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. 2016 Mar 22:11:26.
doi: 10.1186/s13023-016-0408-0.

Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing

Nadège Calmels  1 , Géraldine Greff  2 , Cathy Obringer  3 , Nadine Kempf  2 , Claire Gasnier  2 , Julien Tarabeux  2 , Marguerite Miguet  2 , Geneviève Baujat  4 , Didier Bessis  5 , Patricia Bretones  6 , Anne Cavau  7 , Béatrice Digeon  8 , Martine Doco-Fenzy  9 , Bérénice Doray  10 , François Feillet  11 , Jesus Gardeazabal  12 , Blanca Gener  13 , Sophie Julia  14 , Isabel Llano-Rivas  13 , Artur Mazur  15 , Caroline Michot  16 , Florence Renaldo-Robin  17 , Massimiliano Rossi  18   19 , Pascal Sabouraud  20 , Boris Keren  21   22 , Christel Depienne  21   22 , Jean Muller  2   3 , Jean-Louis Mandel  2 , Vincent Laugel  3   23
Affiliations

Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing

Nadège Calmels et al. Orphanet J Rare Dis. .

Abstract

Background: 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). 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).

Methods: Our 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).

Results: We 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.

Conclusions: Our 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.

Keywords: Cockayne syndrome; ERCC2; ERCC3; ERCC5; ERCC6; ERCC8; NER; NGS; POLH; xeroderma pigmentosum.

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