Absolute quantification reveals the stable transmission of a high copy number variant linked to autoinflammatory disease

A survey on Shar Pei autoinflammatory disease in the United Kingdom

OBJECTIVES

To characterise the fever episodes attributed to Shar Pei autoinflammatory disease and to identify common diagnostic and management strategies in the United Kingdom. A secondary objective was to determine risk factors associated with Shar Pei autoinflammatory disease fever episodes.

METHODS

A retrospective survey was performed to characterise episodes of Shar Pei autoinflammatory disease fever and to identify commonly used treatments in affected dogs. Clinical data were collected from owners and veterinarians. Frequencies of previously proposed risk factors (skin thickness and folding, muzzle conformation) and comorbid conditions were compared between dogs that had exhibited fever episodes consistent with Shar Pei autoinflammatory disease and those who had not.

RESULTS

At least one episode of fever attributed to Shar Pei autoinflammatory disease was reported in 52 of 106 (49%) Shar Pei. Nine other dogs had fever episodes consistent with Shar Pei autoinflammatory disease reported by their owners but not by veterinarians. Median rectal temperature at presentation for Shar Pei autoinflammatory disease fever was 40.1°C [104.2°F] (39.9 to 41.3°C [103.8 to 106.3°F]) and owners reported associated hyporexia (n=33, 63%) and vomiting (n=8, 15%) more frequently than veterinary records (n=22, 42% and n=0, 0%, respectively). The median number of veterinary appointments for Shar Pei autoinflammatory disease was two per dog (1 to 15) while owners reported a median of four episodes per dog per year. None of the assessed phenotypic variants or comorbidities were significantly associated with exhibiting Shar Pei autoinflammatory disease fever episodes.

CLINICAL SIGNIFICANCE

Episodes of Shar Pei autoinflammatory disease fever were reported approximately twice as frequently by owners compared to veterinary records, suggesting the burden of this condition may be underestimated by veterinarians. Specific risk factors for Shar Pei autoinflammatory disease fever were not identified.

A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

We present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine "dark" regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.

Detection and quantitation of copy number variation in the voltage-gated sodium channel gene of the mosquito Culex quinquefasciatus

Insecticide resistance is typically associated with alterations to the insecticidal target-site or with gene expression variation at loci involved in insecticide detoxification. In some species copy number variation (CNV) of target site loci (e.g. the Ace-1 target site of carbamate insecticides) or detoxification genes has been implicated in the resistance phenotype. We show that field-collected Ugandan Culex quinquefasciatus display CNV for the voltage-gated sodium channel gene (Vgsc), target-site of pyrethroid and organochlorine insecticides. In order to develop field-applicable diagnostics for Vgsc CN, and as a prelude to investigating the possible association of CN with insecticide resistance, three assays were compared for their accuracy in CN estimation in this species. The gold standard method is droplet digital PCR (ddPCR), however, the hardware is prohibitively expensive for widespread utility. Here, ddPCR was compared to quantitative PCR (qPCR) and pyrosequencing. Across all platforms, CNV was detected in ≈10% of mosquitoes, corresponding to three or four copies (per diploid genome). ddPCR and qPCR-Std-curve yielded similar predictions for Vgsc CN, indicating that the qPCR protocol developed here can be applied as a diagnostic assay, facilitating monitoring of Vgsc CN in wild populations and the elucidation of association between the Vgsc CN and insecticide resistance.

Whole genome sequencing identifies missense mutation in MTBP in Shar-Pei affected with Autoinflammatory Disease (SPAID)

BACKGROUND

Autoinflammatory diseases in dogs are characterized by complex disease processes with varying clinical signs. In Shar-Pei, signs of inflammation including fever and arthritis are known to be related with a breed-specific predisposition for Shar-Pei Autoinflammatory Disease (SPAID).

RESULTS

Clinical and histopathological examinations of two severely SPAID-affected Shar-Pei revealed signs of inflammation including fever, arthritis, and perivascular and diffuse dermatitis in both dogs. A multifocal accumulation of amyloid in different organs was found in one SPAID-affected case. Whole genome sequencing resulted in 37 variants, which were homozygous mutant private mutations in SPAID-affected Shar-Pei. Nine SNVs with predicted damaging effects and three INDELs were further investigated in 102 Shar-Pei affected with SPAID, 62 unaffected Shar-Pei and 162 controls from 11 different dog breeds. The results showed the missense variant MTBP:g.19383758G > A in MTBP to be highly associated with SPAID in Shar-Pei. In the region of this gene a large ROH (runs of homozygosity) region could be detected exclusively in the two investigated SPAID-affected Shar-Pei compared to control dog breeds. No further SPAID-associated variant with predicted high or moderate effects could be found in genes identified in ROH regions. This MTBP variant was predicted to affect the MDN2-binding protein domain and consequently promote proinflammatory reactions. In the investigated group of Shar-Pei older than six years all dogs with the mutant genotype A/A were SPAID-affected whereas SPAID-unaffected dogs harbored the homozygous wildtype (G/G). Shar-Pei with a heterozygous genotype (G/A) were shown to have a 2.13-fold higher risk for disease development, which gave evidence for an incomplete dominant mode of inheritance.

CONCLUSIONS

The results of this study give strong evidence for a variant in MTBP related with proinflammatory processes via MTBP-MDM2 pathway. Thus, these results enable a reliable detection of SPAID in Shar-Pei dogs.