a family with RE- FECD.
(A) Pedigree of RE- FECD family. Patient 52 (91 years old) and patient 59 (64 year old) had modified Krachmer scores of 6 in both eyes and TCF4 trinucleotide repeat sizes of 18, 24 and 24, 31 respectively. Patient 53 (66 years old) and patient 62 (52 years old) had modified Krachmer scores of 0 in both eyes and TCF4 trinucleotide repeat sizes of 24, 31 and 18, 32 respectively. Outside of the FECD diagnosis, there were no evident medical conditions or syndromic diseases that were common within the pedigree other than solitary skin cancers in 2 of the 4 family members. (B) Sanger sequencing traces of DNA from the vicinity of the R1058H variant are shown. Both affected family members (I-1 and II-2) are confirmed to be heterozygous for the R1058H variant. (C) Schematic diagram showing the filtering strategy used to identify variants in exome sequencing of 4 family members. The number of variants remaining after each filtering step is shown in the boxes.