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ABSTRACT: Genome-wide association study of cruciate rupture in the Labrador Retriever

PROVIDER: PRJEB43243 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	cr397Frontiers_corr.vcf.gz	Vcf
	cr397Frontiers_corr.vcf.gz.tbi	Vcf

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RNA-Seq of anterior cruciate ligament and knee joint synovium in dogs that are affected with cruciate rupture compared to matched controls.

Project description:The intent of the experiment was to identify genes that were differentially expressed between dogs affected with anterior cruciate ligament (ACL) rupture and breed-matched controls. Anterior cruciate ligament and knee synovial tissue biopsies were collected from 4 ACL rupture affected cases and 4 unaffected control dogs. Cases and controls were matched as closely as possible based on breed, sex, neutered status, age, and weight. Medications that the dogs were taking at the time of sample collection were also considered. We prioritized sample size and quality above all other variables, therefore, two matched pairs of Golden Retrievers were chosen with two matched pairs of Labrador Retrievers for this analysis. Tissues from cases were collected during knee stabilization surgery. Tissues from unaffected control dogs were collected from dogs undergoing pelvic limb amputation or euthanasia for reasons unrelated to this study. Illumina TruSeq RNA libraries were constructed and 150bp paired-end sequencing was performed using the Illumina Hi-Seq 2500 platform. Table 1. Breed, sex, age, and weight of matched case and control pairs chosen for RNA sequencing analysis Cases Matched Controls Breed Sex Age (yr) Weight (kg) Breed Sex Age (yr) Weight (kg) GR1 CM 8.8 30.5 GR2 CM 14.9 N/A GR3 CM 5.6 44.0 GR4 CM 3.9 34.0 LR1 CM 9.7 36.0 LR2 CM 12.7 28.5 LR3 CM 13.3 36.0 LR4 CM 13.5 35.0 GR = Golden Retriever. LR = Labrador Retriever. CM= castrated male. Weight at the time of death was not available for one dog.

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Genome-wide association study of cruciate rupture in the Labrador Retriever

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Determining predictive metabolomic biomarkers of meniscal injury in dogs with cranial cruciate ligament disease

Project description:OBJECTIVES: This study used hydrogen nuclear magnetic resonance spectroscopy (1H NMR) for the first-time to examine differences in the metabolomic profile of stifle joint synovial fluid from dogs with cranial cruciate ligament rupture with and without meniscal injuries, in order to identify biomarkers of meniscal injury.METHODS: Stifle joint synovial fluid was collected from dogs undergoing stifle joint surgery or arthrocentesis for lameness investigations at three veterinary hospitals in the North-West of England. Samples underwent 1H NMR spectroscopy and metabolite identification. We used multivariate and univariate statistical analysis to identify differences in the metabolomic profile between dogs with cranial cruciate ligament rupture and meniscal injury, cranial cruciate ligament rupture without meniscal injury, and neither cranial cruciate ligament rupture nor meniscal injury, taking into consideration clinical variables.RESULTS: 154 samples of canine synovial fluid were included in the study. 64 metabolites were annotated to the 1H NMR spectra. Six spectral regions were found to be significantly altered (false discovery rate adjusted p-value <0.05) between groups with cranial cruciate ligament rupture with and without meniscal injury, including three attributed to NMR mobile lipids (mobile lipid -CH3 [p=0.016], mobile lipid -n(CH3)3 [p=0.017], mobile unsaturated lipid [p=0.031]).CLINICAL SIGNIFICANCE: We identified an increase in NMR mobile lipids in the synovial fluid of dogs with meniscal injury which are of interest as potential biomarkers of meniscal injury, as well as understanding the metabolic processes that occur with meniscal injury.

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