A naturally occurring canine model of syndromic congenital microphthalmia

In humans, the prevalence of congenital microphthalmia is estimated to be 0.2 to 3.0 every 10,000 individuals, with non-ocular involvement reported in ~80% of cases. Inherited eye diseases have been widely and descriptively characterized in dogs, and canine models of ocular diseases have played an important role in understanding the pathophysiology and development of new therapies. A naturally occurring canine model of a syndromic disorder characterized by microphthalmia was discovered in the Portuguese Water Dogmodel of a syndromic disorder characterized by microphthalmia in the Portuguese Water Dog (PWD). As non-ocular findings included tooth enamel malformations, stunted growth, anemia, and thrombocytopenia, we hence termed this disorder Canine Congenital Microphthalmos with Hematopoietic Defects (cCMHD). GWAS and homozygosity mapping detected a 2-Mb candidate region on canine chromosome 4. Whole genome sequencing and mapping against the Canfam4 reference revealed a SINE element inse..., Blood samples were gathered of cases and controls - Portuguese Water Dogs affected and unaffected by syndromic congenital microphthalmia. DNA was extracted with standard methods.
A subset of these was genotyped on 220k illumina canine SNP chip for homozygosity mapping and GWAS.
Whole genome sequencing (Illumina Hiseq2000) of a single case was carried out to explore the candidate region., SNP chip data are in plink format, easily convertible to vcf through plink 1.9 or plink 2.0. Also readable as-is (or easily processed) by several R packages.
Whole Genome data are in fastq format, which can be mapped to a reference using standard mappers like BWA., # Data from: A naturally occurring canine model of syndromic congenital microphthalmia

Whole Genome Sequencing, Portuguese water dog, HiSeq2500 paired-end reads (2x 150 bp), of a microphtalmia case:
\"MICR_PWD_R1.fastq.gz\" Forward reads
\"MICR_PWD_R2.fastq.gz\" Reverse reads

Illumina 220k canine SNP chip genotyping:

Files:

\"MICR_PWD_GWAS.tped\" transposed ped file (tped), SNP data in plink format

\"MICR_PWD_GWAS.tfam\" transposed tfam file, ID data in plink format

Following: sample list, cases and controls described in the tfam file

MP001 Case
MP001 Case
MP003 Case
MP004 Case
MP006 Case
MP007 Case
MP008 Case
MP009 Case
MP011 Case
MP012 Case
MP013 Case
MP015 Case
MP016 Case
MP018 Case
MP025 Case
MP026 Case
MP029 Case
MP037 Case
MP038 Case
MP028 Control
MP002 Control
MP010 Control
MP014 Control
MP017 Control
MP027 Control
MP030 Control
MP031 Control
MP032 Control
MP036 Control
MP039 Control
MP040 Control
MP041 Control
MP042 Control
MP043 Control
MP044 Control
MP045 Control
MP046 Control...