Additional file 1: of A genome-wide association study identifies candidate loci associated to syringomyelia secondary to Chiari-like malformation in Cavalier King Charles Spaniels

Table S1. Characteristics and measurements of 96 CKCS of the cohort. This table includes the gender, age, clinical status and all MRI cranial measurements taken on the 96 CKCS dogs included in this study. (XLSX 41 kb

Additional file 3: of A genome-wide association study identifies candidate loci associated to syringomyelia secondary to Chiari-like malformation in Cavalier King Charles Spaniels

Figure S1. P value distribution inside the CFA15 (24537882-26,252,411 bp) associated region. This region spans 1.7 Mb surrounding SNPs associated to ratio F-d/BC and was identified using Haploview V4.2. (PDF 54 kb

Additional file 2: of A genome-wide association study identifies candidate loci associated to syringomyelia secondary to Chiari-like malformation in Cavalier King Charles Spaniels

Table S2. SNPs suggestive of association to SM in the CKCS breed. This table enlists all SNPs suggestive of association with FDR corrected scores between 0.05 and 0.1. These SNPs were identified following a GWAS using a mixed linear model with age as a covariate on the previously identified traits (Line AE, line AI, angle 3, angle 7, ratio F-d/BC and L4 + L7). (DOCX 15 kb

Quantitative Trait Loci (QTL) Study Identifies Novel Genomic Regions Associated to Chiari-Like Malformation in Griffon Bruxellois Dogs

<div><p>Chiari-like malformation (CM) is a developmental abnormality of the craniocervical junction that is common in the Griffon Bruxellois (GB) breed with an estimated prevalence of 65%. This disease is characterized by overcrowding of the neural parenchyma at the craniocervical junction and disturbance of cerebrospinal fluid (CSF) flow. The most common clinical sign is pain either as a direct consequence of CM or neuropathic pain as a consequence of secondary syringomyelia. The etiology of CM remains unknown but genetic factors play an important role. To investigate the genetic complexity of the disease, a quantitative trait locus (QTL) approach was adopted. A total of 14 quantitative skull and atlas measurements were taken and were tested for association to CM. Six traits were found to be associated to CM and were subjected to a whole-genome association study using the Illumina canine high density bead chip in 74 GB dogs (50 affected and 24 controls). Linear and mixed regression analyses identified associated single nucleotide polymorphisms (SNPs) on 5 Canis Familiaris Autosomes (CFAs): CFA2, CFA9, CFA12, CFA14 and CFA24. A reconstructed haplotype of 0.53 Mb on CFA2 strongly associated to the height of the cranial fossa (diameter F) and an haplotype of 2.5 Mb on CFA14 associated to both the height of the rostral part of the caudal cranial fossa (AE) and the height of the brain (FG) were significantly associated to CM after 10 000 permutations strengthening their candidacy for this disease (<i>P = </i>0.0421, <i>P</i> = 0.0094 respectively). The CFA2 QTL harbours the <i>Sall-1</i> gene which is an excellent candidate since its orthologue in humans is mutated in Townes-Brocks syndrome which has previously been associated to Chiari malformation I. Our study demonstrates the implication of multiple traits in the etiology of CM and has successfully identified two new QTL associated to CM and a potential candidate gene.</p></div

Raw and permutation <i>P</i> values for the 5 most frequent CM-associated haplotypes in the CFA2 QTL region.

<p>*Significance threshold set to P value<0.05.</p

QTL significantly associated to Diameter F and Length BC in GB dogs obtained in the linear model and QTL associated to Length AE, Length FG and Angle 5 in the mixed model.

<p>*CFA = Canis familiaris autosome.</p

Manhattan plot of the significant QTL obtained by linear or mixed regression models.

<p>Manhattan plot of the 2 significant QTL obtained by the linear model in traits length BC (panel A) and Diameter F (panel B) and the 4 traits containing the 3 associated regions in the mixed linear model for traits length AE (panel C), Angle 5 (panel D), Diameter F (panel E) and length FG (panel F).</p

Boxplot of CM significantly associated traits and confounding factors.

<p>Boxplot distribution of all 7 CM-significantly associated traits and age code. Boxplots were done on a cohort of 123 GB with unambiguous phenotypes.</p

<i>P</i> value distribution inside the CFA2 (66803513–67333070 bp) QTL region. <i>P</i> value distribution inside the CFA2 QTL region before and after 10 000 permutations.

<p>The black line represents the initial CM association score of the SNPs. The red line represents the association score after permutations.</p

Morphometric measurements of a Griffon Bruxellois skull.

<p>Measurements were chosen to maximize coverage of the possible variation associated with CM. All measurements start from one of those 9 points :(A) the dorsum of sphenoid-occipital synchondrosis, (B) the basion of basioccipital bone, (C) the rostral edge of the dorsal lamina of the atlas, (D) the junction between the supraoccipital bone and the occipital crest, (E) the most dorsal point of intersection of the cerebellum with the occipital lobe circle, (F) the center of occipital lobe circle, (G) the optic nerve, (H) the most caudal point of the olfactory bulb and (I) the intersection point with the HA baseline.</p