Additional file 1 of A LINE-1 insertion situated in the promoter of IMPG2 is associated with autosomal recessive progressive retinal atrophy in Lhasa Apso dogs
Creators: name: Hitti-Malin, Rebekkah J.
name: Burmeister, Louise M.
name: Ricketts, Sally L.
name: Lewis, Thomas W.
name: Pettitt, Louise
name: Boursnell, Mike
name: Schofield, Ellen C.
name: Sargan, David
name: Mellersh, Cathryn S.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 1: Supplementary Table 1. (A) PCR primers used for sequencing amplicons of 18 known canine retinal mutations in the PRA-affected LA sent for WGS. (B) PCR primers used for genotyping seven known canine retinal mutations in the PRA-affected LA sent for WGS (by PCR followed by amplified fragment length polymorphism (AFLP) analysis or by visualisation of PCR product on an agarose gel). Supplementary Table 2. Multiplex PCR amplification using pooled primers. Supplementary Table 3. Thermal cycling conditions for multiplex PCR amplification using pooled primers. Supplementary Table 4. Reaction for IMPG2 LINE-1 insertion amplification for size determination. Supplementary Table 5. Thermal cycling conditions to amplify IMPG2 LINE-1 insertion. Supplementary Table 6. Primer sequences to amplify candidate variant regions. Supplementary Table 7. Amplification of IMPG2 LINE-1 insertion for amplified fragment length polymorphism analysis. Supplementary Table 8. Thermal cycling conditions for amplification of IMPG2 LINE-1 insertion for amplified fragment length polymorphism analysis. Supplementary Table 9. Breed names for 447 dogs of 123 breeds that were screened for the IMPG2 LINE-1 insertion. Supplementary Table 10. Forty-two transcription factor binding site predictions from MatInspector in eye tissue within 150 bp upstream and downstream of the IMPG2 LINE-1 breakpoints. Five of these are bicoid-like homeodomain transcription factors (highlighted in orange) and are specific to photoreceptor cells in the retina. Supplementary Figure 1. A multi-dimensional scaling plot to determine relatedness between the case and control sample sets showed a similar distribution of 15 cases and 27 controls analysed in the GWAS. Supplementary Figure 2. (A) The quantile-quantile (Q-Q) plot of the expected and observed –log10 p values generated from PLINK derived a genomic inflation factor, lambda (λ) =1.36. (B) The Q-Q plot after correcting for population stratification using EMMAX showed a decreased inflation factor, λ =1.02. Supplementary Figure 3. A schematic diagram showing genotypes for four variants across 18 PRA-affected (A1–18) LA and 41 PRA-unaffected (C1–41) LA: homozygous alternate allele (coloured pink), homozygous wild type/reference allele (coloured yellow) or heterozygous (coloured pink and yellow). Supplementary Figure 4. The distribution of the random sample sets mean pairwise kinships (blue histogram), and the AHT PRA4 DNA tested sample set (red dotted line). Supplementary Figure 5. (A-C) Histograms showing the proportion of pairwise relationships across the random sample sets and the AHT PRA4 DNA tested subset; (D) Pedigree drawing of the 16 outliers belonging to two distinct families: circle = female, square = male, diamond = unknown, shaded diamond = not included in our data set. Supplementary Figure 6. (A) Multi-dimensional scaling plot to determine relatedness within each sample set. Red points represent the 261 AHT PRA4 tested samples, blue points represent 1000 randomly selected KC registered dogs born 2009–2017); (B) zoomed in on central cluster in (A) showing the main body of the AHT sample set (red) is representative of a random sample (blue).