Preliminary investigation of potential links between pigmentation variants and opioid analgesic effectiveness in horses during cerebrospinal fluid centesis.

BACKGROUND: The pleiotropic effects of the melanocortin system show promise in overcoming limitations associated with large variations in opioid analgesic effectiveness observed in equine practice. Of particular interest is variation in the melanocortin-1-receptor (MC1R) gene, which dictates pigment type expression through its epistatic interaction with the agouti signalling protein (ASIP) gene. MC1R has previously been implicated in opioid efficacy in other species; however, this relationship is yet to be explored in horses. In this study, analgesic effectiveness was scored (1-3) based on noted response to dura penetration during the performance of cerebrospinal fluid centisis after sedation and tested for association with known genetic regions responsible for pigmentation variation in horses. RESULTS: The chestnut phenotype was statistically significant (P < 0.05) in lowering analgesic effectiveness when compared to the bay base coat colour. The 11bp indel in ASIP known to cause the black base coat colour was not significant (P>0.05); however, six single nucleotide polymorphisms (SNPs) within the genomic region encoding the ASIP gene and one within MC1R were identified as being nominally significant (P<0.05) in association with opioid analgesic effectiveness. This included the location of the known e MC1R variant resulting in the chestnut coat colour. CONCLUSIONS: The current study provides promising evidence for important links between pigmentation genes and opioid effectiveness in horses. The application of an easily identifiable phenotype indicating variable sensitivity presents a promising opportunity for accessible precision medicine in the use of analgesics and warrants further investigation.

An estimation of osteochondrodysplasia prevalence in Australian Scottish Fold cats: a retrospective study using VetCompass Data.

BACKGROUND: All Scottish Fold cats are believed to be affected by osteochondrodysplasia, a painful degenerative joint disorder. This retrospective study aimed to estimate the prevalence of osteochondrodysplasia in Scottish Fold and Scottish Straight cats in Australian veterinary clinics using electronic patient records (EPRs), collected between 1992 and 2018. RESULTS: Consultation events (34,926) in EPRs from veterinary clinics located in New South Wales, Queensland, and Victoria, were collected from 1,131 Scottish Fold and 117 Scottish Shorthair cats. A clinical diagnosis of osteochondrodysplasia was made in 12/1,131 Scottish Fold cats. Additionally, 69 cats were identified with suspected osteochondrodysplasia. Of these, 64 were Scottish Fold and 5 were Scottish Shorthair cats. Male and female cats were equally represented. However, a significant difference was observed for the age clinical signs were first recorded in the EPRs. Cats diagnosed clinically with osteochondrodysplasia were significantly younger (p < 0.0001) compared to cats identified as suspected SFOCD cases. CONCLUSIONS: Findings from this study suggest a relatively low prevalence of clinically diagnosed Scottish Fold osteochondrodysplasia (SFOCD) in the studied Australian Scottish Fold population, with cats generally diagnosed with SFOCD at less than 30 months of age. Further evidence is required to accurately assess the clinical relevance of SFOCD in the Scottish Fold population.

Candidate causative variant for xanthinuria in a Domestic Shorthair cat.

Xanthinuria is a clinically significant form of urolithiasis in cats with poor clinical outcomes and limited treatment options. In humans, xanthinuria has an autosomal recessive mode of inheritance, with variants in xanthine dehydrogenase (XDH) and molybdenum cofactor sulfurase (MOCOS) responsible for cases. While causative genetic variants have not been identified in the domestic cat, a recessive mode of inheritance has been suggested. DNA was extracted from EDTA-stabilised blood obtained from a Domestic Shorthair cat with clinically confirmed xanthinuria. Whole-genome sequencing and variant assessment in XDH and MOCOS identified XDH:c.2042C>T (XDH:p.(A681V)) as a candidate causative variant for xanthinuria in this cat. The variant is located in a highly conserved part of the molybdenum-pterin co-factor domain, responsible for catalysing the hydroxylation of hypoxanthine to xanthine and uric acid. Variants in this domain of XDH have been shown to disrupt enzyme function and to cause xanthinuria in other species. When assessed in the wider cat population, the variant had an allele frequency of 15.8%, with 0.9% of the animals assessed homozygous for the alternative allele. Cats diagnosed with xanthinuria should be tested for this variant to validate its clinical relevance in the wider population.

Correction: Mutations in MITF and PAX3 Cause "Splashed White" and Other White Spotting Phenotypes in Horses.

[This corrects the article DOI: 10.1371/journal.pgen.1002653.].

Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management.

BACKGROUND: While recent advances in genomics has enabled vast improvements in the quantification of genome-wide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits. This has been attributed to the resources and infrastructure required to develop essential genomic datasets such as reference genomes. In the absence of a high-quality reference genome, cross-species alignments can provide reliable, cost-effective methods for single nucleotide variant (SNV) discovery. Here, we demonstrated the utility of cross-species genome alignment methods in gaining insights into population structure and functional genomic features in cheetah (Acinonyx jubatas), snow leopard (Panthera uncia) and Sumatran tiger (Panthera tigris sumatrae), relative to the domestic cat (Felis catus). RESULTS: Alignment of big cats to the domestic cat reference assembly yielded nearly complete sequence coverage of the reference genome. From this, 38,839,061 variants in cheetah, 15,504,143 in snow leopard and 13,414,953 in Sumatran tiger were discovered and annotated. This method was able to delineate population structure but limited in its ability to adequately detect rare variants. Enrichment analysis of fixed and species-specific SNVs revealed insights into adaptive traits, evolutionary history and the pathogenesis of heritable diseases. CONCLUSIONS: The high degree of synteny among felid genomes enabled the successful application of the domestic cat reference in high-quality SNV detection. The datasets presented here provide a useful resource for future studies into population dynamics, evolutionary history and genetic and disease management of big cats. This cross-species method of variant discovery provides genomic context for identifying annotated gene regions essential to understanding adaptive and deleterious variants that can improve conservation outcomes.

Comparison of nostril sizes of newborn infants with outer diameter of endotracheal tubes.

BACKGROUND: Recommendations for endotracheal tube (ETT) size usually refer to the inner diameter (ID). Outer diameters (OD), however, vary greatly between manufacturers, which in some brands might cause difficulties in passing the ETT through the nostrils if choosing the nasal route for intubation. Even though the nostrils are dilatable by an ETT, it might be difficult to pass an ETT through the posterior naris (narrowest point of the nasal passage), if the OD is bigger than the nostrils. Therefore, nostril size may provide some guidance for the appropriate ETT size preventing unsuccessful intubation attempts. This study therefore compares nostril sizes of newborn infants with ODs of ETTs from several manufacturers. METHODS: This is a subgroup analysis of a prospective observational study, performed in a single tertiary perinatal centre in Germany. The diameter of the nostril of infants born between 34 and 41 weeks´ gestation was measured in 3D images using 3dMDvultus software and compared to the OD of ETT from five different manufacturers. RESULTS: Comparisons of nostril sizes with ODs of different ETTs were made for 99 infants with a mean (SD) birthweight of 3058g (559) [range: 1850-4100g]. Mean (SD) nostril size was 5.3mm (0.6). The OD of the 3.5mm ETT of different manufacturers ranged from 4.8-5.3mm and was thus larger than the nostril size of 20-46% of late preterm or term infants. Some OD of a 3.0mm ETT were even bigger than the OD of a 3.5mm ETT (e.g. the 3.0mm ETT from Rüsch® has an OD of 5.0mm while the 3.5mm ETT from Portex® has an OD of 4.8mm). CONCLUSIONS: Clinicians should be aware of the OD of ETTs to reduce unsuccessful intubation attempts caused by ETT sizes not fitting the nasal cavity. Generated data may help to adapt recommendations in future. TRIAL REGISTRATION: Subgroup analysis of the "Fitting of Commonly Available Face Masks for Late Preterm and Term Infants (CAFF)"-study: NCT03369028, www.ClinicalTrials.gov , December 11, 2017.

An approach to define newborns´ sniffing position using an angle based on reproducible facial landmarks.

BACKGROUND: The neutral or sniffing position is advised for mask ventilation in neonates to avoid airway obstruction. As definitions are manifold and often unspecific, we wanted to investigate the reliability and reproducibility of angle measurements based on facial landmarks that may be used in future clinical trials to determine a hypothetical head position with minimal airway obstruction during mask ventilation. METHODS: In a prospective single-center observational study, 2D sagittal photographs of 24 near-term and term infants were taken, with five raters marking facial landmarks to assess interobserver agreement of those landmarks and angle δ, defined as the angle between the line parallel to the lying surface and the line crossing Subnasale (Sn) and Porion' (P'). Angle δ was assessed in sniffing (δsniff ) and physiologic (δphys ) head position, the former based on a published, yet poorly defined head position where the tip of the nose aligns to the ceiling with the head in a supine, relaxed mid-position. RESULTS: Infants had a mean (SD) gestational age of 37.3 (2.3) weeks. Angle δ could be determined in all 48 images taken in either the sniffing or the physiological head position. Interobserver correlation coefficient was 98.6 for all measurements independent of head position. Angle δsniff was 90.5° (5.7) in the sniffing position. CONCLUSIONS: This study provides a new measuring technique using an angle that is reproducible and reliable and may be used in future studies to correlate head position with airway obstruction.

Evaluating practioners' preferences regarding vascular emergency access in newborn infants in the delivery room: a national survey.

BACKGROUND: Venous access during neonatal emergencies in the delivery room (DR) can be accomplished through an umbilical venous catheter (UVC) or an intraosseous (IO) access. Preference of one over the other is unclear. We wanted to evaluate practioners' views. METHODS: An anonymous online questionnaire was circulated to healthcare professionals with different background and experience, all working in neonatal intensive care units in Germany. The web-based survey consisted of 13 questions and data collection was performed using an online tool. RESULTS: We received 502 completed questionnaires, 152 (30%) were from neonatologists, the remainder from residents, fellows and neonatal nurses. For resuscitation of term newborns in the DR 61% of neonatologists vs. 53% of non-neonatologists were in favour of UVC instead of an IO as an emergency access. UVC placement was rated (very) difficult to impossible by 60% of neonatologists and 90% of non-neonatologists (p < 0.05). All respondents cited lack of experience as the main reason for feeling reluctant to place an UVC or IO access, the latter only being taken into consideration in term infants. CONCLUSIONS: UVC placement in the DR is rated more often difficult to use by non-neonatologists than by neonatologists, apparently related to lack of experience. IO access was only considered for resuscitating term infants due to lacking practice and missing approval for birth weights < 3000 g. Frequent training might improve these clinical skills.

Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds.

BACKGROUND: To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. RESULTS: Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation. CONCLUSIONS: Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

Evidence of selection signatures that shape the Persian cat breed.

The Persian cat is mainly characterized by an extremely brachycephalic face as part of the standard body conformation. Despite the popularity, world-wide distribution, and economic importance of the Persian cat as a fancy breed, little is known about the genetics of their hallmark morphology, brachycephaly. Over 800 cats from different breeds including Persian, non-Persian breeds (Abyssinian, Cornish Rex, Bengal, La Perm, Norwegian Forest, Maine Coon, Manx, Oriental, and Siamese), and Persian-derived breeds (British Shorthair, Scottish Fold, Selkirk Rex) were genotyped with the Illumina 63 K feline DNA array. The experimental strategy was composed of three main steps: (i) the Persian dataset was screened for runs of homozygosity to find and select highly homozygous regions; (ii) selected Persian homozygous regions were evaluated for the difference of homozygosity between Persians and those considered non-Persian breeds, and, (iii) the Persian homozygous regions most divergent from the non-Persian breeds were investigated by haplotype analysis in the Persian-derived breeds. Four regions with high homozygosity (H > 0.7) were detected, each with an average length of 1 Mb. Three regions can be considered unique to the Persian breed, with a less conservative haplotype pattern in the Persian-derived breeds. Moreover, two genes, CHL1 and CNTN6 known to determine face shape modification in humans, reside in one of the identified regions and therefore are positional candidates for the brachycephalic face in Persians. In total, the homozygous regions contained several neuronal genes that could be involved in the Persian cat behavior and can provide new insights into cat domestication.

Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker.

SUMMARY: Whole-genome sequencing has revolutionized the study of genetics. Genotyping-by-sequencing is now a viable method of genotyping, yet the bioinformatics involved can be daunting if not prohibitive for some laboratories. Here we present ArrayMaker, a user-friendly tool that extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole-genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms. Using this tool, geneticists with only basic computing ability can genotype samples at any desired list of markers, facilitating genome-wide association analysis, fine mapping, candidate variant assessment, data sharing and compatibility of data sourced from multiple technologies. AVAILABILITY AND IMPLEMENTATION: ArrayMaker is licensed under The MIT License and can be freely obtained at https://github.com/cw2014/ArrayMaker/. The program is implemented in Perl and runs on Linux operating systems. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: cali.willet@sydney.edu.au.

Genome-wide analysis reveals selection for important traits in domestic horse breeds.

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.

Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses.

During fetal development neural-crest-derived melanoblasts migrate across the entire body surface and differentiate into melanocytes, the pigment-producing cells. Alterations in this precisely regulated process can lead to white spotting patterns. White spotting patterns in horses are a complex trait with a large phenotypic variance ranging from minimal white markings up to completely white horses. The "splashed white" pattern is primarily characterized by an extremely large blaze, often accompanied by extended white markings at the distal limbs and blue eyes. Some, but not all, splashed white horses are deaf. We analyzed a Quarter Horse family segregating for the splashed white coat color. Genome-wide linkage analysis in 31 horses gave a positive LOD score of 1.6 in a region on chromosome 6 containing the PAX3 gene. However, the linkage data were not in agreement with a monogenic inheritance of a single fully penetrant mutation. We sequenced the PAX3 gene and identified a missense mutation in some, but not all, splashed white Quarter Horses. Genome-wide association analysis indicated a potential second signal near MITF. We therefore sequenced the MITF gene and found a 10 bp insertion in the melanocyte-specific promoter. The MITF promoter variant was present in some splashed white Quarter Horses from the studied family, but also in splashed white horses from other horse breeds. Finally, we identified two additional non-synonymous mutations in the MITF gene in unrelated horses with white spotting phenotypes. Thus, several independent mutations in MITF and PAX3 together with known variants in the EDNRB and KIT genes explain a large proportion of horses with the more extreme white spotting phenotypes.

Xanthinuria in a familial group of Munchkin cats and an unrelated domestic shorthair cat.

CASE SERIES SUMMARY: Four confirmed cases of xanthinuria in cats, and one suspected case based on pedigree analysis, were identified. Clinical presentations varied and included haematuria, pollakiuria, dysuria, and urethral and ureteral obstruction. All cats had upper urinary tract uroliths. Diagnosis was obtained through infrared mass spectrometry of uroliths or urine. Clinical signs commenced at 3-8 months of age and reduced in all cats in the medium to long term after the introduction of a protein-restricted diet. Four cats were castrated males and one was a spayed female. Cases consisted of four Munchkin pedigree cats and one unrelated domestic shorthair cat. All four affected Munchkin pedigree cats were related, with three cases full siblings and the fourth case a half-sibling. No connection to the Munchkin pedigree could be established for the domestic shorthair cat. A candidate causative genetic variant (XDH p.A681V) proposed for this cat was excluded in the Munchkin family. RELEVANCE AND NOVEL INFORMATION: All affected cats presented diagnostic challenges and routine urinalysis was insufficient to obtain a diagnosis. Cases of feline xanthinuria may be underdiagnosed due to situations where uroliths cannot be retrieved for analysis and there is an inability to make a diagnosis using crystal morphology alone on routine urinalysis. Metabolic screening of urine may provide an effective mechanism to confirm xanthinuria in suspected cases where uroliths are inaccessible or absent. In this case series, male cats were more common. Their anatomy may increase the risk of lower urinary tract signs and urethral obstruction developing secondary to xanthine urolithiasis. A protein-restricted diet appears to reduce clinical signs as part of long-term management. PLAIN LANGUAGE SUMMARY: Four closely related Munchkin cats and one domestic shorthair cat were found with a suspected genetic disease causing high levels of xanthine in their urine. The case series looks at similarities and differences in their clinical signs, as well as difficulties experienced in obtaining a correct diagnosis. All cats had upper urinary tract stones and required metabolic testing of the stones or urine to diagnose. All cats were young when their clinical signs started and were on a high-protein diet. Four cats were desexed males and one was a desexed female. A genetic variant that may have caused the disease in the domestic shorthair cat was ruled out in the Munchkin family. Cases of high xanthine levels in feline urine may be underdiagnosed as the stones may not be accessed for testing. In this case series, male cats were more common. Their anatomy may increase the risk of lower urinary tract signs. A protein-restricted diet appears to reduce clinical signs as part of long-term management.

Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.

Variants in the EDNRB, KIT, MITF, PAX3 and TRPM1 genes are known to cause white spotting phenotypes in horses, which can range from the common white markings up to completely white horses. In this study, we investigated these candidate genes in 169 horses with white spotting phenotypes not explained by the previously described variants. We identified a novel missense variant, PAX3:p.Pro32Arg, in Appaloosa horses with a splashed white phenotype in addition to their leopard complex spotting patterns. We also found three novel variants in the KIT gene. The splice site variant c.1346+1G>A occurred in a Swiss Warmblood horse with a pronounced depigmentation phenotype. The missense variant p.Tyr441Cys was present in several part-bred Arabians with sabino-like depigmentation phenotypes. Finally, we provide evidence suggesting that the common and widely distributed KIT:p.Arg682His variant has a very subtle white-increasing effect, which is much less pronounced than the effect of the other described KIT variants. We termed the new KIT variants W18-W20 to provide a simple and unambiguous nomenclature for future genetic testing applications.