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Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis

Abstract

The contribution of cis-regulatory mutations to human disease remains poorly understood. Whole-genome sequencing can identify all noncoding variants, yet the discrimination of causal regulatory mutations represents a formidable challenge. We used epigenomic annotation in human embryonic stem cell (hESC)-derived pancreatic progenitor cells to guide the interpretation of whole-genome sequences from individuals with isolated pancreatic agenesis. This analysis uncovered six different recessive mutations in a previously uncharacterized 400-bp sequence located 25 kb downstream of PTF1A (encoding pancreas-specific transcription factor 1a) in ten families with pancreatic agenesis. We show that this region acts as a developmental enhancer of PTF1A and that the mutations abolish enhancer activity. These mutations are the most common cause of isolated pancreatic agenesis. Integrating genome sequencing and epigenomic annotation in a disease-relevant cell type can thus uncover new noncoding elements underlying human development and disease.

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Figure 1: Epigenome annotation of variants from genome sequencing identifies a shared variant in a putative enhancer element.
Figure 2: Families with mutations in the PTF1A enhancer.
Figure 3: Pancreas agenesis–associated mutations disrupt the function of a transcriptional enhancer that is specifically active in pancreatic progenitors.

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Acknowledgements

The authors thank M. Day, A. Damhuis and J. Garcia-Hurtado for technical assistance and R. Tearle (Complete Genomics), J. Tena and J.L. Skarmeta (Centro Andaluz de Biología del Desarrollo) for advice. J.F., S.E. and A.T.H. are supported by Wellcome Trust Senior Investigator awards. M.N.W. is supported by the Wellcome Trust as part of WT Biomedical Informatics Hub funding. E.D.F. is funded by the BOLD grant (European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement FP7-PEOPLE-ITN-2008 (Marie Curie Initial Training Networks, Biology of Liver and Pancreatic Development and Disease)). This work was supported by the National Institute for Health Research Exeter Clinical Research Facility through funding for S.E. and A.T.H. and general infrastructure and by the Ministerio de Economía y Competitividad (SAF2011-27086, PLE2009-0162 to J.F.). The views expressed here are those of the authors and not necessarily those of the National Health Service, the National Institute for Health Research or the Department of Health, UK.

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M.N.W., S.E., J.F. and A.T.H. designed the study. M.N.W., A.-M.P., J.A.L.H. and H.L.A. performed bioinformatic analyses. I.C., S.A.R.-S., C.H.-H.C., A.M., L.V. and J.F. performed functional studies. A.-M.P., J.A.L.H., E.D.F., R. Caswell, S.E.F. and S.E. performed Sanger sequencing or deletion analysis and interpreted the results. S.E.F., C.S.-S., K.H., C.L.R., R. Chen, P.M. and A.T.H. analyzed the clinical data. M.N.W., I.C., A.-M.P., S.E., J.F. and A.T.H. prepared the draft manuscript. All authors contributed to discussion of the results and to manuscript preparation.

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Correspondence to Jorge Ferrer or Andrew T Hattersley.

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Weedon, M., Cebola, I., Patch, AM. et al. Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis. Nat Genet 46, 61–64 (2014). https://doi.org/10.1038/ng.2826

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