Abstract
BackgroundDeficient nucleotide excision repair (NER) activity causes a variety of autosomal recessive diseases including xeroderma pigmentosum (XP) a disorder which pre-disposes to skin cancer, and the severe multisystem condition known as Cockayne syndrome (CS). In view of the clinical overlap between NER-related disorders, as well as the existence of multiple phenotypes and the numerous genes involved, we developed a new diagnostic approach based on the enrichment of 16 NER-related genes by multiplex amplification coupled with next-generation sequencing (NGS).MethodsOur test cohort consisted of 11 DNA samples, all with known mutations and/or non pathogenic SNPs in two of the tested genes. We then used the same technique to analyse samples from a prospective cohort of 40 patients. Multiplex amplification and sequencing were performed using AmpliSeq protocol on the Ion Torrent PGM (Life Technologies).ResultsWe identified causative mutations in 17 out of the 40 patients (43 %). Four patients showed biallelic mutations in the ERCC6(CSB) gene, five in the ERCC8(CSA) gene: most of them had classical CS features but some had very mild and incomplete phenotypes. A small cohort of 4 unrelated classic XP patients from the Basque country (Northern Spain) revealed a common splicing mutation in POLH (XP-variant), demonstrating a new founder effect in this population. Interestingly, our results also found ERCC2(XPD), ERCC3(XPB) or ERCC5(XPG) mutations in two cases of UV-sensitive syndrome and in two cases with mixed XP/CS phenotypes.ConclusionsOur study confirms that NGS is an efficient technique for the analysis of NER-related disorders on a molecular level. It is particularly useful for phenotypes with combined features or unusually mild symptoms. Targeted NGS used in conjunction with DNA repair functional tests and precise clinical evaluation permits rapid and cost-effective diagnosis in patients with NER-defects.Electronic supplementary materialThe online version of this article (doi:10.1186/s13023-016-0408-0) contains supplementary material, which is available to authorized users.
Highlights
Deficient nucleotide excision repair (NER) activity causes a variety of autosomal recessive diseases including xeroderma pigmentosum (XP) a disorder which pre-disposes to skin cancer, and the severe multisystem condition known as Cockayne syndrome (CS)
We describe our findings, based on the enrichment of 16 genes of the NER pathway by multiplex amplification coupled with next-generation sequencing (NGS)
We chose a multiplex amplification approach coupled with NGS to focus on genomic sequencing of all NER genes known to be involved in human diseases at the time the study was designed, as well as on their direct interactors (Table 2)
Summary
Deficient nucleotide excision repair (NER) activity causes a variety of autosomal recessive diseases including xeroderma pigmentosum (XP) a disorder which pre-disposes to skin cancer, and the severe multisystem condition known as Cockayne syndrome (CS). Trichothiodystrophy (Orpha number 33364) is a very rare heterogeneous group of disorders characterized by brittle hair with low-sulfur content associated with neurodevelopmental impairment. The spectrum of symptoms observed in TTD patients ranges from mild forms of the disease, characterized by normal development with brittle hair and scaling skin only, to very severe cases, characterized by high mortality at a young age combined with severe neurodevelopmental defects. Cockayne syndrome (Orpha number 191) is a multisystem disorder characterized by intellectual disability, microcephaly, severe growth failure, sensory impairment, peripheral neuropathy and cutaneous photosensitivity [7].
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