Computational protocol: Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2

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Protocol publication

[…] We used whole exome sequences from the Generation Scotland: Scottish Family Health Study (GS:SFHS). Study participants had been originally recruited for population-based studies of complex traits. Details regarding the design and sequencing of human participants is described elsewhere. We extracted all sequence variants in SMOC2 which passed GATK recalibration []. Putative regulatory elements and functional roles of the extracted variants were assessed by the ENCODE-based prediction tool HaploReg (v4.1) []. To assess the predicted consequences of the variants, we examined their C-scores, which indicate the ‘deleteriousness’ of a given mutation using combined annotation dependent depletion (CADD, v3.1) []. […]

Pipeline specifications

Software tools GATK, HaploReg, CADD
Applications WGS analysis, WES analysis
Organisms Canis lupus familiaris, Homo sapiens
Diseases Craniosynostoses, Osteochondrodysplasias