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The semidominant Danforth's short tail ( Sd ) mutation arose spontaneously in the 1920s. The homozygous  Sd  phenotype includes severe malformations of the axial skeleton with an absent tail, kidney agenesis, anal atresia, and persistent cloaca. The  Sd  mutant phenotype mirrors features seen in human caudal malformation syndromes including urorectal septum malformation, caudal regression, VACTERL association, and persistent cloaca. The  Sd  mutation was previously mapped to a 0.9 cM region on mouse chromosome 2qA3. We performed Sanger sequencing of exons and intron/exon boundaries mapping to the  Sd  critical region and did not identify any mutations. We then performed DNA enrichment/capture followed by next-generation sequencing (NGS) of the critical genomic region. Standard bioinformatic analysis of paired-end sequence data did not reveal any causative mutations. Interrogation of reads that had been discarded because only a single end mapped correctly to the  Sd  locus identified an early transposon (ETn) retroviral insertion at the  Sd  locus, located 12.5 kb upstream of the  Ptf1a  gene. We show that  Ptf1a  expression is significantly upregulated in  Sd  mutant embryos at E9.5. The identification of the  Sd  mutation will lead to improved understanding of the developmental pathways that are misregulated in human caudal malformation syndromes.

Next-Generation Sequencing Identifies the Danforth's Short Tail Mouse Mutation as a Retrotransposon Insertion Affecting Ptf1a Expression