A novel genomic rearrangement on chr19q13.42 leads to PRPF31‐associated retinitis pigmentosa

The authors declare no conflicts of interest. The data that support the findings of this study are available from the corresponding author upon reasonable request. Data S1. Supporting Information. FIGURE S1: Clinical manifestations of the RP-11 patient III-3. (A) The younger daughter showed midperipheral and posterior (outside the arcades) clumps of black pigment in bone spicule configuration, with macular alteration, attenuated retinal vessels, and pallor of the optic nerve. (B) OCT examination suggested loss of the delineation between the ellipsoid zone and cone outer segment tips and cystoid macular edema. (C) ERG examination demonstrated severely decreased a-waves and b-waves. FIGURE S2: Significant downregulation of exons 1–3 of PRPF31 and VSTM1 were detected in the proband and RP-11 patient III-3. (A and B) The expression levels of exons 1–3 of VSTM1 and PRPF31 in the patients were measured by q PCR. Significant downregulation of exons 1–3 of PRPF31 and VSTM1 was observed in the proband and patient III-3 versus that of an unrelated non-RP control (NC) at genomic level. (C) Upregulation of exons 1–3 of PRPF31 however, no downregulation of exons 1–3 of VSTM1 were detected in the I-1 individual by q PCR. (D, E and F) No downregulation of exons 1–3 of PRPF31 and VSTM1 was found by qPCR in the I-2, II-3 and III-2 individuals in the RP-11 family. (G) Significant downregulation of PRPF31 at transcriptional level was detected in the proband and patient III-3′ peripheral blood. The primers were designed to span 330 bp-CDS sequence of the PRPF31 gene 5′ end to reflect downregulation induced by the deletion of PRPF31 1–3. FIGURE S3: The rearrangement of the Alu Y element on VSTM1 and the Alu Yh3 element on PRPF31 causes the large fragment deletion on chr19q13.42. (A and B) Sanger sequencing chromatograms demonstrated that the breakpoints of the deletion fragment between the region of chr19:54051736–54 119 836 were located at chr19:54052244 and chr19:54119229. The PCR fragments of two patients' genomic DNA were amplified by the KP0609 primers sequence indicated in Table S1, and the sequences of the PCR fragments were directly identified by Sanger sequencing. The sequencing results showed that the breakpoints in the proband and patient III-3 samples were located at chr19:54052244 and chr19:54119229, respectively. The breakpoint of the deletion fragment is marked by a red dashed line. The sequences flanking the fusion point contained a typical A(5)_TAC_A(6) chimeric construct. (C) The alignment of the partial sequencing result of two RP-11 patients' genomic DNA and the two CNV-Alus. The sequence of the Alu Y element, Alu Yh3 element, and the genomic DNA sequence of the proband were aligned using DNAMAN Version 6. The linker sequence of the two CNV-Alus sequence and the A(5)_TAC_A(6) chimeric construct are framed in red. FIGURE S4: The chimeric Alu Y/Alu Yh3 hybrid is formed by an Alu/Alu-mediated rearrangement (AAMR) event. Structure of the large deletion event detected in the RP-11 family patients. The proximal and distal breakpoints resided within Alu Y of VSTM1 intron 4 and Alu Yh3 of PRPF31 intron 3, respectively. Alu Y/Alu Yh3-mediated homologous recombination produced a chimeric Alu, which contained a 27-bp region of microhomology. The microhomology is represented as green rectangle and shown in chromatograph with a grey background. Table S1: The primer sequence used in this study. Table S2: Overview of PRPF31-involved genomic rearrangements. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.