Background 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.
Methods Shallow whole-genome mate pair sequencing (SGMPS) together with long-range PCR and Sanger sequencing. In one case (BCT disrupting BAHD1 and RET) cDNA analysis was used to verify expression of a fusion transcript in cultured fibroblasts.
Results In all nine probands 11 disrupted genes were found, that is, EFNA5, EBF3, LARGE, PPP2R5E, TXNDC5, ZNF423, NIPBL, BAHD1, RET, TRPS1 and SLC4A10. Five subjects had translocations that disrupted genes with so far unknown (EFNA5, BAHD1, PPP2R5E, TXNDC5) or poorly delineated impact on the phenotype (SLC4A10, two previous reports of BCT disrupting the gene). The four genes with no previous disease associations (EFNA5, BAHD1, PPP2R5E, TXNDC5), 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 EFNA5, BAHD1 and PPP2R5E were particularly good candidates for novel disease loci. The pathomechanism for BAHD1 may involve deregulation of expression due to fusion with RET promoter.
Conclusion SGMPS in symptomatic carriers of BCTs is a powerful approach to delineate novel human gene–disease associations.
- next-generation sequencing
- de novo balanced translocations
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VMP, MK and MM contributed equally.
Contributors VMP, KS, RPo, RPl, MKW, RS, AG, JC, BP and AS wrote the manuscript. VMP, MK and MM performed the experiments. RPl, MR, AG, KC and MKW designed the experiment. VMP, MK and MM designed the pipeline. VMP, BP, AG and MS performed bioinformatic analysis. MM, MK, AS, RPo, PK, JC, EW, RS, KC and MKW contacted the patients. VMP, MR, AAK, AB, AW and JK performed next-generation sequencing. EJ preformed MRI analysis.
Funding The research was supported by the National Science Centre (NCN) grant number 2016/21/B/NZ5/02541.
Competing interests None declared.
Patient consent Parental/guardian consent obtained.
Ethics approval Ethics approval for the study was granted by the Ethical Committee at the Medical University of Warsaw (KB/127/2017).
Provenance and peer review Not commissioned; externally peer reviewed.
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