Simulated validation of intron-less transgene detection using DELLY for gene-doping control in horse sports.

Gene doping is prohibited in horseracing. In a previous study, we developed a method for non-targeted transgene detection using DELLY, which is based on split-read (SR) and paired-end (PE) algorithms to detect structural variants, on WGS data. In this study, we validated the detection sensitivity of DELLY using artificially generated sequence data of 12 target genes. With DELLY, at least one intron was detected as a deletion in eight targeted genes using the 150 bp PE read WGS data, whereas all targeted genes were detected by DELLY using the 100 bp PE read data. The detection sensitivity was higher in 100 bp PE reads than in 150 bp PE reads, despite a lower total sequence coverage, probably because of mismatch tolerance between the mapped reads and reference genome. In addition, it was observed that the average intron size detected by SR alone was 293 bp and that that detected by both SR and PE was 8924 bp. Thus, we showed that transgenes with various intron-exon structures could be detected using DELLY, suggesting its application in gene-doping control in horses.

A candidate-SNP retrospective cohort study for fracture risk in Japanese Thoroughbred racehorses.

Fractures are medical conditions that compromise the athletic potential of horses and/or the safety of jockeys. Therefore, the reduction of fracture risk is an important horse and human welfare issue. The present study used molecular genetic approaches to determine the effect of genetic risk for fracture at four candidate SNPs spanning the myostatin (MSTN) gene on horse chromosome 18. Among the 3706 Japanese Thoroughbred racehorses, 1089 (29.4%) had experienced fractures in their athletic life, indicating the common occurrence of this injury in Thoroughbreds. In the case/control association study, fractures of the carpus (carpal bones and distal radius) were statistically associated with g.65809482T/C (P = 1.17 x 10-8 ), g.65868604G/T (P = 2.66 x 10-9 ), and g.66493737C/T (P = 6.41 x 10-8 ). In the retrospective cohort study using 1710 racehorses born in 2000, the relative risk (RR) was highest for male horses at g.65868604G/T, based on the dominant allele risk model (RR = 2.251, 95% confidence interval 1.407-3.604, P = 0.00041), and for female horses at g.65868604G/T, based on the recessive allele risk model (RR = 2.313, 95% confidence interval 1.380-3.877, P = 0.00163). Considering the association of these SNPs with racing performance traits such as speed, these genotypes may affect the occurrence of carpus fractures in Japanese Thoroughbred racehorses as a consequence of the non-genetic influence of the genotype on the distance and/or intensity of racing and training. The genetic information presented here may contribute to the development of strategic training programs and racing plans for racehorses that improve their health and welfare.

Genetic diversity and relationships among native Japanese horse breeds, the Japanese Thoroughbred and horses outside of Japan using genome-wide SNP data.

Eight horse breeds-Hokkaido, Kiso, Misaki, Noma, Taishu, Tokara, Miyako and Yonaguni-are native to Japan. Although Japanese native breeds are believed to have originated from ancient Mongolian horses imported from the Korean Peninsula, the phylogenetic relationships among these breeds are not well elucidated. In the present study, we compared genetic diversity among 32 international horse breeds previously evaluated by the Equine Genetic Diversity Consortium, the eight Japanese native breeds and Japanese Thoroughbreds using genome-wide SNP genotype data. The proportion of polymorphic loci and expected heterozygosity showed that the native Japanese breeds, with the exception of the Hokkaido, have relatively low diversity compared to the other breeds sampled. Phylogenetic and cluster analyses demonstrated relationships among the breeds that largely reflect their geographic distribution in Japan. Based on these data, we suggest that Japanese horses originated from Mongolian horses migrating through the Korean Peninsula. The Japanese Thoroughbreds were distinct from the native breeds, and although they maintain similar overall diversity as Thoroughbreds from outside Japan, they also show evidence of uniqueness relative to the other Thoroughbred samples. This is the first study to place the eight native Japanese breeds and Japanese Thoroughbred in context with an international sample of diverse breeds.

A Kirschner wire as a transverse-axis guide to improve acetabular cup positioning.

PURPOSE: To compare cup-positioning accuracy in total hip arthroplasty (THA) with or without use of a Kirschner wire as a transverse-axis guide for pelvic alignment. METHODS: Records of 18 men and 73 women (mean age, 60 years) who underwent primary THA with (n=49) or without (n=42) use of a Kirschner wire as a transverse-axis guide for pelvic alignment were reviewed. A 2.4-mm Kirschner wire as a transversea-xis guide was inserted to the anterior superior iliac spine and was parallel to a line linking the left and right anterior superior iliac spine. The safe zone for cup positioning was defined as 30º to 50° abduction and 10º to 30º anteversion. Of the 5 operative surgeons, 2 were classified as experienced (total surgical volume >300) and 3 as inexperienced (total surgical volume of <50). The proportion of patients with the cup in the safe zone was compared in patients with or without use of the transverse-axis guide and in experienced and inexperienced surgeons. RESULTS: For inexperienced surgeons, the use of the transverse-axis guide significantly improved the proportion of patients with the cup in the safe zone from 90% to 100% for abduction, from 50% to 82.4% for anteversion, and from 40% to 82.4% for both. Patients with the cup inside or outside the safe zone were comparable in terms of body height, weight, BMI, subcutaneous fat thickness, incision length, and acetabular cup size. CONCLUSION: The use of the transverse-axis guide improved the accuracy of cup positioning by inexperienced surgeons.

Heritability estimates for racing performance in Japanese Thoroughbred racehorses using linear and non-linear model analyses.

This study evaluated the differences between linear and non-linear modelled heritability estimates of racing performance based on lifetime earnings (LE) and lifetime ranking (LR) in Japanese Thoroughbred racehorses. The heritability estimate (h(2) = 0.25) obtained from a non-linear model based on formal Japan Racing Association ranking was much higher than that obtained from a linear model based on the original trait phenotype (h(2) = 0.11). The linear models showed slightly higher heritability estimates under the trait categorizations than under the original phenotypes, while the non-linear categorical trait models showed much higher heritability estimates than the linear models, especially for binary trait categorizations (h(2) = 0.34) with non-winning and winning horses. The binary trait categorizations were consistent with the case and control classifications in the previous genome-wide association study (GWAS), which identified possible sequence variants on ECA18 that affect racing performance in Japanese Thoroughbred racehorses. Those findings suggested that the different heritability estimates obtained from several trait categorizations would reflect the possible presence of susceptibility gene segregations in the analyzed population, indicating that heritability estimates from non-linear models are useful for the selection of case and control populations in GWAS.

A cohort study of racing performance in Japanese Thoroughbred racehorses using genome information on ECA18.

Using 1710 Thoroughbred racehorses in Japan, a cohort study was performed to evaluate the influence of genotypes at four single nucleotide polymorphisms (SNPs) on equine chromosome 18 (ECA18), which were associated in a previous genome-wide association study for racing performance with lifetime earnings and performance rank. In males, both g.65809482T>C and g.65868604G>T were related to performance rank (P= 0.005). In females, g.65809482T>C (P = 1.76E-6), g.65868604G>T (P=6.81E-6) and g.66493737C>T (P=4.42E-5) were strongly related to performance rank and also to lifetime earnings (P < 0.05). When win-race distance (WRD) among all winning racehorses and best race distance (BRD) among elite racehorses were considered as the phenotypes, significant associations (P<0.001) were observed for all four SNPs. The favourable race distance of both elite (BRD) and novice racehorses (WRD) was also associated with genotypes in the ECA18 region, indicating the presence of a gene in this region influencing optimum race distance in Thoroughbred racehorses. Therefore, the association with performance rank is likely due to the bias in the race distances. The location of the SNPs within and proximal to the gene encoding myostatin (MSTN) strongly suggests that regulation of the MSTN gene affects racing performance. In particular, the g.65809482T>C, g.65868604G>T and g.66493737C>T SNPs, or their combinations, may be genetic diagnostic markers for racing performance indicators such as WRD and BRD.

A genome-wide association study for racing performances in Thoroughbreds clarifies a candidate region near the MSTN gene.

Using 1400 microsatellites, a genome-wide association study (GWAS) was performed to identify genomic regions associated with lifetime earnings and performance ranks, as determined by the Japan Racing Association (JRA). The minimum heritability (h(2) ) was estimated at 7-8% based on the quantitative trait model, suggesting that the racing performance is heritable. Following GWAS with microsatellites, fine mapping led to identification of three SNPs on ECA18, namely, g.65809482T>C (P=1.05E-18), g.65868604G>T (P=6.47E-17), and g.66539967A>G (P=3.35E-14) associated with these performance measures. The haplotype of these SNPs, together with a recently published nearby SNP, g.66493737C>T (P=9.06E-16) in strong linkage disequilibrium, also showed a very clear association with the performance (P<1E-05). The candidate genomic region contained eight genes annotated by ENSEMBL, including the myostatin gene (MSTN). These findings suggest the presence of a gene affecting the racing performance in Thoroughbred racehorses in this region on ECA18.

Development of a method for simultaneously genotyping multiple horse coat colour loci and genetic investigation of basic colour variation in Thoroughbred and Misaki horses in Japan.

In order to develop a genotyping method that can be used in the registration procedure for Thoroughbreds, we developed a method for simultaneously genotyping multiple coat colour genes on the basis of single nucleotide polymorphism typing by using the SNaPshot(TM) technique. This method enabled precise and reasonable detection of causal mutations; it was effective for genotyping of MC1R, ASIP, and SLC45A2 at the Extension (E), Agouti (A), Cream dilution (C) loci, and the possibility of identification of rare variants of MC1R, EDNRB and KIT at the E, Overo (O) and Sabino 1 (SB1) loci, respectively, was also indicated. It was considered that this genotyping method would provide information not only for the registration of Thoroughbreds but also for the preservation of phenotypic characters, such as coat colour, of endangered Misaki native horses in Japan. Therefore, genetic variations at the five coat colour loci were investigated in 1111 Thoroughbred and 99 Misaki native horses. Allele frequencies at the polymorphic E and A loci were estimated, and the proportions of basic coat colours that could be expected in the Thoroughbred population were bay, 0.662; black, 0.070; chestnut, 0.268. In the Misaki population, they were bay, 0.792; black, 0.129; chestnut, 0.080. The data presented were the first of its kind on genetic coat colour variation, and will be important with regard to the registration of Thoroughbreds and the management of Misaki horses.

Antibiotic selection patterns in acutely febrile new outpatients with or without immediate testing for C reactive protein and leucocyte count.

BACKGROUND: Excessive use of broad spectrum antibiotics is related to the spread of drug resistant bacterial strains in the community. AIM/METHODS: The effects of immediate testing for C reactive protein (CRP) and white blood cell count (WBC) on physicians' choices of antibiotic was investigated in patients with acute infection. Acutely febrile new outpatients were randomised into two groups: group 1 (147 patients) underwent CRP and WBC testing before initial consultation (advance testing). Prescriptions were compared with those in group 2 (no advance testing; 154 patients). RESULTS: In non-pneumonic acute respiratory tract infections, 61 (58%) and 122 (91%) of group 1 and 2 patients were prescribed antibiotics, respectively. Cefcapene pivoxil (third generation cephalosporin) and amoxicillin were the most frequently chosen drugs for group 1 and 2, respectively. Total prescriptions of newer, extended spectrum antibiotics (cefcapene pivoxil and clarithromycin (advanced macrolide)) were reduced by 25% in group 1, although they increased in rate (41 (67%) v 55 (45%) prescriptions) because of the decreased prescription of amoxicillin. In group 1, cefcapene pivoxil was preferentially selected when WBC values were greater than 9 x 10(9)/litre. Prescription shifted to macrolides (mainly clarithromycin) in patients without leucocytosis. Patient treatment outcome did not significantly differ between the two groups. CONCLUSIONS: The availability of CRP and WBC data during initial consultation greatly reduced prescription of amoxicillin, but had a lesser effect on newer, potent, broad spectrum antibiotics.

Genetic diagnosis of sex chromosome aberrations in horses based on parentage test by microsatellite DNA and analysis of X- and Y-linked markers.

REASONS FOR PERFORMING STUDY: Sex chromosome aberrations are often associated with clinical signs that affect equine health and reproduction. However, abnormal manifestation with sex chromosome aberration usually appears at maturity and potential disorders may be suspected infrequently. A reliable survey at an early stage is therefore required. OBJECTIVES: To detect and characterise sex chromosome aberrations in newborn foals by the parentage test and analysis using X- and Y-linked markers. METHODS: We conducted a genetic diagnosis combined with a parentage test by microsatellite DNA and analysis of X- and Y-linked genetic markers in newborn light-breed foals (n = 17, 471). The minimum incidence of sex chromosome aberration in horses was estimated in the context of available population data. RESULTS: Eighteen cases with aberrations involving 63,XO, 65,XXY and 65,XXX were found. The XO, XXY (pure 65,XXY and/or mosaics/chimaeras) and XXX were found in 0.15, 0.02 and 0.01% of the population, respectively, based solely on detection of abnormal segregation of a single X chromosome marker, LEX003. CONCLUSIONS AND POTENTIAL RELEVANCE: Detection at an early age and understanding of the prevalence of sex chromosome aberrations should assist in the diagnosis and managment of horses kept for breeding. Further, the parental origin of the X chromosome of each disorder could be proved by the results of genetic analysis, thereby contributing to cytogenetic characterisation.

Population study and validation of paternity testing for Thoroughbred horses by 15 microsatellite loci.

Microsatellite 15 TKY System was characterized for parentage verification of horse registry. The Microsatellite 15 TKY System was constructed by using 15 microsatellites, TKY279, TKY287, TKY294, TKY297, TKY301, TKY312, TKY321, TKY325, TKY333, TKY337, TKY341, TKY343, TKY344, TKY374, and TKY394, to provide stringent PCR-based microsatellite typing specifically optimized for multicolor fluorescence detection. The Microsatellite 15 TKY System showed good resolutions for 250 unrelated Thoroughbred horses, and the probability of exclusion (PE) at each microsatellite ranged from 0.437 to 0.621, resulting in a total PE value of 99.998% for Thoroughbred horses. These results indicated that the Microsatellite 15 TKY System is useful for paternity testing of Thoroughbred horses. A paternity testing case for a Thoroughbred horse family, in which candidate sires had close relations, was analyzed using the Microsatellite 15 TKY System. In this case, the Microsatellite 15 TKY System excluded paternity of a false sire. We concluded that the Microsatellite 15 TKY System can give sufficient and reliable information for paternity testing.

[Effect of inflation of the eustachian tube on tinnitus].

The purposes of this study were to evaluate the effect of inflating the Eustachian tube in patients with tinnitus, and to identify diseases in which tubal inflation is indicated. Fifty-four ears of as many patients complaining of tinnitus were examined by pure tone audiometry and decreases in pitch and loudness associated with tinnitus were also evaluated by tinnitus audiometry (Danac-100, DanaJapan). Tinnitus was associated with sensorineural hearing loss (SNHL) in 44 ears and not associated in the remaining 10. The subjects were classified further into two groups: the higher tone group showed a pitch range with tinnitus of 1000 Hz or higher, and the lower tone group showed a pitch range of less than 1000 Hz. In the higher tone tinnitus group with SNLH, the tubal inflation was effective in 3 of 31 ears (10%), and in the lower tone group, 10 of 13 ears (77%). On the other hand, in the tinnitus group with no hearing loss, the method relieved tinnitus in 6 of 10 ears (60%). In the higher tone tinnitus group with no hearing loss, the tubal inflation was effective in 3 of 6 ears (50%), and in the lower tone group, 3 of 4 ears (75%). In this study, however, no ears were permanently relieved of tinnitus with tubal inflation. In the higher tone group, the duration of the reduced tinnitus was less than 10 minutes. In 69% of the lower tone group, the reduction was from 20 minutes to 2 hours. The effect did not continue for more than 2 hours at the longest. In conclusion, Eustachian tubal inflation is indicated in diseases with tinnitus as follows: 1. Lower tone tinnitus with SNHL, particularly in Meniere's disease and acute onset low-tone type SNHL, may be temporarily relieved with tubal inflation. 2. Tinnitus in an ear without SNHL that may gain transitory relief from ringing with the tubal inflation.