GTPBP2 in-frame deletion in a canine model with progressive retinal degeneration

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 >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 tha..., Blood samples were gathered and DNA extracted as for standard protocol (BACC2 kit)
SNPdata:  genotype data Type from 220k CanineHD array (Illumina). 
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). , , # 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 sequenc...,