POSTER ABSTRACTS
Genome-wide significance was evaluated with SimpleM to correct for multiple testing. We identified two genome-wide significant loci for focal epilepsy (FE) and PD in chromosomes 5 and 37. Both loci contain GABAergic signaling-related candidate genes: GABRD in chromosome 5 and ADAM23 in chromosome 37. ADAM23 has been associated with IE in multiple breeds, including LRs. Neither of these loci were associated with generalized epilepsy in LRs. The following steps will validate the associations in an independent cohort of 50 cases and 50 controls. In addition, we will utilize our existing WGS data of 25 LRs with FE or PD to identify variants from the associated loci. This study has the potential to improve the understanding, diagnostics, and care of IE and PD in dogs and possibly also in humans. #59 Towards a method for feline class I and class II MHC typing with selective Nanopore sequencing Thomas K. Hiron1,2, Sara Falcone2, Sophie Binks2, Marsha D. Wallace1,2, Anja Kipar3, Chris A. O’Callaghan2, Emi. N. Barker4, Lorna J. Kennedy5, Lucy J. Davison1,2,6 thiron@rvc.ac.uk 1Royal Veterinary College, London, UK; 2University of Oxford, Oxford, UK; 3Universität Zürich, Zurich, Switzerland; 4University of Bristol, Bristol, UK; 5The University of Manchester, Manchester, UK; 6MASCOT consortium The highly polymorphic class I and class II major histocompatibility complex (MHC) genes encode proteins essential for cell-surface presentation of self and foreign antigens. Certain MHC haplo- types are associated with specific immune-mediated diseases in humans, but the homologous region in the feline genome is complex, repetitive, and poorly resolved. This locus is therefore challenging to sequence, so the role of MHC variability in many feline diseases remains unexplored. The aim of this study was to develop a novel method for feline MHC genotyping to facilitate explora- tion of MHC genotype in cats with Feline Infectious Peritonitis (FIP) – a potentially fatal complication of feline coronavirus infection. Initially, the MASCOT (Mapping Animal Susceptibility to Coronaviruses: Outcomes and Transcriptomics) consortium assembled a highly contiguous feline genome sequence (2.43 Gb, contig N50 = 74.8 Mb), from a domestic short-hair cat with FIP. This used a hybrid assembly approach incorporating both long-read Nanopore sequencing and high accuracy Illumina short reads from the same patient. The MHC was mapped to 2 contigs containing sequence from feline chromosome B2 and notably the MHC class I region, which is highly fragmented in the felCat9 reference assembly, was intact. Using local alignment, known FLA-DRB alleles were detected in phased long reads. Contiguous, polished sequence corresponding to the MHC was subsequently used to guide ‘Read Until’ adaptive sampling and targeted long-read sequencing of the MHC in a further 9 cats with FIP. An analysis pipeline for focused MHC assembly, read phasing and haplo- type-aware variant calling has been developed and is currently being refined.
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