Dataset Information

Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis.

ABSTRACT: There has been considerable interest in studying cancer in dogs and its potential as a model system for humans. One area of research has been the search for genetic risk variants in canine lymphoma, which is amongst the most common canine cancers. Previous studies have focused on a limited number of breeds, but none have included Border Collies. The aims of this study were to identify relationships between Border Collie lymphoma cases through an extensive pedigree investigation and to utilise relationship information to conduct genome-wide association study (GWAS) analyses to identify risk regions associated with lymphoma. The expanded pedigree analysis included 83,000 Border Collies, with 71 identified lymphoma cases. The analysis identified affected close relatives, and a common ancestor was identified for 54 cases. For the genomic study, a GWAS was designed to incorporate lymphoma cases, putative "carriers", and controls. A case-control GWAS was also conducted as a comparison. Both analyses showed significant SNPs in regions on chromosomes 18 and 27. Putative top candidate genes from these regions included DLA-79, WNT10B, LMBR1L, KMT2D, and CCNT1.

SUBMITTER: Soh PXY

PROVIDER: S-EPMC10536503 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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Publications

Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis.

Soh Pamela Xing Yi PXY Khatkar Mehar Singh MS Williamson Peter P

Veterinary sciences 20230919 9

There has been considerable interest in studying cancer in dogs and its potential as a model system for humans. One area of research has been the search for genetic risk variants in canine lymphoma, which is amongst the most common canine cancers. Previous studies have focused on a limited number of breeds, but none have included Border Collies. The aims of this study were to identify relationships between Border Collie lymphoma cases through an extensive pedigree investigation and to utilise re ...[more]

PMID: 37756103

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Project description:Since most analysis software for genome-wide association studies (GWAS) currently exploit only unrelated individuals, there is a need for efficient applications that can handle general pedigree data or mixtures of both population and pedigree data. Even datasets thought to consist of only unrelated individuals may include cryptic relationships that can lead to false positives if not discovered and controlled for. In addition, family designs possess compelling advantages. They are better equipped to detect rare variants, control for population stratification, and facilitate the study of parent-of-origin effects. Pedigrees selected for extreme trait values often segregate a single gene with strong effect. Finally, many pedigrees are available as an important legacy from the era of linkage analysis. Unfortunately, pedigree likelihoods are notoriously hard to compute. In this paper, we reexamine the computational bottlenecks and implement ultra-fast pedigree-based GWAS analysis. Kinship coefficients can either be based on explicitly provided pedigrees or automatically estimated from dense markers. Our strategy (a) works for random sample data, pedigree data, or a mix of both; (b) entails no loss of power; (c) allows for any number of covariate adjustments, including correction for population stratification; (d) allows for testing SNPs under additive, dominant, and recessive models; and (e) accommodates both univariate and multivariate quantitative traits. On a typical personal computer (six CPU cores at 2.67 GHz), analyzing a univariate HDL (high-density lipoprotein) trait from the San Antonio Family Heart Study (935,392 SNPs on 1,388 individuals in 124 pedigrees) takes less than 2 min and 1.5 GB of memory. Complete multivariate QTL analysis of the three time-points of the longitudinal HDL multivariate trait takes less than 5 min and 1.5 GB of memory. The algorithm is implemented as the Ped-GWAS Analysis (Option 29) in the Mendel statistical genetics package, which is freely available for Macintosh, Linux, and Windows platforms from http://genetics.ucla.edu/software/mendel.

Project description:Recent studies suggest that the relationship between endogenous oxytocin and social affiliative behavior can be critically moderated by contextual and individual factors in humans. While oxytocin has been shown to influence human-directed affiliative behaviors in dogs, no study investigated yet how such factors moderate these effects. Our study aimed to investigate whether the context and the dogs' individual characteristics moderate the associations between the social affiliative (greeting) behavior and four single-nucleotide polymorphisms (SNPs) of the oxytocin receptor (OXTR) gene. We recorded the greeting behavior in three contexts: (1) when the dog first met an unfamiliar experimenter, (2) during a separation from the owner, and (3) after the experimenter approached the dog in a threatening manner. In the latter two contexts (during separation and after threatening), we categorized the dogs into stressed and non-stressed groups based on their behavior in the preceding situations. In line with previous studies, we found that polymorphisms in the OXTR gene are related to the greeting behavior of dogs. However, we also showed that the analyzed SNPs were associated with greeting in different contexts and in different individuals, suggesting that the four SNPs might be related to different functions of the oxytocin system. The -213A/G was associated with greeting only when the dog had no prior negative experience with the experimenter. The rs8679682 was found in association with greeting in all three contexts but these associations were significant only in non-stressed dogs. The -94T/C was associated with greeting only when the dog was stressed and had an interaction with the sex of the dog. The -74C/G SNP was associated with greeting only when the dog was stressed during separation and also had a sex interaction. Taken together, our results suggest that, similarly to humans, the effects of oxytocin on the dogs' social behavior are not universal, but constrained by features of situations and individuals. Understanding these constraints helps further clarify how oxytocin mediates social behavior which, in the long run, could improve the application of oxytocin in pharmacotherapy.

Project description:Simple Summary Dog agility is a canine sport that has gained popularity among pet owners in recent decades. Because of the high-performance level, injuries to dogs competing in this sport are becoming frequent. The need for better knowledge of the anatomy of the structures involved in athletic movements is an essential starting point for correctly managing agility-related injuries. The aim of this paper was to investigate the ultrasonographic anatomy of the carpal joint, creating a baseline reference for the Border Collie, which is the breed most utilised in agility competitions. The data acquired could be of use in future studies regarding sport-induced injuries in the canine carpus. Abstract Recent literature has demonstrated that high-resolution ultrasonographic anatomy of the canine carpus is possible; however, only the structures of the dorsal face were described. The aims of this prospective study were: (1) to describe the normal ultrasonographic appearance of the carpal tendons in sporting Border Collies; (2) to measure the height, length, and thickness of the tendon at the radial ulnar notch level in order to create a baseline reference for the breed, and (3) to describe a standardised protocol to ultrasonographically evaluate the carpal faces and visible tendinous structures. A pilot study based on ten cadaveric front limbs was used to identify the structures. A subsequent clinical phase of the study using twenty-six Border Collies was recorded. The tendons of the Extensor Carpi Radialis, Extensor Digitorum Communis, and Extensor Digitorum Lateralis were identified and followed from the tenomuscular junction to the distal insertion on the dorsal face of the digits. On the lateral face, the tendon of the Extensor Carpi Ulnaris was recognised and followed. On the palmar face, the two heads of the Flexor Carpi Ulnaris tendon ending on the accessory carpal bone, the adjacent Flexor Digitorum Superficialis tendon, and the deep and medially located Flexor Digitorum Profundus tendon were seen and followed. The Flexor Carpi Radialis and the Abductor Pollicis Longus tendons were seen in the medial carpal face. The ulnar notch of the radius was used as the measurement and starting point of the ultrasonography. These data could be used as a standard reference in the case of chronic overuse and trauma-induced changes in the canine carpus.

Dataset Information

Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis.

Publications

Lymphoma in Border Collies: Genome-Wide Association and Pedigree Analysis.

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