title: Uncommon nucleotide excision repair phenotypes revealed by targeted high-throughput sequencing.
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.
authors.affiliation: Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France. nadege.calmels@chru-strasbourg.fr.
authors.forename: Nadège
authors.initials: N
authors.lastname: Calmels
authors.affiliation: Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France.
authors.forename: Géraldine
authors.initials: G
authors.lastname: Greff
authors.affiliation: Laboratoire de Génétique Médicale - INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de médecine de Strasbourg, 11 rue Humann, Strasbourg, France.
authors.forename: Cathy
authors.initials: C
authors.lastname: Obringer
authors.affiliation: Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France.
authors.forename: Nadine
authors.initials: N
authors.lastname: Kempf
authors.affiliation: Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Gasnier
authors.affiliation: Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Tarabeux
authors.affiliation: Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France.
authors.forename: Marguerite
authors.initials: M
authors.lastname: Miguet
authors.affiliation: Centre de Référence Maladies Osseuses Constitutionnelles, Département de Génétique, Hôpital Necker-Enfants malades, Paris, France.
authors.forename: Geneviève
authors.initials: G
authors.lastname: Baujat
authors.affiliation: Département de Dermatologie, Hôpital Saint-Éloi, 80 avenue Augustin-Fliche, 34295, Montpellier, France.
authors.forename: Didier
authors.initials: D
authors.lastname: Bessis
authors.affiliation: Service d'Endocrinologie Pédiatrique, diabète et maladies héréditaires du métabolisme, Hôpital Femme Mère enfant, GH Est, 59 boulevard Pinel, Bron, France.
authors.forename: Patricia
authors.initials: P
authors.lastname: Bretones
authors.affiliation: Service de Pédiatrie Générale, Hôpital Necker-Enfants malades, Paris, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Cavau
authors.affiliation: Service de Pédiatrie, CHU de Reims, Hôpital Maison Blanche, 45 rue Cognacq-Jay, Reims, France.
authors.forename: Béatrice
authors.initials: B
authors.lastname: Digeon
authors.affiliation: Service de Génétique et Biologie de la Reproduction CHU de Reims, Hôpital Maison Blanche, 45 rue Cognacq-Jay, Reims, France.
authors.forename: Martine
authors.initials: M
authors.lastname: Doco-Fenzy
authors.affiliation: Service de Génétique, CHU La Réunion, Hôpital Félix Guyon, Allée des Topazes, Saint-Denis, France.
authors.forename: Bérénice
authors.initials: B
authors.lastname: Doray
authors.affiliation: Centre de Référence des Maladies Héréditaires du Métabolisme, Service de Médecine Infantile, INSERM NGERE 954, CHU Brabois Enfants, Allée du Morvan, Vandœuvre les Nancy, France.
authors.forename: François
authors.initials: F
authors.lastname: Feillet
authors.affiliation: Servicio de Dermatología, Cruces University Hospital, BioCruces Health Research Institute, Baracaldo Vizcaya, Spain.
authors.forename: Jesus
authors.initials: J
authors.lastname: Gardeazabal
authors.affiliation: Servicio de Genética, Cruces University Hospital, BioCruces Health Research Institute, Baracaldo Vizcaya, Spain.
authors.forename: Blanca
authors.initials: B
authors.lastname: Gener
authors.affiliation: Service de Génétique Médicale, CHU de Toulouse - Hôpital Purpan, Place du Docteur Baylac, Toulouse, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Julia
authors.affiliation: Servicio de Genética, Cruces University Hospital, BioCruces Health Research Institute, Baracaldo Vizcaya, Spain.
authors.forename: Isabel
authors.initials: I
authors.lastname: Llano-Rivas
authors.affiliation: Department of Pediatrics, Pediatric Endocrinology and Diabetes, Faculty of Medicine, University of Rzeszów, Rzeszów, Poland.
authors.forename: Artur
authors.initials: A
authors.lastname: Mazur
authors.affiliation: Service de Génétique Médicale, Hôpital Necker Enfants-Malades, 24 Bd du Montparnasse, Paris, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Michot
authors.affiliation: Service de Neurologie, Hôpital Robert Debré, 48 boulevard Serurier, Paris, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Renaldo-Robin
authors.affiliation: Centre de Référence des Anomalies du Développement, Service de Génétique, Hospices Civils de Lyon, Lyon, France.|INSERM U1028; CNRS UMR5292; CNRL TIGER Team, Lyon, France.
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Rossi
authors.affiliation: Service de Pédiatrie A - Neurologie pédiatrique, CHU de Reims - American Memorial Hospital, 47 rue Cognacq Jay, Reims, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Sabouraud
authors.affiliation: AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France.|Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, UM 75, U 1127, UMR 7225, ICM, F-75013, Paris, France.
authors.forename: Boris
authors.initials: B
authors.lastname: Keren
authors.affiliation: AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, F-75013, Paris, France.|Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, UM 75, U 1127, UMR 7225, ICM, F-75013, Paris, France.
authors.forename: Christel
authors.initials: C
authors.lastname: Depienne
authors.affiliation: Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France.|Laboratoire de Génétique Médicale - INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de médecine de Strasbourg, 11 rue Humann, Strasbourg, France.
authors.forename: Jean
authors.initials: J
authors.lastname: Muller
authors.affiliation: Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 1 place de l'hôpital, Strasbourg, France.
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Mandel
authors.affiliation: Laboratoire de Génétique Médicale - INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de médecine de Strasbourg, 11 rue Humann, Strasbourg, France.|Service de Pédiatrie, Hôpitaux Universitaires de Strasbourg, 1 avenue Molière, Strasbourg, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Laugel
mesh_terms: D003057:Cockayne Syndrome / Q000235:genetics; D004265:DNA Helicases / Q000235:genetics; D004260:DNA Repair / Q000235:genetics*; D045643:DNA Repair Enzymes / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D004259:DNA-Directed DNA Polymerase / Q000235:genetics; D004720:Endonucleases / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics; D010641:Phenotype; D000075223:Poly-ADP-Ribose Binding Proteins; D014157:Transcription Factors / Q000235:genetics; D051759:Xeroderma Pigmentosum Group D Protein / Q000235:genetics; D000099250:DNA Excision Repair Protein ERCC-5; D000099270:Y-Family DNA Polymerases
chemical_list: D004265:DNA Helicases; D045643:DNA Repair Enzymes; D004268:DNA-Binding Proteins; D004259:DNA-Directed DNA Polymerase; D004720:Endonucleases; D009687:Nuclear Proteins; D000075223:Poly-ADP-Ribose Binding Proteins; D014157:Transcription Factors; D051759:Xeroderma Pigmentosum Group D Protein; D000099250:DNA Excision Repair Protein ERCC-5; C095472:ERCC8 protein, human; C112338:Rad30 protein; D000099270:Y-Family DNA Polymerases; C078673:ERCC6 protein, human; C497292:ERCC2 protein, human
keywords: Cockayne syndrome; ERCC2; ERCC3; ERCC5; ERCC6; ERCC8; NER; NGS; POLH; xeroderma pigmentosum