Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes OPEN

By limiting sequencing to those sequences transcribed as mRNA, whole exome sequencing is a costefficient technique often used in disease-association studies. We developed two target enrichment designs based on the recently released annotation of the canine genome: the exome-plus design and the exome-CDS design. The exome-plus design combines the exons of the CanFam 3.1 Ensembl annotation, more recently discovered protein-coding exons and a variety of non-coding RNA regions (microRNAs, long non-coding RNAs and antisense transcripts), leading to a total size of ≈152 Mb. The exome-CDS was designed as a subset of the exome-plus by omitting all 3' and 5' untranslated regions. This reduced the size of the exome-CDS to ≈71 Mb. To test the capturing performance, four exome-plus captures were sequenced on a NextSeq 500 with each capture containing four precapture pooled, barcoded samples. At an average sequencing depth of 68.3x, 80% of the regions and well over 90% of the targeted base pairs were completely covered at least 5 times with high reproducibility. Based on the performance of the exome-plus, we estimated the performance of the exome-CDS. Overall, these designs provide flexible solutions for a variety of research questions and are likely to be reliable tools in disease studies. In 2014, the first report detailing the design and performance of a whole exome sequencing (WES) enrichment assay for the dog was published by our group 1 . Aiming to selectively sequence all the regions that are transcribed to mRNA, WES is a reliable tool used to identify disease-causing or predisposing mutations at a fraction of the price of whole genome sequencing (WGS) studies. A limitation of WES is that it is based on our current knowledge of the annotation of the genome and that many disease causing mutations are likely to fall outside protein-coding regions. With new information becoming available, updates and extensions are required. Recently, an improved annotation for the dog genome has been published and new data on non-protein coding genes has been obtained 2 . Based on this data, two new target enrichment designs for dogs, called the exome-plus and the exome-CDS, were developed. The exome-plus offers the most comprehensive design. The exome-CDS is a subset of the exome-plus, focusing on the coding DNA sequences (CDS) by excluding the 3′ and 5′ untranslated regions (UTRs). Thes

Classification of feline hypertrophic cardiomyopathy-associated gene variants according to the American College of Medical Genetics and Genomics guidelines

INTRODUCTION: The correct labeling of a genetic variant as pathogenic is important as breeding decisions based on incorrect DNA tests can lead to the unwarranted exclusion of animals, potentially compromising the long-term health of a population. In human medicine, the American college of Medical Genetics (ACMG) guidelines provide a framework for variant classification. This study aims to apply these guidelines to six genetic variants associated with hypertrophic cardiomyopathy (HCM) in certain cat breeds and to propose a modified criterion for variant classification. METHODS: Genetic samples were sourced from five cat breeds: Maine Coon, Sphynx, Ragdoll, Devon Rex, and British Short- and Longhair. Allele frequencies were determined, and in the subset with phenotypes available, odds ratios to determine the association with HCM were calculated. In silico evaluation followed with joint evidence and data from other publications assisting in the classification of each variant. RESULTS: Two variants, MYBPC3:c.91G > C [A31P] and MYBPC3:c.2453C > T [R818W], were designated as pathogenic. One variant, MYH7:c.5647G > A [E1883K], was found likely pathogenic, while the remaining three were labeled as variants of unknown significance. DISCUSSION: Routine genetic testing is advised solely for the MYBPC3:c.91G > C [A31P] in the Maine Coon and MYBPC3:c.2453C > T [R818W] in the Ragdoll breed. The human ACMG guidelines serve as a suitable foundational tool to ascertain which variants to include; however, refining them for application in veterinary medicine might be beneficial

Classification of feline hypertrophic cardiomyopathy-associated gene variants according to the American College of Medical Genetics and Genomics guidelines

IntroductionThe correct labeling of a genetic variant as pathogenic is important as breeding decisions based on incorrect DNA tests can lead to the unwarranted exclusion of animals, potentially compromising the long-term health of a population. In human medicine, the American college of Medical Genetics (ACMG) guidelines provide a framework for variant classification. This study aims to apply these guidelines to six genetic variants associated with hypertrophic cardiomyopathy (HCM) in certain cat breeds and to propose a modified criterion for variant classification.MethodsGenetic samples were sourced from five cat breeds: Maine Coon, Sphynx, Ragdoll, Devon Rex, and British Short- and Longhair. Allele frequencies were determined, and in the subset with phenotypes available, odds ratios to determine the association with HCM were calculated. In silico evaluation followed with joint evidence and data from other publications assisting in the classification of each variant.ResultsTwo variants, MYBPC3:c.91G > C [A31P] and MYBPC3:c.2453C > T [R818W], were designated as pathogenic. One variant, MYH7:c.5647G > A [E1883K], was found likely pathogenic, while the remaining three were labeled as variants of unknown significance.DiscussionRoutine genetic testing is advised solely for the MYBPC3:c.91G > C [A31P] in the Maine Coon and MYBPC3:c.2453C > T [R818W] in the Ragdoll breed. The human ACMG guidelines serve as a suitable foundational tool to ascertain which variants to include; however, refining them for application in veterinary medicine might be beneficial

VariantscanR: an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals

Abstract Background Since the introduction of next-generation sequencing (NGS) techniques, whole-exome sequencing (WES) and whole-genome sequencing (WGS) have not only revolutionized research, but also diagnostics. The gradual switch from single gene testing to WES and WGS required a different set of skills, given the amount and type of data generated, while the demand for standardization remained. However, most of the tools currently available are solely applicable for human analysis because they require access to specific databases and/or simply do not support other species. Additionally, a complicating factor in clinical genetics in animals is that genetic diversity is often dangerously low due to the breeding history. Combined, there is a clear need for an easy-to-use, flexible tool that allows standardized data processing and preferably, monitoring of genetic diversity as well. To fill these gaps, we developed the R-package variantscanR that allows an easy and straightforward identification and prioritization of known phenotype-associated variants identified in dogs and other domestic animals. Results The R-package variantscanR enables the filtering of variant call format (VCF) files for the presence of known phenotype-associated variants and allows for the estimation of genetic diversity using multi-sample VCF files. Next to this, additional functions are available for the quality control and processing of user-defined input files to make the workflow as easy and straightforward as possible. This user-friendly approach enables the standardisation of complex data analysis in clinical settings. Conclusion We developed an R-package for the identification of known phenotype-associated variants and calculation of genetic diversity

Prevalence of knowledge about the OC.

<p>Prevalence of knowing the period of the highest fertility during the ovulatory cycle. Data from six cross-sectional surveys during 1988–2008 in Egyptian women aged 15–49.</p

Population-wide modelling reveals prospects of marker-assisted selection for parasitic mite resistance in honey bees

Abstract In 2019, a joint eight-variant model was published in which eight single nucleotide polymorphisms (SNPs) in seven Apis mellifera genes were associated with Varroa destructor drone brood resistance (DBR, i.e. mite non-reproduction in drone brood). As this model was derived from only one Darwinian Black Bee Box colony, it could not directly be applied on a population-overarching scale in the northern part of Belgium (Flanders), where beekeepers prefer the carnica subspecies. To determine whether these eight SNPs remained associated with the DBR trait on a Flemish colony-broad scope, we performed population-wide modelling through sampling of various A. mellifera carnica colonies, DBR scoring of Varroa-infested drone brood and variant genotyping. Novel eight-variant modelling was performed and the classification performance of the eight SNPs was evaluated. Besides, we built a reduced three-variant model retaining only three genetic variants and found that this model classified 76% of the phenotyped drones correctly. To examine the spread of beneficial alleles and predict the DBR probability distribution in Flanders, we determined the allelic frequencies of the three variants in 292 A. mellifera carnica queens. As such, this research reveals prospects of marker-assisted selection for Varroa drone brood resistance in honeybees

Veterinarians' Competence in Applying Basic Genetic Principles and Daily Implementation of Clinical Genetics: A Study in a University Environment

Veterinarian competency in genetics is vital for a meaningful application of the rapidly growing number of genetic tests available for animals. We evaluated the use of genetic tests in the daily veterinary practice and the competency of university-employed veterinarians in applying basic principles of genetics in a clinical setting through an electronic survey with 14 cases and 7 statements on genetics. Ninety-one non-geneticist veterinarians from two veterinary faculties in two different countries responded. Almost half of the participants apply genetic tests during their daily work, with frequencies varying between weekly and once a year. The most common indication to request a genetic test was diagnostic testing of clinically ill patients. Although 80% of the veterinarians communicated the result of a genetic test themselves, only 56% of them found it "very to rather easy" to find the correct test, and only 32% of them always felt competent to interpret the result of the test. The number of correctly answered questions varied widely, with median scores of 9/14 (range 0-14) and 5/7 (range 0-7) for the cases and statements, respectively. Most difficulties were seen with recognition of pedigree inheritance patterns, while veterinarians scored better in breeding advice and probability of disease estimations. Veterinarians scored best on questions related to autosomal recessive inheritance, followed by complex, autosomal dominant, X-linked recessive, and X-linked dominant inheritance. This study exposed pain points in veterinarians' knowledge and has led to the formulation of recommendations for future education and communication between laboratories, geneticists, and veterinarians

High-frequency ultrasound, computed tomography and computed tomography arthrography of the cranial cruciate ligament, menisci and cranial meniscotibial ligaments in 10 radiographically normal canine cadaver stifles

Abstract Background Bilateral non-traumatic cranial cruciate disease is frequently seen in originally unilateral cruciate pathology. Untreated cranial cruciate ligament disease and concurrent meniscal lesions cause progressive osteoarthritis and pain of the stifle joint. Early presurgical diagnosis is important, but remains difficult. The purpose of this ex vivo study was (1) to describe the ultrasonographic appearance of the canine cranial cruciate ligament (CrCrL), menisci and meniscal ligaments using a high-frequency linear transducer, (2) to determine the length of the CrCrL seen on ultrasonography (US) and (3) to describe and compare the appearance of the CrCrL, menisci and meniscal ligaments on US, computed tomography (CT) and computed tomography arthrography (CTA). Results US and CT examinations were performed on 10 radiographically normal cadaveric stifles of adult dogs weighing more than 15 kg, followed by macroscopic and histologic evaluations. The CrCrL had a parallel hyperechoic fibrillar pattern at the insertion on the tibia and a hypoechoic structure more proximally in all stifles. This pattern was visible over 35% (median) of the total length of the ligament, with 50% (median) of the total length CrCrL that could be outlined. All medial menisci and 8 out of 10 of the lateral menisci showed hypoechoic lines within their bodies oriented obliquely to the direction of the ultrasound beam. Fifteen of the 20 cranial meniscotibial ligaments were detected, showing a hyperechoic fibrillar pattern. Normal macro- and microscopic appearance was observed in all menisci, with the radial bundles of collagen fibers at the level of and with similar orientation as the intrameniscal hypoechoic lines on US. The CrCrL, menisci and meniscal ligaments were of intermediate density on CT, but marked improvement of the border detection was obtained using CTA. Contrast within the CrCrL was observed in 4/10 stifles using CT and confirmed in 3/4 stifles on histology. One of these ligaments had a partial tear (5–10%) on macroscopic evaluation. None of the menisci showed any abnormalities on CTA. Conclusions Normal canine menisci are heterogeneous on high-frequency US and a fibrillar pattern may be observed in the cranial meniscotibial ligaments and the distal portion of the CrCrL. Linear areas of contrast may be detected within the cranial cruciate ligament of radiographically normal stifles

Pharmacokinetics of cannabidiol following intranasal, intrarectal, and oral administration in healthy dogs

The therapeutic potential of cannabidiol (CBD), a non-psychtropic component of the Cannabis sativa plant, is substantiated more and more. We aimed to determine the pharmacokinetic behavior of CBD after a single dose via intranasal (IN) and intrarectal (IR) administration in six healthy Beagle dogs age 3-8 years old, and compare to the oral administration route (PO). Standardized dosages applied for IN, IR and PO were 20, 100, and 100 mg, respectively. Each dog underwent the same protocol but received CBD through a different administration route. CBD plasma concentrations were determined by ultra-high performance liquid chromatography-tandem mass spectrometry before and at fixed time points after administration. Non-compartmental analysis was performed on the plasma concentration-time profiles. Plasma CBD concentrations after IR administration were below the limit of quantification. The mean area under the curve (AUC) after IN and PO CBD administration was 61 and 1,376 ng/mL*h, respectively. The maximal plasma CBD concentration (C-max) after IN and PO CBD administration was 28 and 217 ng/mL reached after 0.5 and 3.5 h (T-max), respectively. Significant differences between IN and PO administration were found in the T-max (p = 0.04). Higher AUC and C-max were achieved with 100 mg PO compared to 20 mg IN, but no significant differences were found when AUC (p = 0.09) and C-max (p = 0.44) were normalized to 1 mg dosages. IN administration of CBD resulted in faster absorption when compared to PO administration. However, PO remains the most favorable route for CBD delivery due to its more feasible administration. The IR administration route is not advised for clinical application