DOI: 10.5061/dryad.xwdbrv1kd
title: GTPBP2 in-frame deletion in a canine model with progressive retinal degeneration

description: Progressive retinal atrophy (PRA), caused by aberrant functioning of
 rod/cone photoreceptors leads to blindness. Different types of
 photoreceptor abnormalities with different ages of onset and progression
 have been reported in dogs, even in the same breed, and new ones are
 constantly discovered in Labrador retriever. We collected samples from 3
 affected dogs and 3 unaffected siblings, along with the unaffected parents
 of the same litter. Homozygosity mapping detected six candidate regions
 &gt;1Mb. Whole-genome sequencing detected an homozygous 3-bp deletion
 in the coding region of GTPBP2, CFA12 - a GTP-binding protein
 (CFA12:12,246,348) c.1606_1608del, p.Ala536del).
       
             The variant was absent from the online EVA database, the Dog Biomedical Variants Database, and the Dog10k variants database. Testing 75 healthy dogs from the same kennel detected wild type and carrier individuals. More than 600 Labradors from the general population (USA) were genotyped wild type for the variant. The variant was absent from the online EVA database, the Dog Biomedical Variants Database, and the Dog10k variants database. GTPBP2 is associated with Jaberi-Elahi syndrome in Homo sapiens, and splice variants in Mus musculus are associated with neurodegeneration; in both cases photoreceptor degeneration may be included in its manifestation.                      Heterologous cellular systems were transfected with cDNA encoding WT or A536del mutant GTPBP2 protein and immunoblot analysis of total cell lysate with antibodies to GTPBP2 showed that the expression level of the GTPBP2 mutant protein A536del is slightly but not significantly reduced, compared to the WT form. Instead, the cellular distribution of GTPBP2 protein was investigated by using immunofluorescent methods and confocal analysis of cells transfected with WT or A536del GTPBP2 protein revealed that the WT form is diffuse throughout the cytoplasm of cells, while the mutant form resulted in the formation of cytosolic aggregates in almost 70-80% of cells. We therefore show a non-syndromic, retinal-specific phenotype occurring in a large animal model, associated with a deletion in a conserved Alanine, in a conserved interval outside the GTP domain of GTPBP2, suggesting a potentially novel role of the sequence on cellular localization of the protein.
description: Blood samples were gathered and DNA extracted as for standard
 protocol (BACC2 kit) SNPdata:  genotype data Type
 from <em>220k</em> CanineHD array
 (<em>Illumina</em>).  Libraries of 300 bp
 insert size were prepared and illumina HiSeq2500 paired-end reads (2x100
 bp) were collected (one lane per sample). Fastq files were generated using
 Casava 1.8. A total of 561.77 millions reads (100 bp paired-end reads) for
 the four libraries were collected for the sequenced dogs from a shotgun
 fragment library (corresponding to an average coverage of the genome of
 28.2x and 27.6x for the cases, and 26.7x and 28.4x for the
 parents). 
description: # GTPBP2 in-frame deletion in a canine model with progressive retinal
 degeneration Whole Genome Sequencing - 2 cases of Labrador Retriever,
 siblings (*Canis lupus familiaris*) affected with a retinal condition.
 HiSeq2500 paired-end reads 2x100 bp. Compatible with whole-genome mappers
 like bwa. Whole Genome Sequencing - 2 cases GEB113_R1_001.fastq.gz
 GEB113_R2_001.fastq.gz GEB130_R1_001.fastq.gz GEB130_R2_001.fastq.gz Whole
 Genome Sequencing - 2 controls GEB128_R1_001.fastq.gz
 GEB128_R2_001.fastq.gz GEB129_R1_001.fastq.gz GEB129_R2_001.fastq.gz SNP
 chip genotyping - cases and controls marked as plink document (transposed
 format). Two cases and two parents whole-genome sequenced (see other part
 of the submission) are also contained here.  SNP chip data plink
 transposed format GEB_PRA.tfam GEB_PRA.tped ## Data details The fastq.gz
 files are gzipped fastq files. Definition (wiki): "FASTQ format is a
 text-based format for storing both a biological sequence (usually
 nucleotide sequence) and its corresponding quality scores. Both the
 sequence letter and quality score are each encoded with a single ASCII
 character for brevity." More
 info [https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002211](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002211) (accessed Nov 24 2024) tfam is a list of identifications (one dog each) used to read the tped file. The tped file contains information about the genotype of each locus, two bases per marker, used for GWAS, homozygosity mapping, and linkage. More information about [https://www.cog-genomics.org/plink/](https://www.cog-genomics.org/plink/) (accessed Nov 24 2024)