Variation in genes related to cochlear biology is strongly associated with adult-onset deafness in border collies.

Domestic dogs can suffer from hearing losses that can have profound impacts on working ability and quality of life. We have identified a type of adult-onset hearing loss in Border Collies that appears to have a genetic cause, with an earlier age of onset (3-5 years) than typically expected for aging dogs (8-10 years). Studying this complex trait within pure breeds of dog may greatly increase our ability to identify genomic regions associated with risk of hearing impairment in dogs and in humans. We performed a genome-wide association study (GWAS) to detect loci underlying adult-onset deafness in a sample of 20 affected and 28 control Border Collies. We identified a region on canine chromosome 6 that demonstrates extended support for association surrounding SNP Chr6.25819273 (p-value = 1.09 × 10(-13)). To further localize disease-associated variants, targeted next-generation sequencing (NGS) of one affected and two unaffected dogs was performed. Through additional validation based on targeted genotyping of additional cases (n = 23 total) and controls (n = 101 total) and an independent replication cohort of 16 cases and 265 controls, we identified variants in USP31 that were strongly associated with adult-onset deafness in Border Collies, suggesting the involvement of the NF-κB pathway. We found additional support for involvement of RBBP6, which is critical for cochlear development. These findings highlight the utility of GWAS-guided fine-mapping of genetic loci using targeted NGS to study hereditary disorders of the domestic dog that may be analogous to human disorders.

Marker panels for genealogy-based mapping, breed demographics, and inference-of-ancestry in the dog.

Short tandem repeat polymorphisms (STRPs) are robust and informative markers for a range of genetic applications. STRPs are advantageous in experimental designs that derive power from sampling many individuals rather than many loci (e.g., pedigree-based studies, fine-scale mapping, and conservation genetics). STRPs have proven useful for vetting samples prior to costly high-density SNP analysis. Here we present validated STRPs (n = 1,012) spanning the canine genome (2.1 +/-1.4 Mb; 2.1 +/-2.1 cM). Standardized design, pre-multiplexing, M13-based dye-labeling, and selection for loci amenable to semi-automated allele-scoring minimize cost and facilitate efficient genotyping. The markers are leveraged from the canine linkage map, and thus are backed by genetic data useful for parametric multipoint analysis and assessment of empiric coverage. We demonstrate several applications with different marker subsets. The complete set provides a genome scan for linkage at ∼5 cM resolution. A subset of the markers measures molecular diversity between domestic and wild canid populations. Another subset reflects ancestry within breeds, uncovering hidden stratification and flagging genetic outliers prior to SNP genotyping. Thus, the markers described here add flexibility and cost effectiveness to several genetic applications in the dog that complement genome-wide SNP genotyping studies. Supplemental material is available for this article. Go to the publisher's online edition of Animal Biotechnology.

Resuscitation of neonates at 23 weeks' gestational age: a cost-effectiveness analysis.

OBJECTIVE: Resuscitation of infants at 23 weeks' gestation remains controversial; clinical practices vary. We sought to investigate the cost effectiveness of resuscitation of infants born 23 0/7-23 6/7 weeks' gestation. DESIGN: Decision-analytic modeling comparing universal and selective resuscitation to non-resuscitation for 5176 live births at 23 weeks in a theoretic U.S. cohort. Estimates of death (77%) and disability (64-86%) were taken from the literature. Maternal and combined maternal-neonatal utilities were applied to discounted life expectancy to generate QALYs. Incremental cost-effectiveness ratios were calculated, discounting costs and QALYs. Main outcomes included number of survivors, their outcome status and incremental cost-effectiveness ratios for the three strategies. A cost-effectiveness threshold of $100 000/QALY was utilized. RESULTS: Universal resuscitation would save 1059 infants: 138 severely disabled, 413 moderately impaired and 508 without significant sequelae. Selective resuscitation would save 717 infants: 93 severely disabled, 279 moderately impaired and 343 without significant sequelae. For mothers, non-resuscitation is less expensive ($19.9 million) and more effective (127 844 mQALYs) than universal resuscitation ($1.2 billion; 126 574 mQALYs) or selective resuscitation ($845 million; 125 966 mQALYs). For neonates, both universal and selective resuscitation were cost-effective, resulting in 22 256 and 15 134 nQALYS, respectively, versus 247 nQALYs for non-resuscitation. In sensitivity analyses, universal resuscitation was cost-effective from a maternal perspective only at utilities for neonatal death <0.42. When analyzed from a maternal-neonatal perspective, universal resuscitation was cost-effective when the probability of neonatal death was <0.95. CONCLUSIONS: Over wide ranges of probabilities for survival and disability, universal and selective resuscitation strategies were not cost-effective from a maternal perspective. Both strategies were cost-effective from a maternal-neonatal perspective. This study offers a metric for counseling and decision-making for extreme prematurity. Our results could support a more permissive response to parental requests for aggressive intervention at 23 weeks' gestation.

Importance of glycosylation and disulfide bonds in hyaluronidase activity of macaque sperm surface PH-20.

PH-20 is a glycoprotein located on the surface of the sperm plasma membrane and on the inner acrosomal membrane. The best understood function of sperm surface PH-20 is its hyaluronidase activity, which results in hydrolysis of the hyaluronic acid-rich cumulus matrix during sperm penetration of this extracellular oocyte investment. In this study, we investigated whether alterations in the secondary and tertiary structures of sperm surface PH-20 would affect its enzyme activity. Proteins were isolated from the sperm plasma membrane by treatment of living cells with phosphatidylinositol-specific phospholipase C (PI-PLC). PH-20 was purified from the PI-PLC released proteins by immunoaffinity chromatography. Two-dimensional electrophoresis of purified PH-20 revealed 6 isoforms with isoelectric points ranging from 5.1 to 6.0. Removal of the N-linked glycans from PH-20 with N-glycosidase F shifted the molecular weight from 64 kd to approximately 54 kd, its deduced molecular weight based on sequence analysis, suggesting that most if not all, of the potential N-glycosylation sites are linked to oligosaccharides. The lectins Con A and PSA recognized purified sperm surface PH-20 after Western blotting, suggesting that mannose is a major sugar within or at the terminal end of the linked glycan. The lectins UEA and LPA did not recognize PH-20 Western blot, suggesting that fucose and sialic acid are not terminal sugars of sperm surface PH-20. Deglycosylation of sperm surface PH-20 resulted in a complete loss of its hyaluronidase activity. The reduction of disulfide bonds with beta-mercaptoethanol or dithiothreitol also resulted in loss of enzyme activity. We conclude that the hyaluronidase activity of sperm surface PH-20 is dependent on structural features established by sulfhydryl linkages, as well as glycosylation.

A comprehensive linkage map of the dog genome.

We have leveraged the reference sequence of a boxer to construct the first complete linkage map for the domestic dog. The new map improves access to the dog's unique biology, from human disease counterparts to fascinating evolutionary adaptations. The map was constructed with approximately 3000 microsatellite markers developed from the reference sequence. Familial resources afforded 450 mostly phase-known meioses for map assembly. The genotype data supported a framework map with approximately 1500 loci. An additional approximately 1500 markers served as map validators, contributing modestly to estimates of recombination rate but supporting the framework content. Data from approximately 22,000 SNPs informing on a subset of meioses supported map integrity. The sex-averaged map extended 21 M and revealed marked region- and sex-specific differences in recombination rate. The map will enable empiric coverage estimates and multipoint linkage analysis. Knowledge of the variation in recombination rate will also inform on genomewide patterns of linkage disequilibrium (LD), and thus benefit association, selective sweep, and phylogenetic mapping approaches. The computational and wet-bench strategies can be applied to the reference genome of any nonmodel organism to assemble a de novo linkage map.

An ADAMTSL2 founder mutation causes Musladin-Lueke Syndrome, a heritable disorder of beagle dogs, featuring stiff skin and joint contractures.

BACKGROUND: Musladin-Lueke Syndrome (MLS) is a hereditary disorder affecting Beagle dogs that manifests with extensive fibrosis of the skin and joints. In this respect, it resembles human stiff skin syndrome and the Tight skin mouse, each of which is caused by gene defects affecting fibrillin-1, a major component of tissue microfibrils. The objective of this work was to determine the genetic basis of MLS and the molecular consequence of the identified mutation. METHODOLOGY AND PRINCIPAL FINDINGS: We mapped the locus for MLS by genome-wide association to a 3.05 Mb haplotype on canine chromosome 9 (CFA9 (50.11-54.26; p(raw) <10(-7))), which was homozygous and identical-by-descent among all affected dogs, consistent with recessive inheritance of a founder mutation. Sequence analysis of a candidate gene at this locus, ADAMTSL2, which is responsible for the human TGFß dysregulation syndrome, Geleophysic Dysplasia (GD), uncovered a mutation in exon 7 (c.660C>T; p.R221C) perfectly associated with MLS (p-value=10(-12)). Murine ADAMTSL2 containing the p.R221C mutation formed anomalous disulfide-bonded dimers when transiently expressed in COS-1, HEK293F and CHO cells, and was present in the medium of these cells at lower levels than wild-type ADAMTSL2 expressed in parallel. CONCLUSIONS/SIGNIFICANCE: The genetic basis of MLS is a founder mutation in ADAMTSL2, previously shown to interact with latent TGF-ß binding protein, which binds fibrillin-1. The molecular effect of the founder mutation on ADAMTSL2 is formation of disulfide-bonded dimers. Although caused by a distinct mutation, and having a milder phenotype than human GD, MLS nevertheless offers a new animal model for study of GD, and for prospective insights on mechanisms and pathways of skin fibrosis and joint contractures.

Breed distribution and history of canine mdr1-1Delta, a pharmacogenetic mutation that marks the emergence of breeds from the collie lineage.

A mutation in the canine multidrug resistance gene, MDR1, has previously been associated with drug sensitivities in two breeds from the collie lineage. We exploited breed phylogeny and reports of drug sensitivity to survey other purebred populations that might be genetically at risk. We found that the same allele, mdr1-1Delta, segregated in seven additional breeds, including two sighthounds that were not expected to share collie ancestry. A mutant haplotype that was conserved among affected breeds indicated that the allele was identical by descent. Based on breed histories and the extent of linkage disequilibrium, we conclude that all dogs carrying mdr1-1Delta are descendants of a dog that lived in Great Britain before the genetic isolation of breeds by registry (ca. 1873). The breed distribution and frequency of mdr1-1Delta have applications in veterinary medicine and selective breeding, whereas the allele's history recounts the emergence of formally recognized breeds from an admixed population of working sheepdogs.