Data from: Combining GWAS and RNA-seq approaches for detection of the causal mutation for hereditary junctional epidermolysis bullosa in sheep

In this study, we demonstrate the use of a genome-wide association mapping
together with RNA-seq in a reduced number of samples, as an efficient
approach to detect the causal mutation for a Mendelian disease. Junctional
epidermolysis bullosa is a recessive genodermatosis that manifests with
neonatal mechanical fragility of the skin, blistering confined to the
lamina lucida of the basement membrane and severe alteration of the
hemidesmosomal junctions. In Spanish Churra sheep, junctional
epidermolysis bullosa (JEB) has been detected in two commercial flocks.
The JEB locus was mapped to Ovis aries chromosome 11 by GWAS and
subsequently fine-mapped to an 868-kb homozygous segment using the
identical-by-descent method. The ITGB4, which is located within this
region, was identified as the best positional and functional candidate
gene. The RNA-seq variant analysis enabled us to discover a 4-bp deletion
within exon 33 of the ITGB4 gene (c.4412_4415del). The c.4412_4415del
mutation causes a frameshift resulting in a premature stop codon at
position 1472 of the integrin β4 protein. A functional analysis of this
deletion revealed decreased levels of mRNA in JEB skin samples and the
absence of integrin β4 labeling in immunohistochemical assays. Genotyping
of c.4412_4415del showed perfect concordance with the recessive mode of
the disease phenotype. Selection against this causal mutation will now be
used to solve the problem of JEB in flocks of Churra sheep. Furthermore,
the identification of the ITGB4 mutation means that affected sheep can be
used as a large mammal animal model for the human form of epidermolysis
bullosa with aplasia cutis. Our approach evidences that RNA-seq offers
cost-effective alternative to identify variants in the species in which
high resolution exome-sequencing is not straightforward.