Additional file 1: Table S1. of Partial uniparental isodisomy of chromosome 16 unmasks a deleterious biallelic mutation in IFT140 that causes Mainzer-Saldino syndrome

Clinical genetic testing summary. Table S2. Whole exome sequencing capture statistics. Table S3. Final variant list following trio-based exome analysis (<1% minor allele frequency (MAF), homozygous, compound heterozygous, de novo, or X-linked). Figure S1. Fundus imaging and full field electroretinograms indicate retinal dystrophy. a. Fundus imaging of the proband at 5 years 6 months in the right (top) and left (bottom) eyes show mottling of the retinal pigmentary epithelium. b. Photopic (light adapted) testing of cone function demonstrated reduced a-wave implicit time and amplitudes with slowed implicit times for the b-wave. c. Scotopic (dark adapted) testing of rod function demonstrated slower implicit time and diminished amplitudes for both a- and b-waves. The a-wave was substantially delayed with reduced incremental increases in a-wave and b-wave. Figure S2. Validation of the ift140 splice-blocking (sb) morpholino (MO). a. Schematic of the D. rerio ift140 locus at chr24:37,937,737-38,013,596 (GRCz10; top) and translated protein (bottom). Exons are depicted as green boxes; untranslated regions are shown as white boxes (ENSDART00000129889.4). The sb-MO targets the splice donor of exon (Ex) 2 (red box). Protein schematic (blue) indicates predicted WD40 repeat (WD40) and tetratricopeptide-like helical domains (TPR). b. ift140 sb-MO induces aberrant splicing of endogenous transcript. ift140 transcript was evaluated by RT-PCR; embryos were injected with 9 ng MO at the one-to-four-cell stage and harvested for RNA extraction at the mid-somitic stage. Resulting cDNA was amplified with primers flanking the MO target site (arrows in panel a), and migrated on a 2.5% agarose gel. β–actin was used as a control to ensure RNA integrity. c. Chromatograms indicate splicing defects in ift140 mRNA in morphants. Sequence analysis of purified PCR product indicates that the majority of ift140 message is missing exon 2 (bottom), which contains the translation initiation codon. Modest amounts of wild type (wt; center) and mRNA containing a 33 nucleotide in-frame intronic insertion (top) are also detectable. d. Representative dose curve of the ift140 sb-MO. Embryo batches were injected at the one-to-four-cell stage with increasing amounts of ift140 sb-MO and scored for gastrulation defects at the mid-somitic stage (eight to ten somites). Embryos were scored live according to previously established phenotypic criteria: class I, modest shortening of the body axis and reduction in size of anterior structures; class II, severe shortening of the body axis and decreased anterior structures accompanied by broadening and/or kinking of the notochord and thinning of the somites (See Figure 3; n = 59–70 embryos/injection; repeated twice). Figure S3. Read depth and variant calls of the homozygous variants called on 16p13. Plot of the 76 maternally inherited homozygous variants identified in the 16p13 region of the proband. Red indicates alternate (alt) reads; blue indicates reference (ref) reads; 49/76 (64%) are comprised only of alternate reads; 27/76 (36%) had one to three reference reads at positions annotated as homozygous. (PDF 20018 kb