Mapping of breakpoints in balanced chromosomal translocations by shallow whole-genome sequencing points to <i>EFNA5</i>, <i>BAHD1</i> and <i>PPP2R5E</i> as novel candidates for genes causing human Mendelian disorders.

Abstract

Mapping the breakpoints in de novo balanced chromosomal translocations (BCT) in symptomatic individuals provides a unique opportunity to identify in an unbiased way the likely causative genetic defect and thus find novel human disease candidate genes. Our aim was to fine-map breakpoints of de novo BCTs in a case series of nine patients. Shallow whole-genome mate pair sequencing (SGMPS) together with long-range PCR and Sanger sequencing. In one case (BCT disrupting <i>BAHD1</i> and <i>RET</i>) cDNA analysis was used to verify expression of a fusion transcript in cultured fibroblasts. In all nine probands 11 disrupted genes were found, that is, <i>EFNA5, EBF3, LARGE, PPP2R5E, TXNDC5, ZNF423, NIPBL, BAHD1, RET, TRPS1</i> and <i>SLC4A10</i>. Five subjects had translocations that disrupted genes with so far unknown (<i>EFNA5, BAHD1, PPP2R5E, TXNDC5</i>) or poorly delineated impact on the phenotype (<i>SLC4A10,</i> two previous reports of BCT disrupting the gene). The four genes with no previous disease associations (<i>EFNA5, BAHD1, PPP2R5E, TXNDC5</i>), when compared with all human genes by a bootstrap test, had significantly higher pLI (p<0.017) and DOMINO (p<0.02) scores indicating enrichment in genes likely to be intolerant to single copy damage. Inspection of individual pLI and DOMINO scores, and local topologically associating domain structure suggested that <i>EFNA5, BAHD1</i> and <i>PPP2R5E</i> were particularly good candidates for novel disease loci. The pathomechanism for <i>BAHD1</i> may involve deregulation of expression due to fusion with <i>RET</i> promoter. SGMPS in symptomatic carriers of BCTs is a powerful approach to delineate novel human gene-disease associations.