A missense mutation (p.Leu2153His) of the factor VIII gene causes cattle haemophilia A

Causative alleles for chondrodysplastic dwarfism, factor XI deficiency, and factor XIII deficiency in the Kumamoto sub-breed of Japanese Brown cattle

Japanese Brown cattle are the second most popular Wagyu breed, and the Kumamoto sub-breed shows better daily gain and carcass weight. One of the breeding objectives for this sub-breed is to reduce genetic defects. Chondrodysplastic dwarfism and factor VIII deficiency have been identified as genetic diseases in the Kumamoto sub-breed. Previously, we detected individuals in the Kumamoto sub-breed with causative alleles of genetic diseases identified in Japanese Black cattle. In the current study, 11 mutations responsible for genetic diseases in the Wagyu breeds were analyzed to evaluate the risk of genetic diseases in the Kumamoto sub-breed. Genotyping revealed the causative mutations of chondrodysplastic dwarfism, factor XI deficiency, and factor XIII deficiency and suggested the appearance of affected animals in this sub-breed. DNA testing for these diseases is needed to prevent economic loses in beef production using the Kumamoto sub-breed.

Prediction of deleterious mutations in coding regions of mammals with transfer learning

The genomes of mammals contain thousands of deleterious mutations. It is important to be able to recognize them with high precision. In conservation biology, the small size of fragmented populations results in accumulation of damaging variants. Preserving animals with less damaged genomes could optimize conservation efforts. In breeding of farm animals, trade-offs between farm performance versus general fitness might be better avoided if deleterious mutations are well classified. In humans, the problem of such a precise classification has been successfully solved, in large part due to large databases of disease-causing mutations. However, this kind of information is very limited for other mammals. Here, we propose to better use information available on human mutations to enable classification of damaging mutations in other mammalian species. Specifically, we apply transfer learning-machine learning methods-improving small dataset for solving a focal problem (recognizing damaging mutations in our companion and farm animals) due to the use of much large datasets available for solving a related problem (recognizing damaging mutations in humans). We validate our tools using mouse and dog annotated datasets and obtain significantly better results in companion to the SIFT classifier. Then, we apply them to predict deleterious mutations in cattle genomewide dataset.

Two novel missense mutations associated with hemophilia A in a family of Boxers, and a German Shepherd dog

BACKGROUND

Hemophilia A is an X-linked disorder caused by a deficiency in coagulation factor VIII. Over 2300 unique mutations in the gene-encoding factor VIII have been documented in people, but limited information is known in dogs. An 11-week-old male Boxer and a 5-year-old male German Shepherd were diagnosed with hemophilia A based on diminished factor VIII activity.

OBJECTIVE

The purpose of the study was to identify genetic mutations associated with hemophilia A in both dogs.

METHODS

Genomic DNA was isolated from EDTA blood samples from the affected German Shepherd and Boxer, the Boxer's dam, 3 female siblings, and one asymptomatic male sibling. Primers were designed in noncoding regions to amplify the 26 exons of the factor VIII gene via PCR.

RESULTS

The affected Boxer sequence revealed a single nucleotide change, cytosine to guanine, at nucleotide position 1412 (1412C>G) in exon 10. The change is predicted to result in the substitution of arginine for proline at amino acid 471 (P471R) in the A2 domain of factor VIII. The dam and female siblings were carriers, the male sibling did not have the mutation. The German Shepherd dog had a single nucleotide change of a guanine to adenine at position 1643 (1643G>A) in exon 11, predicting the substitution of tyrosine for cysteine at amino acid 548 (C548Y) in the A2 domain.

CONCLUSIONS

Here we document 2 mutations associated with canine hemophilia A associated with < 1% factor VIII activity, similar to that in people. Another related Boxer with the P471R mutation was later identified.

In vitro and In vivo Model Systems for Hemophilia A Gene Therapy

Hemophilia A is a hereditary disorder caused by various mutations in factor VIII gene resulting in either a severe deficit or total lack of the corresponding activity. Recent success in gene therapy of a related disease, hemophilia B, gives new hope that similar success can be achieved for hemophilia A as well. To develop a gene therapy strategy for the latter, a variety of model systems are needed to evaluate molecular engineering of the factor VIII gene, vector delivery efficacy and safety-related issues. Typically, a tissue culture cell line is the most convenient way to get a preliminary glimpse of the potential of a vector delivery strategy. It is then followed by extensive testing in hemophilia A mouse and dog models. Newly developed hemophilia A sheep may provide yet another tool for evaluation of factor VIII gene delivery vectors. Hemophilia models based on other species may also be developed since hemophiliac animals have been identified or generated in rat, pig, cattle and horse. Although a genetic nonhuman primate hemophilia A model has yet to be developed, the non-genetic hemophilia A model can also be used for special purposes when specific questions need to be addressed that cannot not be answered in other model systems. Hemophilia A is caused by a functional deficiency in the factor VIII gene. This X-linked, recessive bleeding disorder affects approximately 1 in 5000 males [1–3]. Clinically, it is characterized by frequent and spontaneous joint hemorrhages, easy bruising and prolonged bleeding time. The coagulation activity of FVIII dictates severity of the clinical symptoms. Approximately 50% of all cases are classified as severe with less than 1% of normal levels of factor VIII detected [4]. This deficiency may lead to spontaneous joint hemorrhages or life-threatening bleeding. In contrast, patients with 5–30% of normal factor VIII activity exhibit mild clinical manifestations.

A genetic predisposition for bovine neonatal pancytopenia is not due to mutations in coagulation factor XI

Bovine neonatal pancytopenia (BNP) is a newly emerging disease in many European countries that causes haemorrhagic diathesis and mortality in neonatal calves. This study tested the hypothesis that genetic factors might be involved in BNP, since genetic defects resulting in coagulation disorders have been described in many species, including cattle. A familial pattern of occurrence of BNP cases was observed in an experimental population of cattle in Germany and BNP was diagnosed in nine calves on an experimental dairy herd from May 2007 to December 2009. All affected calves were descendents of a single F(1) sire in a specific F(2) resource population generated from Charolais and German Holstein bloodlines. Sequence analysis of the bovine coagulation factor XI (F11) gene as a functional candidate gene for BNP revealed an unusually high number of non-synonymous mutations within the gene compared to a whole genome mutation screen in cattle targetting random sequences. However, none of the mutations in the F11 gene were concordant with BNP status. Although these data and further pedigree analysis excluded a simple mode of inheritance of the BNP phenotype, there was a statistically significant (P=0.0001) accumulation of BNP cases in the specific pedigree examined, suggesting that a genetic component is involved in the development of BNP.