Improved genetic testing for monogenic diabetes using targeted next-generation sequencing

Abstract

Aims/hypothesisCurrent genetic tests for diagnosing monogenic diabetes rely on selection of the appropriate gene for analysis according to the patient’s phenotype. Next-generation sequencing enables the simultaneous analysis of multiple genes in a single test. Our aim was to develop a targeted next-generation sequencing assay to detect mutations in all known MODY and neonatal diabetes genes.MethodsWe selected 29 genes in which mutations have been reported to cause neonatal diabetes, MODY, maternally inherited diabetes and deafness (MIDD) or familial partial lipodystrophy (FPLD). An exon-capture assay was designed to include coding regions and splice sites. A total of 114 patient samples were tested—32 with known mutations and 82 previously tested for MODY (n = 33) or neonatal diabetes (n = 49) but in whom a mutation had not been found. Sequence data were analysed for the presence of base substitutions, small insertions or deletions (indels) and exonic deletions or duplications.ResultsIn the 32 positive controls we detected all previously identified variants (34 mutations and 36 polymorphisms), including 55 base substitutions, ten small insertions or deletions and five partial/whole gene deletions/duplications. Previously unidentified mutations were found in five patients with MODY (15%) and nine with neonatal diabetes (18%). Most of these patients (12/14) had mutations in genes that had not previously been tested.Conclusions/interpretationOur novel targeted next-generation sequencing assay provides a highly sensitive method for simultaneous analysis of all monogenic diabetes genes. This single test can detect mutations previously identified by Sanger sequencing or multiplex ligation-dependent probe amplification dosage analysis. The increased number of genes tested led to a higher mutation detection rate.Electronic supplementary materialThe online version of this article (doi:10.1007/s00125-013-2962-5) contains peer-reviewed but unedited supplementary material, which is available to authorised users.

An emerging, recognizable facial phenotype in association with mutations in GLI‐similar 3 (GLIS3)

“…Patient 4 was analysed for all the known neonatal diabetes genes using a targeted next generation assay [Ellard et al, 2013]. Mutations identified by this assay were confirmed by Sanger sequencing.…”

Clinical utility gene card for: Maturity-onset diabetes of the young

“…10,11 NGS allows the simultaneous testing of all known genetic subtypes of MODY (including the rare genetic forms described in section 2.3) that is not possible by Sanger sequencing/MLPA. It is recommended that mutations identified by NGS are confirmed by a second method.…”

“…10,12 Routine checking of primer-binding sites for SNPs is essential (https://secure.ngrl.org.uk/SNPCheck/snpcheck.htm). This is particularly important in the context of predictive genetic testing; a repeat test with an alternative primer is recommended for patients where the familial mutation is not detected and a SNP within a primer-binding site is identified by the SNP checker tool.…”

Comprehensive screening shows that mutations in the known syndromic genes are rare in individuals presenting with hyperinsulinaemic hypoglycaemia

“…The targeted analysis of a gene is usually only performed when there is a clinical suspicion of a specific syndrome in an individual and therefore acts to confirm the clinical diagnosis [13]. Consequently the prevalence of mutations in these genes in HH is not known.…”

“…None of these patients had received a clinical diagnosis consistent with a known syndromic form of HH at the time of study. Mutations in the ABCC8, KCNJ11, HADH, HNF4A, HNF1A, GLUD1, GCK and SLC16A1 genes had been excluded in all patients using targeted next generation sequencing [13].…”