Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Quantitative trait loci (QTL) study identifies novel genomic regions associated to Chiari-Like Malformation in Griffon Bruxellois dogs

ABSTRACT: 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 were used to identify quantitative trait loci. To identify the presence of causative haplotype for Chiari-Like Malformation 80 Griffon Bruxellois dogs were genotyped using Illumina CanineHD Beadchip. This cohort consisted of 53 cases and 27 controls. Ten samples were whole genome amplified using the Qiagen Repli-g kit following the protocol. Linear and mixed regression model were used to define association between morphologic traits and genetic data. The sample traits (provided in the sample characteristics field) are described in the 'README_Traits_description.pdf' Processed data were obtained in 3 different normalization batches. The normalization batch/raw data file information is provided in the sample description field.

ORGANISM(S): Canis lupus familiaris

SUBMITTER: Philippe Lemay

PROVIDER: E-GEOD-52221 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Quantitative trait loci (QTL) study identifies novel genomic regions associated to Chiari-like malformation in Griffon Bruxellois dogs.

Lemay Philippe P Knowler Susan P SP Bouasker Samir S Nédélec Yohann Y Platt Simon S Freeman Courtenay C Child Georgina G Barreiro Luis B LB Rouleau Guy A GA Rusbridge Clare C Kibar Zoha Z

PloS one 20140416 4

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 ...[more]

PMID: 24740420

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Project description:Contemporary Jews comprise an aggregate of ethno-religious communities whose worldwide members identify with each other through various shared religious, historical, and cultural traditions1,2. Historical evidence suggests common origins in the Middle East, followed by migrations leading to the establishment of communities of Jews in Europe, Africa, and Asia - in what is termed the Jewish Diaspora3-5. This complex demographic history imposes special challenges in attempting to address the genetic structure of the Jewish people6. While many genetic studies have shed light on Jewish diseases and origins, including those focusing on uniparentally- and biparentally-inherited markers7-16, genome-wide patterns of variation across the vast geographic span of Jewish Diaspora communities and their respective neighbors have yet to be addressed. Here we use high-density bead arrays to genotype individuals from 14 Jewish Diaspora communities, and compare these patterns of genome-wide diversity with those from 69 Old World non-Jewish populations, of which 25 have not been previously reported. These samples were carefully chosen to provide comprehensive comparisons between Jewish and non-Jewish populations in the Diaspora, as well as with non-Jewish populations from the Middle East and North Africa. Principal component and structure-like analyses identify previously unrecognized genetic substructure within the Middle East. Most Jewish samples form a remarkably tight sub-cluster that overlies Druze and Cypriot samples, but not samples from other Levantine populations or paired Diaspora host populations. In contrast, Ethiopian Jews (Beta Israel) and Bene Israel Indian Jews cluster with neighbouring autochthonous populations in Ethiopia and western India, respectively; despite a clear paternal link between the Bene Israel and the Levant. These results cast light on the variegated genetic architecture of the Middle East, and trace the origins of most Jewish Diaspora communities to the Levant. 466 samples are analysed on three different Illumina platforms.

Dataset Information

Quantitative trait loci (QTL) study identifies novel genomic regions associated to Chiari-Like Malformation in Griffon Bruxellois dogs

Publications

Quantitative trait loci (QTL) study identifies novel genomic regions associated to Chiari-like malformation in Griffon Bruxellois dogs.

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