Åke Hedhammar

Efficient mapping of mendelian traits in dogs through genome-wide association

With several hundred genetic diseases and an advantageous genome structure, dogs are ideal for mapping genes that cause disease. Here we report the development of a genotyping array with ∼27,000 SNPs and show that genome-wide association mapping of mendelian traits in dog breeds can be achieved with only ∼20 dogs. Specifically, we map two traits with mendelian inheritance: the major white spotting (S) locus and the hair ridge in Rhodesian ridgebacks. For both traits, we map the loci to discrete regions of <1 Mb. Fine-mapping of the S locus in two breeds refines the localization to a region of ∼100 kb contained within the pigmentation-related gene MITF. Complete sequencing of the white and solid haplotypes identifies candidate regulatory mutations in the melanocyte-specific promoter of MITF. Our results show that genome-wide association mapping within dog breeds, followed by fine-mapping across multiple breeds, will be highly efficient and generally applicable to trait mapping, providing insights into canine and human health.

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

The domestication of dogs was an important episode in the development of human civilization. The precise timing and location of this event is debated and little is known about the genetic changes that accompanied the transformation of ancient wolves into domestic dogs. Here we conduct whole-genome resequencing of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication. Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves. Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs.

Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.

The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease.

Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in Ridgeback dogs

The dorsal hair ridge in Rhodesian and Thai Ridgeback dogs is caused by a dominant mutation that also predisposes to the congenital developmental disorder dermoid sinus. Here we show that the causative mutation is a 133-kb duplication involving three fibroblast growth factor (FGF) genes. FGFs play a crucial role in development, suggesting that the ridge and dermoid sinus are caused by dysregulation of one or more of the three FGF genes during development.

A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs.

Hereditary periodic fever syndromes are characterized by recurrent episodes of fever and inflammation with no known pathogenic or autoimmune cause. In humans, several genes have been implicated in this group of diseases, but the majority of cases remain unexplained. A similar periodic fever syndrome is relatively frequent in the Chinese Shar-Pei breed of dogs. In the western world, Shar-Pei have been strongly selected for a distinctive thick and heavily folded skin. In this study, a mutation affecting both these traits was identified. Using genome-wide SNP analysis of Shar-Pei and other breeds, the strongest signal of a breed-specific selective sweep was located on chromosome 13. The same region also harbored the strongest genome-wide association (GWA) signal for susceptibility to the periodic fever syndrome (praw = 2.3×10−6, pgenome = 0.01). Dense targeted resequencing revealed two partially overlapping duplications, 14.3 Kb and 16.1 Kb in size, unique to Shar-Pei and upstream of the Hyaluronic Acid Synthase 2 (HAS2) gene. HAS2 encodes the rate-limiting enzyme synthesizing hyaluronan (HA), a major component of the skin. HA is up-regulated and accumulates in the thickened skin of Shar-Pei. A high copy number of the 16.1 Kb duplication was associated with an increased expression of HAS2 as well as the periodic fever syndrome (p<0.0001). When fragmented, HA can act as a trigger of the innate immune system and stimulate sterile fever and inflammation. The strong selection for the skin phenotype therefore appears to enrich for a pleiotropic mutation predisposing these dogs to a periodic fever syndrome. The identification of HA as a major risk factor for this canine disease raises the potential of this glycosaminoglycan as a risk factor for human periodic fevers and as an important driver of chronic inflammation.

Breed Risk of Pyometra in Insured Dogs in Sweden

An animal insurance database containing data on over 200,000 dogs was used to study the occurrence of pyometra with respect to breed and age during 1995 and 1996 in Swedish bitches <10 years of age. A total of 1,803 females in 1995 and 1,754 females in 1996 had claims submitted because of pyometra. Thirty breeds with at least 800 bitches insured each year were studied using univariate and multivariate methods. The crude 12-month risk of pyometra for females <10 years of age was 2.0% (95% confidence interval = 1.9-2.1%) in 1995 and 1.9% (1.8-2.0%) in 1996. The occurrence of pyometra differed with age, breed, and geographic location. The risk of developing pyometra was increased (identified using multivariate models) in rough Collies, Rottweilers, Cavalier King Charles Spaniels, Golden Retrievers, Bernese Mountain Dogs, and English Cocker Spaniels compared with baseline (all other breeds, including mixed breed dogs). Breeds with a low risk of developing the disease were Drevers, German Shepherd Dogs, Miniature Dachshunds, Dachshunds (normal size), and Swedish Hounds. Survival rates indicate that on average 23-24% of the bitches in the databases will have experienced pyometra by 10 years of age. In the studied breeds, this proportion ranged between 10 and 54%. Pyometra is a clinically relevant problem in intact bitches, and differences related to breed and age should be taken into account in studies of this disease.

Mortality in over 350,000 Insured Swedish dogs from 1995–2000: I. Breed-, Gender-, Age- and Cause-specific Rates

This study presents data on over 350,000 insured Swedish dogs up to 10 years of age contributing to over one million dog-years at risk (DYAR) during 1995–2000. A total of 43,172 dogs died or were euthanised and of these 72% had a claim with a diagnosis for the cause of death. The overall total mortality was 393 deaths per 10,000 DYAR. Mortality rates are calculated for the 10 most common breeds, 10 breeds with high mortality and a group including all other breeds, crudely and for general causes of death. Proportional mortality is presented for several classifications. Five general causes accounted for 62% of the deaths with a diagnosis (i.e. tumour (18%), trauma (17%), locomotor (13%), heart (8%) and neurological (6%)). Mortality rates for the five most common diagnoses within the general causes of death are presented. These detailed statistics on mortality can be used in breed-specific strategies as well as for general health promotion programs. Further details on survival and relative risk by breed and age are presented in the companion paper [14].SammanfattningMortalitet hos hund baserad på data från över 350 000 svenska hundar försäkrade under 1995 till 2000: 1. Ras-, ålders-, köns- och orsaksspecifika rater.I denna studie presenteras data från över 350 000 försäkrade svenska hundar, med en ålder upp till 10 år, som tillsammans har bidragit med över en miljon hundår av risk (HÅR) under åren 1995 till 2000. Totalt dog eller avlivades 43 172 hundar. Av dessa hade 72% fått en dödsorsaksdiagnos. Den totala mortaliteten var 393 dödsfall per 10 000 HÅR. Mortalitet ututräknades generellt och per dödsorsak för de 10 vanligaste hundraserna, för 10 hundraser med hög mortalitet och för en övrig grupp. Flera typer av proportionell mortalitet presenteras. Fem generella orsaker stod för 62% av alla dödsfall där diagnos förelåg – tumörer (18%), trauma (17%), problem från rörelseapparaten (13%), hjärta (8%) och neurologiska problem (6%). Mortaliteten för de fem vanligaste diagnoserna inom de generella dödsorsakerna presenteras. Denna detaljerade mortalitetsstatistik kan användas både för rasspecifika strategier och för mer generella hälsobefrämjande åtgärder.

Mortality in insured Swedish dogs: rates and causes of death in various breeds

Data on over 222,000 Swedish dogs enrolled in life insurance in 1992 and 1993 were analysed. There were approximately 260 deaths per 10,000 dog-years at risk. Breed-specific mortality rates and causes of death are presented for breeds with more than 500 dogs at risk that had consistently high or low rates. Breed-specific mortality ranged from less than 1 per cent to more than 11 per cent. True rates and proportional statistics for the cause of death were calculated for the entire insured population (250 breeds) and cause-specific mortality rates were calculated for the breeds with the highest risk of dying of the most common causes. Trauma, tumours and problems related to the locomotor system together accounted for more than 40 per cent of all deaths or euthanasias. Although limited to insured dogs, these data cover approximately one-third of all Swedish dogs and provide baseline mortality data for further population-based studies on health and disease.

Validation of computerized Swedish dog and cat insurance data against veterinary practice records

Large computerized medical databases offer great potential for epidemiological research. However, data-quality issues must be addressed. This study evaluated the agreement between veterinary practice records and computerized insurance data in a large Swedish claims database. For the year 1995, the company insured over 320,000 dogs and cats. A total of 470 hard-copy records were sampled from claims for health care (n = 236) and life insurance (n = 234). Computerized insurance data for these claims were accessed and records from the attending veterinary practices were collected. For health and life claims, respectively, 79.2 and 72.8% of practice records were retrieved. Variables compared between the computer and practice records were breed, sex, date of birth and diagnosis for the claim. The degree of agreement was categorized as agreement, minor disagreement, major disagreement or data missing. Multivariable logistic regression was used to examine factors associated with errors. The observed agreement for breed and sex was excellent. There was 28.9 and 33.8% minor disagreement for the date of birth for health and life claims, respectively. This was mainly because, prior to 1993, the date of birth was coded as the first of January when more complete information was unavailable. Major disagreement (different year of birth) was low for both health and life claims. For health and life claims, the observed agreement for diagnosis was 84.0 and 84.9%, minor disagreement was 6.4 and 4.3%, and major disagreement 5.9 and 9.4%, respectively. Although there was no difference based on size of the veterinary clinic involved, there was a tendency for better agreement between the practice record and the computerized insurance data for claims from clinics with computerized practice records (n = 40) than for clinics with manual practice records (n = 286). Rates of discrepancy were affected by the clerk who processed the claims. Records processed by two of the 21 clerks had significantly more disagreements. Given the nature of the data, it was only possible to calculate a measure of observed agreement. In general, the agreement between data in the insurance-company database and from the practice records was excellent for demographic data such as breed and sex and fair for diagnostic information and date of birth. In general, the data are adequate to support ongoing research with due considerations of certain limitations.

Mortality in over 350,000 Insured Swedish Dogs from 1995–2000: II. Breed-Specific Age and Survival Patterns and Relative Risk for Causes of Death

This study continues analysis from a companion paper on over 350,000 insured Swedish dogs up to 10 years of age contributing to more than one million dog-years at risk during 1995–2000. The age patterns for total and diagnostic mortality and for general causes of death (trauma, tumour, locomotor, heart and neurological) are presented for numerous breeds. Survival estimates at five, eight and 10 years of age are calculated. Survival to 10 years of age was 75% or more in Labrador and golden retrievers, miniature and toy poodles and miniature dachshunds and lowest in Irish wolfhounds (91% dead by 10 years). Multivariable analysis was used to estimate the relative risk for general and more specific causes of death between breeds accounting for gender and age effects, including two-way interactions. Older females had tumour as a designated cause of death more often than males in most breeds, but not in the Bernese mountain dog. Information presented in this and the companion paper inform our understanding of the population level burden of disease, and support decision-making at the population and individual level about health promotion efforts and treatment and prognosis of disease events.SammanfattningMortalitet hos hund baserad på data från över 350 000 svenska hundar försäkrade under 1995 till 2000: II. Rasspecifika ålders och överlevnadsmönster och relativ risk för olika dödsorsaker.Detta är del 2 i en studie där data på över 350 000 försäkrade svenska hundar under 10 års ålder analyserats. Resultaten grundas på mer än en miljon hundår av risk under 1995 till 2000. Åldersmönstret för den totala och diagnostiska mortaliteten, och också för generella dödsorsaker (trauma, tumörer, problem från rörelseapparaten, hjärta och neurologiska problem) presenteras för ett flertal hundraser. Beräknad överlevnad vid 5, 8 och 10 års ålder presenteras. Överlevnaden vid 10 års ålder var 75% eller högre hos labrador och golden retriever, dvärg- och mellanpudel samt dvärgtaxar och lägst hos irländska varghundar (91% var döda vid 10 års ålder). Multivariabel analys användes för att beräkna relativ risk för generella och mer specifika dödsorsaker för olika raser, med hänsyn taget till könsoch ålderseffekter vilket också inkluderar två-vägs interaktioner. I de flesta hundraser hade äldre tikar tumör som dödsorsak oftare än äldre hanhundar, med undantag för berner sennen hundar. Information som presenteras i denna del (2) och del 1 ger insikt om dödsorsakspanoramat hos hund. Detta kan ge stöd för beslut på både populations och individuell nivå om vilka åtgärder somkan vidtas för att förbättra hundars hälsa, såväl behandlingsmässigt som prognostiskt.