Integrative genomics reveals that distal cis-regulatory mutations cause isolated pancreatic agenesis

WEEDON, M.N.; CEBOLA, I.; PATCH, A.M.; FLANAGAN, S.; DE FRANCO, E.; CASWELL, R.; RODRÍGUEZ SEGUÍ, S.A.; SHAW-SMITH, C.; CHO, C.; ALLEN, H.L.; HOUGHTON, J.; ROTH, C.L.; CHEN, R.; HUSSAIN, K.; MARSH, P.; VALLIER, L.; MURRAY, A.; ELLARD, S.; FERRER, J.; HATTERSLEY, A.T.

Boston

Encuentro; American Society of Human Genetics (ASHG) Annual Meeting 2013; 2013

American Society of Human Genetics (ASHG)

The contribution of cis-regulatory mutations to human disease remains poorly understood. Whole genome sequencing can identify all non-coding variants, yet discrimination of causal regulatory mutations represents a formidable challenge.We performed whole genome sequencing on probands from two consanguineous families with non-syndromic pancreatic agenesis. We first looked for recessive coding mutations in the exomes of these patients, but no obvious candidate causal mutations were identified.To search for non-coding disease-causing mutations, we annotated the 6,024 rare (<1% frequency in the 1000 genomes project) or novel homozygous variants from these patients using epigenome maps from human pancreatic progenitor cells. Only one variant, a novel SNV, occurred in a functionally annotated region and was shared by both unrelated patients. This variant occurs several tens of kb from PTF1A in a short (~400bp) region of evolutionary conservation. Follow-up sequencing identified four different recessive point mutations and an 8kb deletion spanning the functional element in 9 of 12 non-syndromic pancreatic agenesis cases.A series of experiments including 3C and reporter assays clearly demonstrate that this previously uncharacterised non-coding element acts as a developmental enhancer of PTF1A in human pancreatic progenitor cells. The 6 mutations prevent enhancer activity by abolishing transcription factor binding or deleting the entire enhancer sequence.These results demonstrate that integrating genome sequencing and epigenomic annotation in a disease-relevant cell type can uncover novel non-coding elements underlying human development and disease.