Additional file 1 of Cataracts in Havanese: genome wide association study reveals two loci associated with posterior polar cataract

Additional file 1: Supplementary figure 1. A schematic illustration of LD-stretches in the associated regions on (A) CFA20 and (B) CFA21, showing LD between selected SNPs that span across the associated variants (orange outline) and potential candidate genes (orange). (Additional SNPs show similar values but are not shown). Supplementary figure 2. MDS-plots for the (A) posterior polar cataract and (B) cortical cataract datasets, showing that both cases and controls are represented in each cluster for both phenotypes. Cases = red, controls = blue, unknown status (excluded from the association analysis) = grey. Supplementary figure 3. Regional Manhattan plots, spanning +/- 2 Mb of the top SNP on each chromosome of the association analysis of posterior polar cataract (A+B) and cortical cataracts (C+D). A: CFA20, B: CFA21, C: CFA4, D: CFA30. Supplementary figure 4. Genome wide association result for anterior suture line cataract, including 23 anterior suture line cataract cases and 57 controls. The analysis included 140475 autosomal SNPs that remained after quality control. A: Manhattan plot. B: Quantile-quantile plot. λ = 1.03

Dog_Phenotypes

For each Gordon setter and English setter; information on symmetrical onychomadesis disease status, gender, nationality and DLA class II haplotypes is given

Dogs .map file

Singel nucleotide polymorphism locations are given according to the Canfam 3.1assembly

Dogs .ped file

The nucleotide variant is given at each marker on the 170K CanineHD BeadChip (Illumina), for each Gordon setter and English setter

Additional file 1: Table S1. of Genetics and epidemiology of hypothyroidism and symmetrical onychomadesis in the Gordon setter and the English setter

DLA alleles in the Gordon setter (GS). Table S2. DLA alleles in the English setter (ES). Table S3. DLA haplotypes associated with symmetrical onychomadesis and protection for symmetrical onychomadesis in the Gordon setter. Table S4. Oligonucleotide primers used in the study. (DOCX 26 kb

Tumor_LogR.GCadjusted_qnorm_117

Adjusted Log R Ratio values for the 117 tumour samples studied, after the application of the GC correction method and quantile normalization

Diagnoses and histopathologic scores_ASCAT tumours

Histopathomorphological diagnoses and histopathologic score values for all tumours that achieced an ASCAT output (113 of 117 tumours). These diagnoses/scores were used in further analysis of the ASCAT output

Association results for chromosome 27.

<p><b>(A)</b> Chromosome 27 with association results colour-coded according to pair-wise LD (r²) with the top two SNPs (index 1 = chr27:745,156 bp and 2 = chr27:7,706,463 bp). <b>(B)</b> Minor allele frequency plot over chromosome 27. <b>(C)</b> Association results for the merged and imputed GWAS and sequence candidate SNPs dataset at the 0.7 Mb peak. The top SNP (chr27:735,281 bp) is located 418 bp upstream of <i>LACRT</i>, SNP position indicated by red arrow. Gene annotations are lifted over from the human genome. <b>(D)</b> Association results for the 7.7 Mb region. The top SNP (chr27:7,706,463 bp) is potentially located in an intron of <i>SLC38A4</i>.</p

Top ten GWAS regions defined by linkage disequilibrium (cut-off p<0.1 and r²>0.2).

<p>Top ten GWAS regions defined by linkage disequilibrium (cut-off p<0.1 and r²>0.2).</p

Tumor_BAF_117orig

Original B allele frequency values for the 117 tumour samples studied