Genomic localization of a feline congenital hydrocephalus

Abstract

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] An inherited congenital hydrocephalus (CH) was identified after an Oriental shorthair male with "cobby" ears was used in the development of Toygers, a new breed. Bred for their small ears, hydrocephalic status was discovered after an MRI was conducted on a young kitten. A genetically verified pedigree confirmed an autosomal recessive and fully penetrant mode of inheritance (MOI). Genome-wide association analyses were performed using the Illumina Infinium Feline 63K iSelect DNA array data. A sibTDT analysis, a case control association and region of homozygosity (ROH) scans were performed using 20 affected cases and 20 unaffected controls. The analyses localized the genomic region associated with the phenotype to a 9 Mb region on cat chromosome A3. Visual screening of the region revealed the presence of 55 coding sequences, with no obvious candidate gene. Whole genome sequencing (WGS) of a trio of cats, from the Toyger pedigree, was performed using Illumina sequencing technology at a 30X depth of coverage. Variant calling identified 5,877,171 variants genome wide. Of these, 699,837 variants segregate concordantly with the diseases status and 11,016 were identified within critical region. Eleven healthy cats were used for polymorphism screening via direct sequencing, and the number of exonic variants concordant with the phenotype was reduced to 12. Fine mapping of the region was conducted with the Agena Mass Array technology. Twelve concordant exonic variants and 22 concordant intronic variants were spaced across the 9 Mb haplotype and tested in 96 samples (79 related cats from the pedigree and 17 unrelated cats). Mass Array results reduced the haplotype to a 971 kb critical region. Future endeavors to find this mutation should include de novo assemblies of affected individuals and exploration into different variant discovery algorithms.