C. Thèze

UMD‐CFTR: A database dedicated to CF and CFTR‐related disorders

With the increasing knowledge of cystic fibrosis (CF) and CFTR‐related diseases (CFTR‐RD), the number of sequence variations in the CFTR gene is constantly raising. CF and particularly CFTR‐RD provide a particular challenge because of many unclassified variants and identical genotypes associated with different phenotypes. Using the Universal Mutation Database (UMD®) software we have constructed UMD‐CFTR (freely available at the URL: http://www.umd.be/CFTR/), the first comprehensive relational CFTR database that allows an in‐depth analysis and annotation of all variations identified in individuals whose CFTR genes have been analyzed extensively. The system has been tested on the molecular data from 757 patients (540 CF and 217 CBAVD) including disease‐causing, unclassified, and nonpathogenic alterations (301 different sequence variations) representing 3,973 entries. Tools are provided to assess the pathogenicity of mutations. UMD‐CFTR also offers a number of query tools and graphical views providing instant access to the list of mutations, their frequencies, positions and predicted consequences, or correlations between genotypes, haplotypes, and phenotypes. UMD‐CFTR offers a way to compile not only disease‐causing genotypes but also haplotypes. It will help the CFTR scientific and medical communities to improve sequence variation interpretation, evaluate the putative influence of haplotypes on mutations, and correlate molecular data with phenotypes. Hum Mutat 31:1011–1019, 2010.

Small-scale high-throughput sequencing–based identification of new therapeutic tools in cystic fibrosis

Purpose:Although 97–99% of CFTR mutations have been identified, great efforts must be made to detect yet-unidentified mutations.Methods:We developed a small-scale next-generation sequencing approach for reliably and quickly scanning the entire gene, including noncoding regions, to identify new mutations. We applied this approach to 18 samples from patients suffering from cystic fibrosis (CF) in whom only one mutation had hitherto been identified.Results:Using an in-house bioinformatics pipeline, we could rapidly identify a second disease-causing CFTR mutation for 16 of 18 samples. Of them, c.1680-883A>G was found in three unrelated CF patients. Analysis of minigenes and patients’ transcripts showed that this mutation results in aberrantly spliced transcripts because of the inclusion of a pseudoexon. It is located only three base pairs from the c.1680-886A>G mutation (1811+1.6kbA>G), the fourth most frequent mutation in southwestern Europe. We next tested the effect of antisense oligonucleotides targeting splice sites on these two mutations on pseudoexon skipping. Oligonucleotide transfection resulted in the restoration of the full-length, in-frame CFTR transcript, demonstrating the effect of antisense oligonucleotide-induced pseudoexon skipping in CF.Conclusion:Our data confirm the importance of analyzing noncoding regions to find unidentified mutations, which is essential to designing targeted therapeutic approaches.Genet Med 17 10, 796–806.

A Classification Model Relative to Splicing for Variants of Unknown Clinical Significance: Application to the CFTR Gene

Molecular diagnosis of cystic fibrosis and cystic fibrosis transmembrane regulator (CFTR)‐related disorders led to the worldwide identification of nearly 1,900 sequence variations in the CFTR gene that consist mainly of private point mutations and small insertions/deletions. Establishing their effect on the function of the encoded protein and therefore their involvement in the disease is still challenging and directly impacts genetic counseling. In this context, we built a decision tree following the international guidelines for the classification of variants of unknown clinical significance (VUCS) in the CFTR gene specifically focused on their consequences on splicing. We applied general and specific criteria, including comprehensive review of literature and databases, familial genetics data, and thorough in silico studies. This model was tested on 15 intronic and exonic VUCS identified in our cohort. Six variants were classified as probably nonpathogenic considering their impact on splicing and eight as probably pathogenic, which include two apparent missense mutations. We assessed the validity of our method by performing minigenes studies and confirmed that 93% (14/15) were correctly classified. We provide in this study a high‐performance method that can play a full role in interpreting the results of molecular diagnosis in emergency context, when functional studies are not achievable.

A novel double deletion underscores the importance of characterizing end points of the CFTR large rearrangements

Large genomic rearrangements in patients with cystic fibrosis (CF) account for up to 16–24% of CF alleles negative for point mutations in European populations. Herein, we identified a new large rearrangement removing exon 19 in a young CF patient, who hitherto harbored only the F508del mutation. By using LightCycler technology, we successfully and rapidly delineated the deletion end points by determining the relative copy number of a set CFTR sequence from introns 18 to 19. Fine mapping of the sequences bordering its break points was achieved using direct sequencing. We reported the first complex CFTR rearrangement containing two successive deletion events putatively linked. We evidenced the presence of short direct repeats in the vicinity of the deletions suggesting a possible replication slippage model. In this report, we also discussed the putative molecular mechanism and consequences of this complex gene rearrangement, unprecedented in CF. This complex deletion illustrates the importance of delineating the genomic rearrangement to improve our knowledge of the CFTR mutational spectrum and to better understand the molecular mechanism controlling the CFTR expression.

CFTR-France, a national relational patient database for sharing genetic and phenotypic data associated with rare CFTR variants

Most of the 2,000 variants identified in the CFTR (cystic fibrosis transmembrane regulator) gene are rare or private. Their interpretation is hampered by the lack of available data and resources, making patient care and genetic counseling challenging. We developed a patient‐based database dedicated to the annotations of rare CFTR variants in the context of their cis‐ and trans‐allelic combinations. Based on almost 30 years of experience of CFTR testing, CFTR‐France (https://cftr.iurc.montp.inserm.fr/cftr) currently compiles 16,819 variant records from 4,615 individuals with cystic fibrosis (CF) or CFTR‐RD (related disorders), fetuses with ultrasound bowel anomalies, newborns awaiting clinical diagnosis, and asymptomatic compound heterozygotes. For each of the 736 different variants reported in the database, patient characteristics and genetic information (other variations in cis or in trans) have been thoroughly checked by a dedicated curator. Combining updated clinical, epidemiological, in silico, or in vitro functional data helps to the interpretation of unclassified and the reassessment of misclassified variants. This comprehensive CFTR database is now an invaluable tool for diagnostic laboratories gathering information on rare variants, especially in the context of genetic counseling, prenatal and preimplantation genetic diagnosis. CFTR‐France is thus highly complementary to the international database CFTR2 focused so far on the most common CF‐causing alleles.

Banques de données de mutations : enjeux et perspectives pour les maladies génétiques orphelines

New technologies, which constantly become available for mutation detection and gene analysis, have contributed to an exponential rate of discovery of disease genes and variation in the human genome. The task of collecting and documenting this enormous amount of data in genetic databases represents a major challenge for the future of biological and medical science. The Locus Specific Databases (LSDBs) are so far the most efficient mutation databases. This review presents the main types of databases available for the analysis of mutations responsible for genetic disorders, as well as open perspectives for new therapeutic research or challenges for future medicine. Accurate and exhaustive collection of variations in human genomes will be crucial for research and personalized delivery of healthcare.

4 Valuable collaboration between a molecular CFTR database and a national CF registry: the French experience

4 Valuable collaboration between a molecular CFTR database and a national CF registry: the French experience C. Bareil, L. Lemonnier, C. Dehillotte, V. Colomb-Jung, C. Theze, M.-P. Audrezet, C. Ferec, T. Bienvenu, E. Girodon, P. Fanen, C. Mekki, E. Bieth, V. Gaston, P. Fergelot, M.-P. Reboul, A. Kitzis, G. Lalau, A. Pagin, M.-C. Malinge, C. Raynal, M. Claustres. CHRU de Montpellier, Laboratoire de Genetique Moleculaire, Montpellier, France; Association Vaincre La Mucoviscidose, Paris, France; CHRU Brest, Laboratoire de Genetique Moleculaire, Brest, France; Hopital Cochin, APHP, Service de Genetique et Biologie Moleculaires, Paris, France; GH Henri Mondor, Departement de Genetique, Creteil, France; CHRU de Toulouse, Service de Genetique Medicale, Toulouse, France; Hopital Pellegrin – CHU de Bordeaux, Laboratoire de Genetique Moleculaire, Bordeaux, France; CHU de Poitiers, Service de Genetique, Poitiers, France; CHRU de Lille, Service de Toxicologie et Genopathies, Lille, France; CHU Angers, UF de Genetique Moleculaire – Departement de Biochimie Genetique, Angers, France In 2013 the French CF Registry and CFTR-France database managers started collaborating to address the limitations of each base, due to the lack of genetics and clinical data cross comparison. The aim was to check and update clinical data in CFTR-France and genetic data in the Registry. Records from the two databases were compared using name, date of birth, gender, sex and mutations. Matched and unmatched records were identified. Discrepancies were checked and confirmed by the laboratories and then sent to the CF centres. Comparison of 8807 patients in the Registry and 4617 in CFTR-France identified 1924 full match and 321 partially matched records. Molecular laboratories confirmations added 216 full matches. The remaining 105 patients still need confirmation by laboratories and CF centres. Among the 321 patients, personal data and/or genotype discrepancies were identified for respectively 70 and 129 patients. This database crossing allowed 110 genotypes to be corrected/completed in the Registry, which is of major interest. Indeed, if those incorrect data are also present in the CF centre medical files, they can impact familial genetic counselling and impair patients’ access to optimal mutation targeted therapies. Clinical data provided by the Registry are currently being analysed to complete the CFTR-France phenotypic status of patients. In-depth analysis of these data allows patients to be re-classified in different phenotypic groups (CF, CBAVD, isolated bronchiectasis or pancreatitis) and genotype/phenotype relationships to be refined, in order to better manage rare variants interpretation, medical care strategy and genetic counselling to families.

WS17.2 Identification of CF mutations in deep intronic regions: Design of antisense oligonucleotides for a targeted therapeutic approach

Considering that the extensive study of the CFTR gene classically performed in molecular diagnosis does not detect all disease-causing mutations, we previously developed an approach for a complete resequencing of the CFTR locus to search for mutations deeply located in introns (Bonini et al. Genet Med, 2015). After identifying candidate intronic mutations, we now aim to restore full-length CFTR transcripts by using antisense oligonucleotides also named Target Site Blockers (TSB). DNA from 15 patients with only one CF mutation were collected through a national collaborative study. Enrichments of the CFTR locus (250 kb) by long-range PCR or targeted capture were sequenced using 454 GS Junior and MiSeq Illumina platforms. TSB (Exiqon) were specifically designed for the deleterious variants. Out of 200 variations detected, our in-house pipeline pointed out 10 intronic variations, per DNA in average. In silico analysis tools predicted that 13 variants (for the 15 patients) had a deleterious effect on CFTR splicing by promoting inclusion of pseudoexons. TSB were tested whether the splicing defect was confirmed. For instance, TSB used on bronchial and primary nasal cells transfected with minigene constructs, significantly restored the full-length CFTR transcript for the well-known mutation c.1680–886A>G and a new identified c.1680–883A>G. Two new mutations in introns 18 and 23 are being tested. Finally, our massively parallel sequencing strategy lead to the identification of new CF-causing mutations in introns. Our findings also demonstrate the efficiency of antisense oligonucleotides for a targeted therapeutic for cystic fibrosis. Work supported by Vaincre La Mucoviscidose.

5* Assessing the impact of unclassified variants on splicing of CFTR mRNA: in silico predictions versus ex vivo assays

5* Assessing the impact of unclassified variants on splicing of CFTR mRNA: in silico predictions versus ex vivo assays C. Raynal1,2,3, M. Taulan2,3, V. Viart2,3, C. Theze2,3, J. Miro2,3, S. TufferyGiraud2,3, M. Claustres1,2,3, M. des Georges1,3. 1CHU Montpellier, Laboratoire de Genetique des Maladies Rares, Montpellier, France; 2Universite Montpellier 1, Montpellier, France; 3INSERM − U827, Montpellier, France