Identification of Novel Genetic Risk Loci in Maltese Dogs with Necrotizing Meningoencephalitis and Evidence of a Shared Genetic Risk across Toy Dog Breeds

Necrotizing meningoencephalitis (NME) affects toy and small breed dogs causing progressive, often fatal, inflammation and necrosis in the brain. Genetic risk loci for NME previously were identified in pug dogs, particularly associated with the dog leukocyte antigen (DLA) class II complex on chromosome 12, but have not been investigated in other susceptible breeds. We sought to evaluate Maltese and Chihuahua dogs, in addition to pug dogs, to identify novel or shared genetic risk factors for NME development. Genome-wide association testing of single nucleotide polymorphisms (SNPs) in Maltese dogs with NME identified 2 regions of genome-wide significance on chromosomes 4 (chr4:74522353T>A, p = 8.1×10-7) and 15 (chr15:53338796A>G, p = 1.5×10-7). Haplotype analysis and fine-mapping suggests that ILR7 and FBXW7, respectively, both important for regulation of immune system function, could be the underlying associated genes. Further evaluation of these regions and the previously identified DLA II locus across all three breeds, revealed an enrichment of nominal significant SNPs associated with chromosome 15 in pug dogs and DLA II in Maltese and Chihuahua dogs. Meta-analysis confirmed effect sizes the same direction in all three breeds for both the chromosome 15 and DLA II loci (p = 8.6×10-11 and p = 2.5×10-7, respectively). This suggests a shared genetic background exists between all breeds and confers susceptibility to NME, but effect sizes might be different among breeds. In conclusion, we identified the first genetic risk factors for NME development in the Maltese, chromosome 4 and chromosome 15, and provide evidence for a shared genetic risk between breeds associated with chromosome 15 and DLA II. Last, DLA II and IL7R both have been implicated in human inflammatory diseases of the central nervous system such as multiple sclerosis, suggesting that similar pharmacotherapeutic targets across species should be investigated

Autosomal recessive nonsyndromic hearing impairment in two Finnish families due to the population enriched CABP2 c.637+1G>T variant

Abstract Background: The genetic architecture of hearing impairment in Finland is largely unknown. Here, we investigated two Finnish families with autosomal recessive nonsyndromic symmetrical moderate-to-severe hearing impairment. Methods: Exome and custom capture next-generation sequencing were used to detect the underlying cause of hearing impairment. Results: In both Finnish families, we identified a homozygous pathogenic splice site variant c.637+1G>T in CABP2 that is known to cause autosomal recessive nonsyndromic hearing impairment. Four CABP2 variants have been reported to underlie autosomal recessive nonsyndromic hearing impairment in eight families from Iran, Turkey, Pakistan, Italy, and Denmark. Of these variants, the pathogenic splice site variant c.637+1Ggt;T is the most prevalent. The c.637+1Ggt;T variant is enriched in the Finnish population, which has undergone multiple bottlenecks that can lead to the higher frequency of certain variants including those involved in disease. Conclusion: We report two Finnish families with hearing impairment due to the CABP2 splice site variant c.637+1Ggt;T

Fine mapping of genome wide significant regions on (A) chromosomes 4 and (B) 15 in Maltese dogs by haplotype analysis.

<p>The raw –log₁₀ p-values for each haplotype test are plotted (y axis) against the chromosome position (x axis). The colored lines represent haplotypes formed by a 5-SNP sliding window across the region, and the black lines represent haplotypes formed by the underlying LD structure calculated by the 4-gamete rule. In the bottom, the LD between the SNPs in the region is shown (dark red = high D’; blue = low D’). The haploblocks based on the 4-gamete rule are indicated in black.</p

Manhattan plot of genome wide association analysis in Maltese dogs with necrotizing meningoencephalitis.

<p>The raw –log₁₀ p-values for each SNP as determined by Fisher’s exact tests are plotted (y axis) against the chromosome position (x axis). The horizontal gray line represents the threshold for significant association after Bonferroni correction. Regions that reach genome wide significance are indicated in black.</p

Forest plots of four SNPs in the dog leukocyte antigen II region on chromosome 12 across three toy breeds with necrotizing meningoencephalitis.

<p>(a) BICF2P22942: p = 1.57×10⁻⁷, OR = 0.18 (0.09–0.35), (b) BICF2P738783: p = 4.11×10⁻⁸, OR = 0.18 (0.10–0.34), (c) BICF2P178662: p = 1.11×10⁻⁹, OR = 9.48 (4.19–21.40), and (d) BICF2P608380: p = 8.6×10⁻¹¹, OR = 11.08 (4.72–26.01). The 95% confidence interval for each study is represented by a horizontal line, and the point estimate is given by a square, the height of which is inversely proportional to the standard error of the estimate after each study. The summary OR is indicated by a diamond with horizontal limits as the confidence limits and height inversely proportional to its standard error. The meta-analyses for all these SNPs were significant and effect sizes were in the same direction.</p

Most significantly associated SNPs from genome wide association analysis of Maltese dogs with necrotizing meningoencephalitis.

<p>Chr: chromosome; P_raw: Fisher exact test p-value; BONF: Bonferroni correction for multiple testing; FDR BH: false discovery rate of multiple testing; Max(T): Max(T) permutation of 10,000 permutations as corrected empirical p (EMP2) value; AF: allele frequency; OR: odds ratio; L95 and U95: upper and lower 95% confidence intervals for the OR. Coordinates are based on CanFam2.0 alignment. The SNPs with greatest significance are represented with bold lettering.</p><p>Most significantly associated SNPs from genome wide association analysis of Maltese dogs with necrotizing meningoencephalitis.</p

Exome sequencing reveals predominantly de novo variants in disorders with intellectual disability (ID) in the founder population of Finland

Abstract The genetics of autosomal recessive intellectual disability (ARID) has mainly been studied in consanguineous families, however, founder populations may also be of interest to study intellectual disability (ID) and the contribution of ARID. Here, we used a genotype-driven approach to study the genetic landscape of ID in the founder population of Finland. A total of 39 families with syndromic and non-syndromic ID were analyzed using exome sequencing, which revealed a variant in a known ID gene in 27 families. Notably, 75% of these variants in known ID genes were de novo or suspected de novo (64% autosomal dominant; 11% X-linked) and 25% were inherited (14% autosomal recessive; 7% X-linked; and 4% autosomal dominant). A dual molecular diagnosis was suggested in two families (5%). Via additional analysis and molecular testing, we identified three cases with an abnormal molecular karyotype, including chr21q22.12q22.2 uniparental disomy with a mosaic interstitial 2.7 Mb deletion covering DYRK1A and KCNJ6. Overall, a pathogenic or likely pathogenic variant was identified in 64% (25/39) of the families. Last, we report an alternate inheritance model for 3 known ID genes (UBA7, DDX47, DHX58) and discuss potential candidate genes for ID, including SYPL1 and ERGIC3 with homozygous founder variants and de novo variants in POLR2F and DNAH3. In summary, similar to other European populations, de novo variants were the most common variants underlying ID in the studied Finnish population, with limited contribution of ARID to ID etiology, though mainly driven by founder and potential founder variation in the latter case