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Moore AR, Yu J, Pei Y, Cheng EWY, Taylor Tavares AL, Walker WT, Thomas NS, Kamath A, Ibitoye R, Josifova D, Wilsdon A, Ross A, Calder AD, Offiah AC, Wilkie AOM, Taylor JC, Pagnamenta AT. Use of genome sequencing to hunt for cryptic second-hit variants: analysis of 31 cases recruited to the 100 000 Genomes Project. J Med Genet 2023; 60:1235-1244. [PMID: 37558402 PMCID: PMC10715503 DOI: 10.1136/jmg-2023-109362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Current clinical testing methods used to uncover the genetic basis of rare disease have inherent limitations, which can lead to causative pathogenic variants being missed. Within the rare disease arm of the 100 000 Genomes Project (100kGP), families were recruited under the clinical indication 'single autosomal recessive mutation in rare disease'. These participants presented with strong clinical suspicion for a specific autosomal recessive disorder, but only one suspected pathogenic variant had been identified through standard-of-care testing. Whole genome sequencing (WGS) aimed to identify cryptic 'second-hit' variants. METHODS To investigate the 31 families with available data that remained unsolved following formal review within the 100kGP, SVRare was used to aggregate structural variants present in <1% of 100kGP participants. Small variants were assessed using population allele frequency data and SpliceAI. Literature searches and publicly available online tools were used for further annotation of pathogenicity. RESULTS Using these strategies, 8/31 cases were solved, increasing the overall diagnostic yield of this cohort from 10/41 (24.4%) to 18/41 (43.9%). Exemplar cases include a patient with cystic fibrosis harbouring a novel exonic LINE1 insertion in CFTR and a patient with generalised arterial calcification of infancy with complex interlinked duplications involving exons 2-6 of ENPP1. Although ambiguous by short-read WGS, the ENPP1 variant structure was resolved using optical genome mapping and RNA analysis. CONCLUSION Systematic examination of cryptic variants across a multi-disease cohort successfully identifies additional pathogenic variants. WGS data analysis in autosomal recessive rare disease should consider complex structural and small intronic variants as potentially pathogenic second hits.
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Affiliation(s)
- A Rachel Moore
- Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jing Yu
- Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Yang Pei
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | | | - Woolf T Walker
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- PCD Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - N Simon Thomas
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Arveen Kamath
- All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Rita Ibitoye
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, London, UK
| | - Dragana Josifova
- Department of Clinical Genetics, Guy's and St Thomas' Hospitals NHS Trust, London, UK
| | - Anna Wilsdon
- Clinical Genetics, Nottingham City Hospital, Nottingham, UK
| | - Alison Ross
- Clinical Genetics, NHS Grampian, Aberdeen, UK
| | - Alistair D Calder
- Radiology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Amaka C Offiah
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
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Masson E, Ewers M, Paliwal S, Kume K, Scotet V, Cooper DN, Rebours V, Buscail L, Rouault K, Abrantes A, Aguilera Munoz L, Albouys J, Alric L, Amiot X, Archambeaud I, Audiau S, Bastide L, Baudon J, Bellaiche G, Bellon S, Bertrand V, Bideau K, Billiemaz K, Billioud C, Bonnefoy S, Borderon C, Bournet B, Breton E, Brugel M, Buscail L, Cadiot G, Camus M, Carpentier-Pourquier M, Chamouard P, Chaput U, Chen JM, Cholet F, Ciocan DM, Clavel C, Coffin B, Coimet-Berger L, Cosconea S, Creveaux I, Culetto A, Daboussi O, De Mestier L, Degand T, D'engremont C, Denis B, Dermine S, Drouet D'Aubigny A, Enaud R, Fabre A, Férec C, Gargot D, Gelsi E, Gentilcore E, Gincul R, Ginglinger-Favre E, Giovannini M, Gomercic C, Gondran H, Grainville T, Grandval P, Grasset D, Grimaldi S, Grimbert S, Hagege H, Heissat S, Hentic O, Herber-Mayne A, Hervouet M, Hoibian S, Jacques J, Jais B, Kaassis M, Koch S, Lacaze E, Lacroute J, Lamireau T, Laurent L, Le Guillou X, Le Rhun M, Leblanc S, Levy P, Lievre A, Lorenzo D, Maire F, Marcel K, Masson E, Mauillon J, Morgant S, Moussata D, Muller N, Nambot S, Napoleon B, Olivier A, Pagenault M, Pelletier AL, Pennec O, Pinard F, Pioche M, Prost B, Queneherve L, Rebours V, Reboux N, Rekik S, Riachi G, Rohmer B, Roquelaure B, Rosa Hezode I, Rostain F, Saurin JC, Servais L, Stan-Iuga R, Subtil C, Tanneche J, Texier C, Thomassin L, Tougeron D, Vuitton L, Wallenhorst T, Wangerme M, Zanaldi H, Zerbib F, Bhaskar S, Kikuta K, Rao GV, Hamada S, Reddy DN, Masamune A, Chandak GR, Witt H, Férec C, Chen JM. The PRSS3P2 and TRY7 deletion copy number variant modifies risk for chronic pancreatitis. Pancreatology 2023; 23:48-56. [PMID: 36517351 DOI: 10.1016/j.pan.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND PRSS1 and PRSS2 constitute the only functional copies of a tandemly-arranged five-trypsinogen-gene cluster (i.e., PRSS1, PRSS3P1, PRSS3P2, TRY7 and PRSS2) on chromosome 7q35. Variants in PRSS1 and PRSS2, including missense and copy number variants (CNVs), have been reported to predispose to or protect against chronic pancreatitis (CP). We wondered whether a common trypsinogen pseudogene deletion CNV (that removes two of the three trypsinogen pseudogenes, PRSS3P2 and TRY7) might be associated with CP causation/predisposition. METHODS We analyzed the common PRSS3P2 and TRY7 deletion CNV in a total of 1536 CP patients and 3506 controls from France, Germany, India and Japan by means of quantitative fluorescent multiplex polymerase chain reaction. RESULTS We demonstrated that the deletion CNV variant was associated with a protective effect against CP in the French, German and Japanese cohorts whilst a trend toward the same association was noted in the Indian cohort. Meta-analysis under a dominant model yielded a pooled odds ratio (OR) of 0.68 (95% confidence interval (CI) 0.52-0.89; p = 0.005) whereas an allele-based meta-analysis yielded a pooled OR of 0.84 (95% CI 0.77-0.92; p = 0.0001). This protective effect is explicable by reference to the recent finding that the still functional PRSS3P2/TRY7 pseudogene enhancers upregulate pancreatic PRSS2 expression. CONCLUSIONS The common PRSS3P2 and TRY7 deletion CNV was associated with a reduced risk for CP. This finding provides additional support for the emerging view that dysregulated PRSS2 expression represents a discrete mechanism underlying CP predisposition or protection.
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Affiliation(s)
- Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France; Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Maren Ewers
- Paediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany
| | - Sumit Paliwal
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Kiyoshi Kume
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Virginie Scotet
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Vinciane Rebours
- Pancreatology and Digestive Oncology Department, Beaujon Hospital, APHP - Clichy, Université Paris Cité, Paris, France
| | - Louis Buscail
- Department of Gastroenterology and Pancreatology, CHU Rangueil and University of Toulouse, Toulouse, France
| | - Karen Rouault
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France; Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Marc Hervouet
- Hôpital d'instruction des Armées Percy, Clamart, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Seema Bhaskar
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Kazuhiro Kikuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Shin Hamada
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Giriraj Ratan Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Heiko Witt
- Paediatric Nutritional Medicine & Else Kröner-Fresenius-Centre for Nutritional Medicine (EKFZ), Technical University Munich (TUM), Freising, Germany
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France.
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Woodward AA, Urbanowicz RJ, Naj AC, Moore JH. Genetic heterogeneity: Challenges, impacts, and methods through an associative lens. Genet Epidemiol 2022; 46:555-571. [PMID: 35924480 PMCID: PMC9669229 DOI: 10.1002/gepi.22497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023]
Abstract
Genetic heterogeneity describes the occurrence of the same or similar phenotypes through different genetic mechanisms in different individuals. Robustly characterizing and accounting for genetic heterogeneity is crucial to pursuing the goals of precision medicine, for discovering novel disease biomarkers, and for identifying targets for treatments. Failure to account for genetic heterogeneity may lead to missed associations and incorrect inferences. Thus, it is critical to review the impact of genetic heterogeneity on the design and analysis of population level genetic studies, aspects that are often overlooked in the literature. In this review, we first contextualize our approach to genetic heterogeneity by proposing a high-level categorization of heterogeneity into "feature," "outcome," and "associative" heterogeneity, drawing on perspectives from epidemiology and machine learning to illustrate distinctions between them. We highlight the unique nature of genetic heterogeneity as a heterogeneous pattern of association that warrants specific methodological considerations. We then focus on the challenges that preclude effective detection and characterization of genetic heterogeneity across a variety of epidemiological contexts. Finally, we discuss systems heterogeneity as an integrated approach to using genetic and other high-dimensional multi-omic data in complex disease research.
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Affiliation(s)
- Alexa A. Woodward
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ryan J. Urbanowicz
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jason H. Moore
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
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Dilernia D, Amin P, Flores J, Stecenko A, Sorscher E. Mutation profiling of the c.1521_1523delCTT (p.Phe508del, F508del) CFTR allele using haplotype-resolved long-read next generation sequencing. Hum Mutat 2022; 43:595-603. [PMID: 35170824 DOI: 10.1002/humu.24352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022]
Abstract
Current approaches to characterize the mutational profile of the cystic fibrosis transmembrane conductance regulator (CFTR) gene are based on targeted mutation analysis (TMA) or whole gene studies derived from short-read next generation sequencing (NGS). However, these methods lack phasing capability which, in certain scenarios, can provide clinically valuable information. In the present work, we performed near-full length CFTR using Single-Molecule Real-Time Sequencing to produce haplotype-resolved data from both homozygous and heterozygous individuals for mutation c.1521_1523delCTT (p.Phe508del, F508del). This approach utilizes target enrichment of the CFTR gene using biotinylated probes, facilitates multiplexing samples in the same sequencing run, and utilizes fully-automated bioinformatics pipelines for error correction and variant calling. We show a remarkable conservation of F508del haplotype, consistent with the single gene founder effect, as well as diverse mutational profiles in non-F508del alleles. By the same method, 105 single nucleotide polymorphisms (SNPs) exhibiting invariant linkage to F508del CFTR (which better define the founder haplotype) were identified. High level homology between F508del sequences derived from heterozygotes, and those obtained from homozygous individuals, demonstrate accuracy of this method to produce haplotype resolved sequencing. The studies provide a new diagnostic technology for detailed analysis of complex CFTR alleles linked to disease severity. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Dario Dilernia
- Department of Pathology, School of Medicine, Emory University.,Emory Vaccine Center, Emory University
| | | | - Julie Flores
- Department of Pediatrics, School of Medicine, Emory University, and the Emory + Children's Center for Cystic Fibrosis and Airways Disease Research
| | - Arlene Stecenko
- Department of Pediatrics, School of Medicine, Emory University, and the Emory + Children's Center for Cystic Fibrosis and Airways Disease Research
| | - Eric Sorscher
- Department of Pediatrics, School of Medicine, Emory University, and the Emory + Children's Center for Cystic Fibrosis and Airways Disease Research
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Analysis of rearrangements of the CFTR gene in patients from Turkey with CFTR-related disorders: frequent exon 2 deletion. J Hum Genet 2020; 66:315-320. [PMID: 33093640 DOI: 10.1038/s10038-020-00859-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/23/2020] [Accepted: 10/06/2020] [Indexed: 11/09/2022]
Abstract
Cystic fibrosis is a hereditary disease that mostly affects the sweat glands, respiratory system, digestive system, and reproductive system. Many and various types of mutations have been reported in CFTR in different ethnicities and countries/regions. Analysis of CFTR gene rearrangements is recommended in patients with unidentified mutated alleles in CFTR sequencing analysis. We collected MLPA analyses of 527 patients from Turkey who had at least one unidentified mutation in CFTR sequence analysis. Heterozygous/homozygous deletions were detected in the CFTR gene in 49 individuals (9.2%) from 35 families. Twelve different single/multi exon deletions were demonstrated, two of which were not previously reported in the literature. Mutations have previously reported in patients from various regions including Asia, Europe, and Africa, and Turkey is located at a crossroads between them. The most frequent mutation was the exon 2 deletion, accounting for 60%. Moreover, patients with exon 2 deletions, were especially originated from northern Turkey. This finding is valuable in leading and shaping planned screening programs in Turkey. Our study, the most comprehensive study for rearrangement analysis in patients from Tukey, revealed a candidate hotspot region of patients suspected of having CFTR-related disorders from Turkey.
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Paranjapye A, Ruffin M, Harris A, Corvol H. Genetic variation in CFTR and modifier loci may modulate cystic fibrosis disease severity. J Cyst Fibros 2020; 19 Suppl 1:S10-S14. [PMID: 31734115 PMCID: PMC7036019 DOI: 10.1016/j.jcf.2019.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022]
Abstract
In patients with cystic fibrosis (CF), genetic variants within and outside the CFTR locus contribute to the variability of the disease severity. CFTR transcription is tightly regulated by cis-regulatory elements (CREs) that control the three-dimensional structure of the locus, chromatin accessibility and transcription factor recruitment. Variants within these CREs may contribute to the pathophysiology and to the phenotypic heterogeneity by altering CFTR transcript abundance. In addition to the CREs, variants outside the CFTR locus, namely "modifiers genes", may also be associated with the clinical variability. This review addresses variants at the CFTR locus itself and CFTR CREs, together with the outcomes of the latest modifier gene studies with respect to the different CF phenotypes.
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Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University Medical School, 10900 Euclid Avenue, Cleveland, OH, USA
| | - Manon Ruffin
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University Medical School, 10900 Euclid Avenue, Cleveland, OH, USA.
| | - Harriet Corvol
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France; AP-HP, Hôpital Trousseau, Service de Pneumologie Pédiatrique, Paris, France.
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Pierandrei S, Blaconà G, Fabrizzi B, Cimino G, Cirilli N, Caporelli N, Angeloni A, Cipolli M, Lucarelli M. Two novel and correlated CF-causing insertions in the (TG)mTn tract of the CFTR gene. PLoS One 2019; 14:e0222838. [PMID: 31593572 PMCID: PMC6782095 DOI: 10.1371/journal.pone.0222838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/06/2019] [Indexed: 02/05/2023] Open
Abstract
Two novel and related pathogenic variants of the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene were structurally and functionally characterized. These alterations have not been previously described in literature. Two patients with diagnosis of Cystic Fibrosis (CF) based on the presence of one mutated allele, p.Phe508del, pathological sweat test and clinical symptoms were studied. To complete the genotypes of both patients, an extensive genetic and functional analysis of the CFTR gene was performed. Extensive genetic characterization confirmed the presence of p.Phe508del pathogenic variant and revealed, in both patients, the presence of an insertion of part of intron 10 in intron 9 of the CFTR gene, within the (TG)m repeat, with a variable poly-T stretch. The molecular lesions resulted to be very similar in both patients, with only a difference in the number of T in the poly-T stretch. The functional characterization at RNA level revealed a complete anomalous splicing, without exon 10, from the allele with the insertion of both patients. Consequently, the alleles with the insertions are expected not to contribute to the formation of a functional CFTR protein. Molecular and functional features of these alterations are compatible with the definition of novel CF-causing variants of the CFTR gene. This also allowed the completion of the genetic characterization of both patients.
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Affiliation(s)
- Silvia Pierandrei
- Dept. of Mother-Child and Urologic Sciences, Sapienza University of Rome, Rome, Italy
| | - Giovanna Blaconà
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Benedetta Fabrizzi
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Giuseppe Cimino
- Cystic Fibrosis Care Center, Umberto I Hospital, Rome, Italy
| | - Natalia Cirilli
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Nicole Caporelli
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Antonio Angeloni
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Marco Cipolli
- Cystic Fibrosis Care Center, Mother - Child Department, United Hospitals, Ancona, Italy
| | - Marco Lucarelli
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Pasteur Institute Cenci Bolognetti Foundation, Rome, Italy
- * E-mail:
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8
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Atag E, Bas Ikizoglu N, Ergenekon AP, Gokdemir Y, Eralp EE, Ata P, Ersu R, Karakoc F, Karadag B. Novel mutations and deletions in cystic fibrosis in a tertiary cystic fibrosis center in Istanbul. Pediatr Pulmonol 2019; 54:743-750. [PMID: 30938940 DOI: 10.1002/ppul.24299] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 02/02/2019] [Accepted: 02/10/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Cystic fibrosis (CF) genotyping has garnered increased attention since the discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in 1989 led to the identification of over 1700 mutations on chromosome 7. Yet, little is known about the genetic profile of CF patients in Turkey. This study sought to determine the mutation distribution among CF patients seeking care at Marmara University. METHODS Two hundred fifty previously diagnosed CF patients were included in the study. CFTR gene exons 1 to 27 were amplified by a polymerase chain reaction and whole DNA sequencing was performed. Duplications and deletions were investigated by the multiplex ligation-dependent probe amplification (MLPA) technique in patients with one or two unidentified mutations in sequence analysis. RESULTS CFTR mutation analysis revealed 80 mutations and five large deletions were present in our study population. The five most common mutations were (delta) F508 (c.1521-1523delCTT) (28.4%), 1677delTA (c.1545-1546delTA) (6.4%), 2789 + 5G- > A (c.2657 + 5G > A) (5.8%), N1303K (c.3909C > G) (2.4%), and c.2183AA- > G (c.2051-2052delAAinsG) (4.0%). Large deletions were found in 16 patients. Four novel mutations and two novel deletions were detected in this study. CONCLUSIONS We have identified four novel mutations and two novel deletions using next-generation DNA sequencing and the MLPA technique and obtained an overall mutation detection rate of 91.4%. Detection of novel variants in CF patients will assist in genetic counseling and in determining appropriate patients for new therapies.
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Affiliation(s)
- Emine Atag
- Division of Pediatric Pulmonology, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Nilay Bas Ikizoglu
- Division of Pediatric Pulmonology, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Almala Pinar Ergenekon
- Division of Pediatric Pulmonology, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Yasemin Gokdemir
- Division of Pediatric Pulmonology, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Ela Erdem Eralp
- Division of Pediatric Pulmonology, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Pinar Ata
- Department of Medical Genetics, School of Medicine, Marmara University, Istanbul, Turkey
| | - Refika Ersu
- Division of Pediatric Pulmonology, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Fazilet Karakoc
- Division of Pediatric Pulmonology, Faculty of Medicine, Marmara University, Istanbul, Turkey
| | - Bulent Karadag
- Division of Pediatric Pulmonology, Faculty of Medicine, Marmara University, Istanbul, Turkey
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Kerschner JL, Ghosh S, Paranjapye A, Cosme WR, Audrézet MP, Nakakuki M, Ishiguro H, Férec C, Rommens J, Harris A. Screening for Regulatory Variants in 460 kb Encompassing the CFTR Locus in Cystic Fibrosis Patients. J Mol Diagn 2018; 21:70-80. [PMID: 30296588 DOI: 10.1016/j.jmoldx.2018.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/18/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
It is estimated that up to 5% of cystic fibrosis transmembrane conductance regulator (CFTR) pathogenic alleles are unidentified. Some of these errors may lie in noncoding regions of the locus and affect gene expression. To identify regulatory element variants in the CFTR locus, SureSelect targeted enrichment of 460 kb encompassing the gene was optimized to deep sequence genomic DNA from 80 CF patients with an unequivocal clinical diagnosis but only one or no CFTR-coding region pathogenic variants. Bioinformatics tools were used to identify sequence variants and predict their impact, which were then assayed in transient reporter gene luciferase assays. The effect of five variants in the CFTR promoter and four in an intestinal enhancer of the gene were assayed in relevant cell lines. The initial analysis of sequence data revealed previously known CF-causing variants, validating the robustness of the SureSelect design, and showed that 85 of 160 CF alleles were undefined. Of a total 1737 variants revealed across the extended 460-kb CFTR locus, 51 map to known CFTR cis-regulatory elements, and many of these are predicted to alter transcription factor occupancy. Four promoter variants and all those in the intestinal enhancer significantly repress reporter gene activity. These data suggest that CFTR regulatory elements may harbor novel CF disease-causing variants that warrant further investigation, both for genetic screening protocols and functional assays.
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Affiliation(s)
- Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Sujana Ghosh
- Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Wilmel R Cosme
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | | | - Miyuki Nakakuki
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroshi Ishiguro
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Johanna Rommens
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio; Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.
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10
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Claustres M, Thèze C, des Georges M, Baux D, Girodon E, Bienvenu T, Audrezet MP, Dugueperoux I, Férec C, Lalau G, Pagin A, Kitzis A, Thoreau V, Gaston V, Bieth E, Malinge MC, Reboul MP, Fergelot P, Lemonnier L, Mekki C, Fanen P, Bergougnoux A, Sasorith S, Raynal C, Bareil C. CFTR-France, a national relational patient database for sharing genetic and phenotypic data associated with rare CFTR variants. Hum Mutat 2017; 38:1297-1315. [PMID: 28603918 DOI: 10.1002/humu.23276] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/31/2017] [Accepted: 06/04/2017] [Indexed: 11/09/2022]
Abstract
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.
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Affiliation(s)
- Mireille Claustres
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Corinne Thèze
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Marie des Georges
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Emmanuelle Girodon
- Service de Génétique et Biologie Moléculaires, Groupe Hospitalier Cochin-Broca-Hotel Dieu, Paris, France
| | - Thierry Bienvenu
- Service de Génétique et Biologie Moléculaires, Groupe Hospitalier Cochin-Broca-Hotel Dieu, Paris, France
| | - Marie-Pierre Audrezet
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire, Brest, France
| | - Ingrid Dugueperoux
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire, Brest, France
| | - Claude Férec
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire, Brest, France
| | - Guy Lalau
- Centre de Biologie Pathologie Génétique, Centre Hospitalier Régional Universitaire, Lille, France
| | - Adrien Pagin
- Centre de Biologie Pathologie Génétique, Centre Hospitalier Régional Universitaire, Lille, France
| | - Alain Kitzis
- Département de Génétique, Centre Hospitalier Universitaire, Poitiers, France
| | - Vincent Thoreau
- Département de Génétique, Centre Hospitalier Universitaire, Poitiers, France
| | - Véronique Gaston
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Toulouse, France
| | - Eric Bieth
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Toulouse, France
| | - Marie-Claire Malinge
- Département de Biochimie Génétique, Institut de Biologie en Santé, Centre Hospitalier Universitaire, Angers, France
| | - Marie-Pierre Reboul
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Régional Universitaire, Bordeaux, France
| | - Patricia Fergelot
- Laboratoire Maladies Rares, Génétique et Métabolisme, Bordeaux, France
| | - Lydie Lemonnier
- Registre français de la mucoviscidose, Vaincre la Mucoviscidose, Paris, France
| | - Chadia Mekki
- Laboratoire de Génétique, Hôpital Henri Mondor, Créteil, France
| | - Pascale Fanen
- Laboratoire de Génétique, Hôpital Henri Mondor, Créteil, France
| | - Anne Bergougnoux
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Souphatta Sasorith
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Caroline Raynal
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
| | - Corinne Bareil
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire et Université de Montpellier, Montpellier, France
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11
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Abstract
Cystic fibrosis (CF) is the most frequent lethal genetic disorder among Caucasians, but is considered to be a very rare disease in Chinese population. Here, we present an 11-year-old Chinese CF patient with disseminated bronchiectasis and salty sweat, for whom exon sequencing followed by multiplex ligation-dependent probe amplification analysis of the CFTR gene was applied for mutation screening. A homozygous deletion involving exon 20 of CFTR was observed in the patient's genome. Molecular characterization of the breakpoints indicated that both alleles of this locus had an identical novel complex rearrangement (c.3140-454_c.3367+249del931ins13, p.R1048_G1123del), leading to an in-frame removal of 76 amino acid residues in the second transmembrane domains of the CFTR protein. Although a same haplotype containing this complex rearrangement was observed on both of the maternal and paternal alleles, the parents denied any blood relationship as far as they know. Genome-wide homozygosity mapping was performed through SNP microarray and only a single homozygous interval of ~14.1 Mb at chromosome 7 containing the CFTR gene was observed, indicating the possible origin of the deletion from a common ancestor many generations ago. This study expands the mutation spectrum of CFTR in patients of Chinese origin and further emphasizes the necessity of MLPA analysis in mutation screening for CF patients.
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12
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Lefterova MI, Shen P, Odegaard JI, Fung E, Chiang T, Peng G, Davis RW, Wang W, Kharrazi M, Schrijver I, Scharfe C. Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis. J Mol Diagn 2016; 18:267-82. [PMID: 26847993 DOI: 10.1016/j.jmoldx.2015.11.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 10/21/2015] [Accepted: 11/19/2015] [Indexed: 12/19/2022] Open
Abstract
Newborn screening for cystic fibrosis enables early detection and management of this debilitating genetic disease. Implementing comprehensive CFTR analysis using Sanger sequencing as a component of confirmatory testing of all screen-positive newborns has remained impractical due to relatively lengthy turnaround times and high cost. Here, we describe CFseq, a highly sensitive, specific, rapid (<3 days), and cost-effective assay for comprehensive CFTR gene analysis from dried blood spots, the common newborn screening specimen. The unique design of CFseq integrates optimized dried blood spot sample processing, a novel multiplex amplification method from as little as 1 ng of genomic DNA, and multiplex next-generation sequencing of 96 samples in a single run to detect all relevant CFTR mutation types. Sequence data analysis utilizes publicly available software supplemented by an expert-curated compendium of >2000 CFTR variants. Validation studies across 190 dried blood spots demonstrated 100% sensitivity and a positive predictive value of 100% for single-nucleotide variants and insertions and deletions and complete concordance across the polymorphic poly-TG and consecutive poly-T tracts. Additionally, we accurately detected both a known exon 2,3 deletion and a previously undetected exon 22,23 deletion. CFseq is thus able to replace all existing CFTR molecular assays with a single robust, definitive assay at significant cost and time savings and could be adapted to high-throughput screening of other inherited conditions.
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Affiliation(s)
- Martina I Lefterova
- Department of Pathology, Stanford University Medical Center, Stanford, California
| | - Peidong Shen
- Stanford Genome Technology Center, Stanford University, Palo Alto, California
| | - Justin I Odegaard
- Department of Pathology, Stanford University Medical Center, Stanford, California
| | - Eula Fung
- Department of Pathology, Stanford University Medical Center, Stanford, California
| | - Tsoyu Chiang
- Department of Pathology, Stanford University Medical Center, Stanford, California
| | - Gang Peng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ronald W Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, California
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Martin Kharrazi
- California Department of Public Health, Environmental Health Investigations Branch, Richmond, California
| | - Iris Schrijver
- Department of Pathology, Stanford University Medical Center, Stanford, California; Department of Pediatrics, Stanford University Medical Center, Stanford, California
| | - Curt Scharfe
- Department of Pathology, Stanford University Medical Center, Stanford, California; Stanford Genome Technology Center, Stanford University, Palo Alto, California.
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13
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Identifying Highly Penetrant Disease Causal Mutations Using Next Generation Sequencing: Guide to Whole Process. BIOMED RESEARCH INTERNATIONAL 2015; 2015:923491. [PMID: 26106619 PMCID: PMC4461748 DOI: 10.1155/2015/923491] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/17/2015] [Indexed: 01/10/2023]
Abstract
Recent technological advances have created challenges for geneticists and a need to adapt to a wide range of new bioinformatics tools and an expanding wealth of publicly available data (e.g., mutation databases, and software). This wide range of methods and a diversity of file formats used in sequence analysis is a significant issue, with a considerable amount of time spent before anyone can even attempt to analyse the genetic basis of human disorders. Another point to consider that is although many possess “just enough” knowledge to analyse their data, they do not make full use of the tools and databases that are available and also do not fully understand how their data was created. The primary aim of this review is to document some of the key approaches and provide an analysis schema to make the analysis process more efficient and reliable in the context of discovering highly penetrant causal mutations/genes. This review will also compare the methods used to identify highly penetrant variants when data is obtained from consanguineous individuals as opposed to nonconsanguineous; and when Mendelian disorders are analysed as opposed to common-complex disorders.
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14
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Characterization of 26 deletion CNVs reveals the frequent occurrence of micro-mutations within the breakpoint-flanking regions and frequent repair of double-strand breaks by templated insertions derived from remote genomic regions. Hum Genet 2015; 134:589-603. [DOI: 10.1007/s00439-015-1539-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
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15
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Aygun N. Correlations between long inverted repeat (LIR) features, deletion size and distance from breakpoint in human gross gene deletions. Sci Rep 2015; 5:8300. [PMID: 25657065 PMCID: PMC4319165 DOI: 10.1038/srep08300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/14/2015] [Indexed: 11/09/2022] Open
Abstract
Long inverted repeats (LIRs) have been shown to induce genomic deletions in yeast. In this study, LIRs were investigated within ±10 kb spanning each breakpoint from 109 human gross deletions, using Inverted Repeat Finder (IRF) software. LIR number was significantly higher at the breakpoint regions, than in control segments (P < 0.001). In addition, it was found that strong correlation between 5' and 3' LIR numbers, suggesting contribution to DNA sequence evolution (r = 0.85, P < 0.001). 138 LIR features at ±3 kb breakpoints in 89 (81%) of 109 gross deletions were evaluated. Significant correlations were found between distance from breakpoint and loop length (r = -0.18, P < 0.05) and stem length (r = -0.18, P < 0.05), suggesting DNA strands are potentially broken in locations closer to bigger LIRs. In addition, bigger loops cause larger deletions (r = 0.19, P < 0.05). Moreover, loop length (r = 0.29, P < 0.02) and identity between stem copies (r = 0.30, P < 0.05) of 3' LIRs were more important in larger deletions. Consequently, DNA breaks may form via LIR-induced cruciform structure during replication. DNA ends may be later repaired by non-homologous end-joining (NHEJ), with following deletion.
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Affiliation(s)
- Nevim Aygun
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir, Turkey
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16
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Lee J, Kim YJ, Mun S, Kim HS, Han K. Identification of human-specific AluS elements through comparative genomics. Gene 2014; 555:208-16. [PMID: 25447892 DOI: 10.1016/j.gene.2014.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 11/03/2014] [Accepted: 11/05/2014] [Indexed: 01/08/2023]
Abstract
Mobile elements are responsible for ~45% of the human genome. Among them is the Alu element, accounting for 10% of the human genome (>1.1million copies). Several studies of Alu elements have reported that they are frequently involved in human genetic diseases and genomic rearrangements. In this study, we investigated the AluS subfamily, which is a relatively old Alu subfamily and has the highest copy number in primate genomes. Previously, a set of 263 human-specific AluS insertions was identified in the human genome. To validate these, we compared each of the human-specific AluS loci with its pre-insertion site in other primate genomes, including chimpanzee, gorilla, and orangutan. We obtained 24 putative human-specific AluS candidates via the in silico analysis and manual inspection, and then tried to verify them using PCR amplification and DNA sequencing. Through the PCR product sequencing, we were able to detect two instances of near-parallel Alu insertions in nearby sites that led to computational false negatives. Finally, we computationally and experimentally verified 23 human-specific AluS elements. We reported three alternative Alu insertion events, which are accompanied by filler DNA and/or Alu retrotransposition mediated-deletion. Bisulfite sequencing was carried out to examine DNA methylation levels of human-specific AluS elements. The results showed that fixed AluS elements are hypermethylated compared with polymorphic elements, indicating a possible relation between DNA methylation and Alu fixation in the human genome.
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Affiliation(s)
- Jae Lee
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea
| | - Yun-Ji Kim
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea.
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17
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Audrézet MP, Munck A, Scotet V, Claustres M, Roussey M, Delmas D, Férec C, Desgeorges M. Comprehensive CFTR gene analysis of the French cystic fibrosis screened newborn cohort: implications for diagnosis, genetic counseling, and mutation-specific therapy. Genet Med 2014; 17:108-16. [DOI: 10.1038/gim.2014.113] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/06/2014] [Indexed: 11/09/2022] Open
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18
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Does Integration of Various Ion Channel Measurements Improve Diagnostic Performance in Cystic Fibrosis? Ann Am Thorac Soc 2014; 11:562-70. [DOI: 10.1513/annalsats.201311-412oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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19
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Ooi CY, Dupuis A, Ellis L, Jarvi K, Martin S, Ray PN, Steele L, Kortan P, Gonska T, Dorfman R, Solomon M, Zielenski J, Corey M, Tullis E, Durie P. Does extensive genotyping and nasal potential difference testing clarify the diagnosis of cystic fibrosis among patients with single-organ manifestations of cystic fibrosis? Thorax 2013; 69:254-60. [PMID: 24149827 DOI: 10.1136/thoraxjnl-2013-203832] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND The phenotypic spectrum of cystic fibrosis (CF) has expanded to include patients affected by single-organ diseases. Extensive genotyping and nasal potential difference (NPD) testing have been proposed to assist in the diagnosis of CF when sweat testing is inconclusive. However, the diagnostic yield of extensive genotyping and NPD and the concordance between NPD and the sweat test have not been carefully evaluated. METHODS We evaluated the diagnostic outcomes of genotyping (with 122 mutations included as disease causing), sweat testing and NPD in a prospectively ascertained cohort of undiagnosed patients who presented with chronic sino-pulmonary disease (RESP), chronic/recurrent pancreatitis (PANC) or obstructive azoospermia (AZOOSP). RESULTS 202 patients (68 RESP, 42 PANC and 92 AZOOSP) were evaluated; 17.3%, 22.8% and 59.9% had abnormal, borderline and normal sweat chloride results, respectively. Only 17 (8.4%) patients were diagnosable as having CF by genotyping. Compared to sweat testing, NPD identified more patients as having CF (33.2%) with fewer borderline results (18.8%). The level of agreement according to kappa statistics (and the observed percentage of agreement) between sweat chloride and NPD in RESP, PANC and AZOOSP subjects was 'moderate' (65% observed agreement), 'poor' (33% observed agreement) and 'fair' (28% observed agreement), respectively. The degree of agreement only improved marginally when subjects with borderline sweat chloride results were excluded from the analysis. CONCLUSIONS The diagnosis of CF or its exclusion is not always straightforward and may remain elusive even with comprehensive evaluation, particularly among individuals who present at an older age with single-organ manifestations suggestive of CF.
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Affiliation(s)
- Chee Y Ooi
- Physiology and Experimental Medicine, Research Institute, The Hospital for Sick Children, , Toronto, Canada
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20
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Masson E, Chen JM, Audrézet MP, Cooper DN, Férec C. A conservative assessment of the major genetic causes of idiopathic chronic pancreatitis: data from a comprehensive analysis of PRSS1, SPINK1, CTRC and CFTR genes in 253 young French patients. PLoS One 2013; 8:e73522. [PMID: 23951356 PMCID: PMC3738529 DOI: 10.1371/journal.pone.0073522] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/30/2013] [Indexed: 12/21/2022] Open
Abstract
Idiopathic chronic pancreatitis (ICP) has traditionally been defined as chronic pancreatitis in the absence of any obvious precipitating factors (e.g. alcohol abuse) and family history of the disease. Studies over the past 15 years have revealed that ICP has a highly complex genetic architecture involving multiple gene loci. Here, we have attempted to provide a conservative assessment of the major genetic causes of ICP in a sample of 253 young French ICP patients. For the first time, conventional types of mutation (comprising coding sequence variants and variants at intron/exon boundaries) and gross genomic rearrangements were screened for in all four major pancreatitis genes, PRSS1, SPINK1, CTRC and CFTR. For the purposes of the study, synonymous, intronic and 5'- or 3'-untranslated region variants were excluded from the analysis except where there was persuasive evidence of functional consequences. The remaining sequence variants/genotypes were classified into causative, contributory or neutral categories by consideration of (i) their allele frequencies in patient and normal control populations, (ii) their presumed or experimentally confirmed functional effects, (iii) the relative importance of their associated genes in the pathogenesis of chronic pancreatitis and (iv) gene-gene interactions wherever applicable. Adoption of this strategy allowed us to assess the pathogenic relevance of specific variants/genotypes to their respective carriers to an unprecedented degree. The genetic cause of ICP could be assigned in 23.7% of individuals in the study group. A strong genetic susceptibility factor was also present in an additional 24.5% of cases. Taken together, up to 48.2% of the studied ICP patients were found to display evidence of a genetic basis for their pancreatitis. Whereas these particular proportions may not be extrapolable to all ICP patients, the approach employed should serve as a useful framework for acquiring a better understanding of the role of genetic factors in causing this oligogenic disease.
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Affiliation(s)
- Emmanuelle Masson
- Institut National de la Santé et de la Recherche Médicale, U1078, Brest, France
- Laboratoire de Génétique Moléculaire et d’Histocompatibilité, Centre Hospitalier Régional Universitaire Brest, Hôpital Morvan, Brest, France
| | - Jian-Min Chen
- Institut National de la Santé et de la Recherche Médicale, U1078, Brest, France
- Etablissement Français du sang – Bretagne, Brest, France
- * E-mail: (J-MC); (CF)
| | - Marie-Pierre Audrézet
- Institut National de la Santé et de la Recherche Médicale, U1078, Brest, France
- Laboratoire de Génétique Moléculaire et d’Histocompatibilité, Centre Hospitalier Régional Universitaire Brest, Hôpital Morvan, Brest, France
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Claude Férec
- Institut National de la Santé et de la Recherche Médicale, U1078, Brest, France
- Laboratoire de Génétique Moléculaire et d’Histocompatibilité, Centre Hospitalier Régional Universitaire Brest, Hôpital Morvan, Brest, France
- Etablissement Français du sang – Bretagne, Brest, France
- Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale, Brest, France
- * E-mail: (J-MC); (CF)
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21
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Vasson A, Leroux C, Orhant L, Boimard M, Toussaint A, Leroy C, Commere V, Ghiotti T, Deburgrave N, Saillour Y, Atlan I, Fouveaut C, Beldjord C, Valleix S, Leturcq F, Dodé C, Bienvenu T, Chelly J, Cossée M. Custom oligonucleotide array-based CGH: a reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes. Eur J Hum Genet 2013; 21:977-87. [PMID: 23340513 PMCID: PMC3746255 DOI: 10.1038/ejhg.2012.279] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/31/2012] [Accepted: 11/13/2012] [Indexed: 11/09/2022] Open
Abstract
The frequency of disease-related large rearrangements (referred to as copy-number mutations, CNMs) varies among genes, and search for these mutations has an important place in diagnostic strategies. In recent years, CGH method using custom-designed high-density oligonucleotide-based arrays allowed the development of a powerful tool for detection of alterations at the level of exons and made it possible to provide flexibility through the possibility of modeling chips. The aim of our study was to test custom-designed oligonucleotide CGH array in a diagnostic laboratory setting that analyses several genes involved in various genetic diseases, and to compare it with conventional strategies. To this end, we designed a 12-plex CGH array (135k; 135 000 probes/subarray) (Roche Nimblegen) with exonic and intronic oligonucleotide probes covering 26 genes routinely analyzed in the laboratory. We tested control samples with known CNMs and patients for whom genetic causes underlying their disorders were unknown. The contribution of this technique is undeniable. Indeed, it appeared reproducible, reliable and sensitive enough to detect heterozygous single-exon deletions or duplications, complex rearrangements and somatic mosaicism. In addition, it improves reliability of CNM detection and allows determination of boundaries precisely enough to direct targeted sequencing of breakpoints. All of these points, associated with the possibility of a simultaneous analysis of several genes and scalability 'homemade' make it a valuable tool as a new diagnostic approach of CNMs.
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Affiliation(s)
- Aurélie Vasson
- Assistance Publique-Hôpitaux de Paris, Laboratoire de Biochimie et Génétique Moléculaire, Hôpital Cochin, APHP, Paris, France
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22
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Ward LD, Kellis M. Interpreting noncoding genetic variation in complex traits and human disease. Nat Biotechnol 2012; 30:1095-106. [PMID: 23138309 PMCID: PMC3703467 DOI: 10.1038/nbt.2422] [Citation(s) in RCA: 340] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 10/16/2012] [Indexed: 12/13/2022]
Abstract
Association studies provide genome-wide information about the genetic basis of complex disease, but medical research has primarily focused on protein-coding variants, due to the difficulty of interpreting non-coding mutations. This picture has changed with advances in the systematic annotation of functional non-coding elements. Evolutionary conservation, functional genomics, chromatin state, sequence motifs, and molecular quantitative trait loci all provide complementary information about non-coding function. These functional maps can help prioritize variants on risk haplotypes, filter mutations encountered in the clinic, and perform systems-level analyses to reveal processes underlying disease associations. Advances in predictive modeling can enable dataset integration to reveal pathways shared across loci and alleles, and richer regulatory models can guide the search for epistatic interactions. Lastly, new massively parallel reporter experiments can systematically validate regulatory predictions. Ultimately, advances in regulatory and systems genomics can help unleash the value of whole-genome sequencing for personalized genomic risk assessment, diagnosis, and treatment.
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Affiliation(s)
- Lucas D Ward
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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23
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Ehret G, Lamparter D, Hoggart C, Whittaker J, Beckmann J, Kutalik Z, Kutalik Z. A multi-SNP locus-association method reveals a substantial fraction of the missing heritability. Am J Hum Genet 2012; 91:863-71. [PMID: 23122585 DOI: 10.1016/j.ajhg.2012.09.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 07/23/2012] [Accepted: 09/21/2012] [Indexed: 10/27/2022] Open
Abstract
There are many known examples of multiple semi-independent associations at individual loci; such associations might arise either because of true allelic heterogeneity or because of imperfect tagging of an unobserved causal variant. This phenomenon is of great importance in monogenic traits but has not yet been systematically investigated and quantified in complex-trait genome-wide association studies (GWASs). Here, we describe a multi-SNP association method that estimates the effect of loci harboring multiple association signals by using GWAS summary statistics. Applying the method to a large anthropometric GWAS meta-analysis (from the Genetic Investigation of Anthropometric Traits consortium study), we show that for height, body mass index (BMI), and waist-to-hip ratio (WHR), 3%, 2%, and 1%, respectively, of additional phenotypic variance can be explained on top of the previously reported 10% (height), 1.5% (BMI), and 1% (WHR). The method also permitted a substantial increase (by up to 50%) in the number of loci that replicate in a discovery-validation design. Specifically, we identified 74 loci at which the multi-SNP, a linear combination of SNPs, explains significantly more variance than does the best individual SNP. A detailed analysis of multi-SNPs shows that most of the additional variability explained is derived from SNPs that are not in linkage disequilibrium with the lead SNP, suggesting a major contribution of allelic heterogeneity to the missing heritability.
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Tang S, Moonnumakal SP, Stevens B, Douglas G, Mason S, Schmitt ES, Eng CM, Katz M, Fang P. Characterization of a recurrent 3.8kb deletion involving exons 17a and 17b within the CFTR gene. J Cyst Fibros 2012; 12:290-4. [PMID: 22998936 DOI: 10.1016/j.jcf.2012.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/29/2012] [Accepted: 08/29/2012] [Indexed: 12/17/2022]
Abstract
BACKGROUND Large deletions within CFTR have been estimated to constitute 1-2% pathogenic alleles, but the occurrence could be much higher in classical cystic fibrosis (CF) patients with one mutation detectable by the routine screening/sequencing work-up. Currently, evaluation of major CFTR rearrangements is not included in the mutation analysis for the reproductive partner of a CF patient/carrier. METHODS Exon sequencing and Multiplex Ligation-dependent Amplification (MLPA) analyses were used to make a molecular diagnosis of two unrelated CF patients. Long PCR, restriction mapping, cloning, and hot start sequencing were employed to accurately annotate the rearrangement junctions. RESULTS Both patients had a heterozygous single amino acid deletion mutation identified by sequencing, and a heterozygous deletion of CFTR exons 17a and 17b detected by MLPA. Molecular characterization of the rearrangement breakpoints indicated that the two patients had an identical complex c.2988+1616_c.3367+356del3796ins62 change, flanked by a pair of perfectly inverted repeats of 32 nucleotides. CONCLUSIONS The c.2988+1616_c.3367+356del3796ins62 complex rearrangement is a recurrent mutation from patients of different ethnic backgrounds. This mutation can be detected through a simple PCR based analysis.
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Affiliation(s)
- Sha Tang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030, United States
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25
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Abstract
Cystic fibrosis (CF) is defined as the most common life shortening genetic disorder in the Caucasian populations. The cloning of the gene responsible for the disease - the CFTR (Cystic Fibrosis Transmembrane conductance Regulator) gene - twenty years ago has greatly improved our knowledge of the pathophysiology of CF. That disease is characterized by a highly phenotypic variability and the CFTR mutations cannot explain all the variability observed in the disease severity. The possible influence of the environment and modifier genes has therefore been evocated. Several genetic variants coding for genes involved in the physiopathology of the disease have been studied, like genes involve in the immunity and the inflammatory response. Some of these genes have indeed been shown to influence the disease severity. A new approach has also been developed, analyzing the whole genome. This review summarizes the genetic basis of CF in its classical and atypical forms, as well as the work performed in the field of modifier genes.
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Norek A, Stremska M, Sobczyńska-Tomaszewska A, Wertheim-Tysarowska K, Dmeńska H, Jurek M. Novel de novo large deletion in cystic fibrosis transmembrane conductance regulator gene results in a severe cystic fibrosis phenotype. J Pediatr 2011; 159:343-6.e1. [PMID: 21663921 DOI: 10.1016/j.jpeds.2011.04.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 03/22/2011] [Accepted: 04/18/2011] [Indexed: 01/24/2023]
Abstract
We identified c.1521_1523delCTT and c.1679+94_2619+986del8118 in trans in a 6-year-old boy with a severe cystic fibrosis phenotype. The first deletion was inherited maternally, but the latter had arisen de novo.
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Affiliation(s)
- Aleksandra Norek
- Institute of Mother and Child, Department of Medical Genetics, Warsaw, Poland.
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Characterization of a novel isolated deletion of the exon 3 within the CFTR gene: Relevance for phenotypic expression and genetic counseling. Clin Biochem 2011; 44:799-803. [DOI: 10.1016/j.clinbiochem.2011.03.140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 03/14/2011] [Accepted: 03/29/2011] [Indexed: 11/18/2022]
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Vargas-Poussou R, Dahan K, Kahila D, Venisse A, Riveira-Munoz E, Debaix H, Grisart B, Bridoux F, Unwin R, Moulin B, Haymann JP, Vantyghem MC, Rigothier C, Dussol B, Godin M, Nivet H, Dubourg L, Tack I, Gimenez-Roqueplo AP, Houillier P, Blanchard A, Devuyst O, Jeunemaitre X. Spectrum of mutations in Gitelman syndrome. J Am Soc Nephrol 2011; 22:693-703. [PMID: 21415153 DOI: 10.1681/asn.2010090907] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Gitelman's syndrome (GS) is a rare, autosomal recessive, salt-losing tubulopathy caused by mutations in the SLC12A3 gene, which encodes the thiazide-sensitive NaCl cotransporter (NCC). Because 18 to 40% of suspected GS patients carry only one SLC12A3 mutant allele, large genomic rearrangements may account for unidentified mutations. Here, we directly sequenced genomic DNA from a large cohort of 448 unrelated patients suspected of having GS. We found 172 distinct mutations, of which 100 were unreported previously. In 315 patients (70%), we identified two mutations; in 81 patients (18%), we identified one; and in 52 patients (12%), we did not detect a mutation. In 88 patients, we performed a search for large rearrangements by multiplex ligation-dependent probe amplification (MLPA) and found nine deletions and two duplications in 24 of the 51 heterozygous patients. A second technique confirmed each rearrangement. Based on the breakpoints of seven deletions, nonallelic homologous recombination by Alu sequences and nonhomologous end-joining probably favor these intragenic deletions. In summary, missense mutations account for approximately 59% of the mutations in Gitelman's syndrome, and there is a predisposition to large rearrangements (6% of our cases) caused by the presence of repeated sequences within the SLC12A3 gene.
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Affiliation(s)
- Rosa Vargas-Poussou
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service de Génétique, Paris, France.
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Houdayer C, Dehainault C, Gauthier-Villars M, Stoppa-Lyonnet D. Screening for genomic rearrangements by multiplex PCR/liquid chromatography. Methods Mol Biol 2011; 688:127-42. [PMID: 20938836 DOI: 10.1007/978-1-60761-947-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Screening for large gene rearrangements has become established as an important part of molecular medicine; however, it is also challenging as these rearrangements range from an extra copy of a complete chromosome(s) to deletion or duplication of a single exon. In this chapter, we describe a versatile and robust method to assess exon copy number, called multiplex PCR/liquid chromatography (MP/LC) assay. Multiple genomic fragments are amplified under semiquantitative conditions using unlabeled primers, then separated by ion-pair reversed-phase high-performance liquid chromatography, and quantitated by fluorescent detection using a postcolumn intercalation dye. The relative peak intensities for each target directly reflect DNA copy number. This technique can be used not only to screen intronic, exonic, and intergenic parts of the genome but also for transcript quantitation. MP/LC appears to be an easy, versatile, and cost-effective method, which is particularly relevant to DHPLC users, as it broadens the spectrum of available applications on a DHPLC system. The authors describe a detailed protocol for large rearrangement screening in the RB1 gene.
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Affiliation(s)
- Claude Houdayer
- Service de Génétique Oncologique, Institut Curie Hôpital, Paris, France.
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Ooi CY, Dorfman R, Cipolli M, Gonska T, Castellani C, Keenan K, Freedman SD, Zielenski J, Berthiaume Y, Corey M, Schibli S, Tullis E, Durie PR. Type of CFTR mutation determines risk of pancreatitis in patients with cystic fibrosis. Gastroenterology 2011; 140:153-61. [PMID: 20923678 DOI: 10.1053/j.gastro.2010.09.046] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 08/20/2010] [Accepted: 09/17/2010] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Different mutations in the cystic fibrosis gene (CFTR) are associated with different functional status of the exocrine pancreas. We investigated whether CFTR genotypes determine the risk of pancreatitis in patients with cystic fibrosis (CF). METHODS Patients with pancreatic-sufficient CF were identified from 2 CF population-based databases (N = 277; 62 with pancreatitis and 215 without pancreatitis); patients' genotypes and clinical characteristics were analyzed. The loss of pancreatic function associated with each CFTR genotype was determined based on the pancreatic insufficiency prevalence (PIP) score. RESULTS Patients with pancreatitis were more likely to have genotypes associated with mild (70%) than moderate-severe (30%) PIP scores (P = .004). The cumulative proportion of patients who developed pancreatitis through to the age of 50 years was significantly greater for genotypes associated with mild (50%) than moderate-severe (27%) PIP scores (P = .006). The genotype associated with mild PIP scores had a hazard ratio of 2.4 for pancreatitis (95% confidence interval, 1.3-4.5; P = .006). Patients with pancreatitis were diagnosed with CF at an older median age than those without pancreatitis (14.9 years [interquartile range, 9.5-27.7] vs 9.3 years [interquartile range, 1.5-21.4]; P = .003) and had lower mean levels of sweat chloride than patients without pancreatitis (74.5 ± 26.2 mmol/L vs 82.8 ± 25.2 mmol/L; P = .03). CONCLUSIONS Specific CFTR genotypes are significantly associated with pancreatitis. Patients with genotypes associated with mild phenotypic effects have a greater risk of developing pancreatitis than patients with genotypes associated with moderate-severe phenotypes. This observation provides further insight into the complex pathogenesis of pancreatitis.
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Affiliation(s)
- Chee Y Ooi
- Physiology and Experimental Medicine, The Research Institute, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
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Comprehensive description of CFTR genotypes and ultrasound patterns in 694 cases of fetal bowel anomalies: a revised strategy. Hum Genet 2010; 129:387-96. [DOI: 10.1007/s00439-010-0933-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 12/10/2010] [Indexed: 02/02/2023]
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Scotet V, Duguépéroux I, Audrézet MP, Audebert-Bellanger S, Muller M, Blayau M, Férec C. Focus on cystic fibrosis and other disorders evidenced in fetuses with sonographic finding of echogenic bowel: 16-year report from Brittany, France. Am J Obstet Gynecol 2010; 203:592.e1-6. [PMID: 20932506 DOI: 10.1016/j.ajog.2010.08.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 04/30/2010] [Accepted: 08/17/2010] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Pregnancies medical follow-up and ultrasonography development have enabled detection of fetal echogenic bowel, a sign associated with various pathologies, including cystic fibrosis. Based on the long experience of a region where cystic fibrosis is frequent (Brittany, France), we describe disorders diagnosed in fetal echogenic bowel fetuses and assess ultrasonography ability in detecting cystic fibrosis in utero. STUDY DESIGN We reviewed the cases of fetal echogenic bowel diagnosed in pregnant women living in Brittany and referred for CFTR gene analysis over the 1992-2007 period (n = 289). RESULTS A disorder was diagnosed in 32.2% of the fetuses, cystic fibrosis being the most commonly identified (7.6%). We also found digestive malformations (7.0%), chromosomal abnormalities (3.7%), and maternofetal infections (3.7%). Combining these data with our ongoing newborn screening program since 1989 showed that ultrasonography enabled diagnosis of 10.7% of the cystic fibrosis cases. CONCLUSION This study highlights the importance of pregnancy ultrasound examinations and their efficiency in detecting cystic fibrosis.
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Sermet-Gaudelus I, Girodon E, Sands D, Stremmler N, Vavrova V, Deneuville E, Reix P, Bui S, Huet F, Lebourgeois M, Munck A, Iron A, Skalicka V, Bienvenu T, Roussel D, Lenoir G, Bellon G, Sarles J, Macek M, Roussey M, Fajac I, Edelman A. Clinical Phenotype and Genotype of Children with Borderline Sweat Test and Abnormal Nasal Epithelial Chloride Transport. Am J Respir Crit Care Med 2010; 182:929-36. [DOI: 10.1164/rccm.201003-0382oc] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Quemener S, Chen JM, Chuzhanova N, Bénech C, Casals T, Macek M, Bienvenu T, McDevitt T, Farrell PM, Loumi O, Messaoud T, Cuppens H, Cutting GR, Stenson PD, Giteau K, Audrézet MP, Cooper DN, Férec C. Complete ascertainment of intragenic copy number mutations (CNMs) in the CFTR gene and its implications for CNM formation at other autosomal loci. Hum Mutat 2010; 31:421-8. [PMID: 20052766 DOI: 10.1002/humu.21196] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Over the last 20 years since the discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, more than 1,600 different putatively pathological CFTR mutations have been identified. Until now, however, copy number mutations (CNMs) involving the CFTR gene have not been methodically analyzed, resulting almost certainly in the underascertainment of CFTR gene duplications compared with deletions. Here, high-resolution array comparative genomic hybridization (averaging one interrogating probe every 95 bp) was used to analyze the entire length of the CFTR gene (189 kb) in 233 cystic fibrosis chromosomes lacking conventional mutations. We succeeded in identifying five duplication CNMs that would otherwise have been refractory to analysis. Based upon findings from this and other studies, we propose that deletion and duplication CNMs in the human autosomal genome are likely to be generated in the proportion of approximately 2-3:1. We further postulate that intragenic gene duplication CNMs in other disease loci may have been routinely underascertained. Finally, our analysis of +/-20 bp flanking each of the 40 CFTR breakpoints characterized at the DNA sequence level provide support for the emerging concept that non-B DNA conformations in combination with specific sequence motifs predispose to both recurring and nonrecurring genomic rearrangements.
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Affiliation(s)
- Sylvia Quemener
- INSERM U613, and Université de Bretagne Occidentale, 46 rue Félix Le Dantec, Brest, France
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35
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Svensson AM, Chou LS, Miller CE, Robles JA, Swensen JJ, Voelkerding KV, Mao R, Lyon E. Detection of large rearrangements in the cystic fibrosis transmembrane conductance regulator gene by multiplex ligation-dependent probe amplification assay when sequencing fails to detect two disease-causing mutations. Genet Test Mol Biomarkers 2010; 14:171-4. [PMID: 20059381 DOI: 10.1089/gtmb.2009.0099] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AIMS Most of the over 1600 mutations and sequence variants identified to date in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are point mutations or small deletions/insertions detectable by conventional sequencing. However, large rearrangements (deletions, duplications, or insertion/deletion mutations) have recently been reported to constitute 1-2% of CFTR mutations. The CFTR sequencing protocol at ARUP Laboratories interrogates the coding regions of all 27 exons and all intron/exon boundaries of the gene. This study was undertaken to determine whether testing for large gene rearrangements could improve the mutation detection rate. RESULTS Nine cases with abnormal quantitative pilocarpine iontophoresis sweat chloride (SC) values (>60 mEq/L) and 20 cases with borderline SC levels (40-60 mEq/L) with only one or no mutations detected by the ARUP 32 mutation panel, including the 23 mutations recommended by American College of Medical Genetics (ACMG) for carrier screening, followed by sequencing, were tested using a multiplex ligation-dependent probe amplification (MLPA) assay. MLPA analysis identified one deletion among nine patients with SC >60 who had previously been tested with sequencing. None of the cases with borderline SC levels showed rearrangements. CONCLUSION The MLPA assay for detection of large rearrangements may be valuable in individuals with positive SC levels where one or no mutations have been identified by sequencing.
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Affiliation(s)
- Annika M Svensson
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.
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Chen JM, Férec C, Cooper DN. LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease: mutation detection bias and multiple mechanisms of target gene disruption. J Biomed Biotechnol 2010; 2006:56182. [PMID: 16877817 PMCID: PMC1510945 DOI: 10.1155/jbb/2006/56182] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
LINE-1 (L1) elements are the most abundant autonomous non-LTR retrotransposons in the human genome. Having recently performed a meta-analysis of L1 endonuclease-mediated retrotranspositional events causing human genetic disease, we have extended this study by focusing on two key issues, namely, mutation detection bias and the multiplicity of mechanisms of target gene disruption. Our analysis suggests that whereas an ascertainment bias may have generally militated against the detection of autosomal L1-mediated insertions, autosomal L1 direct insertions could have been disproportionately overlooked owing to their unusually large size. Our analysis has also indicated that the mechanisms underlying the functional disruption of target genes by L1-mediated retrotranspositional events are likely to be dependent on several different factors such as the type of insertion (L1 direct, L1 trans-driven Alu, or SVA), the precise locations of the inserted sequences within the target gene regions, the length of the inserted sequences, and possibly also their orientation.
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Affiliation(s)
- Jian-Min Chen
- INSERM U613, Génétique
Moléculaire et Génétique Épidémiologique,
29220 Brest, France
- Faculté de Médecine de Brest
et des Sciences de la Santé, Université de Bretagne Occidentale, 29238
Brest, France
- Etablissement Français du Sang-Bretagne,
35000 Rennes, France
- *Jian-Min Chen:
| | - Claude Férec
- INSERM U613, Génétique
Moléculaire et Génétique Épidémiologique,
29220 Brest, France
- Faculté de Médecine de Brest
et des Sciences de la Santé, Université de Bretagne Occidentale, 29238
Brest, France
- Etablissement Français du Sang-Bretagne,
35000 Rennes, France
- Hôpital Morvan, CHRU Brest, Laboratoire de
Génétique Moléculaire et d'Histocompatibilité, 29200 Brest, France
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine,
Cardiff University, Heath Park Campus, Cardiff CF14 4XN, UK
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Abstract
Cystic fibrosis is a chronic condition for which genetic testing offers much for the individuals affected in terms of an early diagnosis and offers timely additional information for families with regard to family planning and prenatal testing. Genetic counselling encompasses a range of clinical issues for families and forms a complementary resource for clinicians caring for people with cystic fibrosis. This review will discuss the range of genetic information readily available to patients and families through genetic counselling.
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Affiliation(s)
- Bronwyn Culling
- Department of Molecular and Clinical Genetics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
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de Becdelièvre A, Costa C, LeFloch A, Legendre M, Jouannic JM, Vigneron J, Bresson JL, Gobin S, Martin J, Goossens M, Girodon E. Notable contribution of large CFTR gene rearrangements to the diagnosis of cystic fibrosis in fetuses with bowel anomalies. Eur J Hum Genet 2010; 18:1166-9. [PMID: 20512161 DOI: 10.1038/ejhg.2010.80] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Grade III fetal bowel hyperechogenicity and/or loop dilatation observed at the second trimester of pregnancy can be due to several disease conditions, including cystic fibrosis (CF). Screening for frequent CF mutations is performed as a first step and, in certain situations, such as when a frequent CF mutation is found in the fetus, the increased risk of CF justifies an in-depth study of the second allele. To determine the contribution of large CFTR gene rearrangements in such cases, detected using a semiquantitative fluorescent multiplex PCR (QFM-PCR) assay, we collated data on 669 referrals related to suspicion of CF in fetuses from 1998 to 2009. Deletions were found in 5/70 cases in which QFM-PCR was applied, dele19, dele22_23, dele2_6b, dele14b_15 and dele6a_6b, of which the last three remain undescribed. In 3/5 cases, hyperechogenicity was associated with dilatation and/or gallbladder anomalies. Of the total cases of CF recognized in the subgroup of first-hand referrals, deletions represent 16.7% of CF alleles. Our study thus strengthens the need to consider large CFTR gene rearrangements in the diagnosis strategy of fetal bowel anomalies, in particular in the presence of multiple anomalies.
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Affiliation(s)
- Alix de Becdelièvre
- Service de Biochimie-Génétique et Inserm U955 Equipe 11, Groupe Hospitalier Henri Mondor-Albert Chenevier, APHP, Créteil, France
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Masson E, Paliwal S, Bhaskar S, Prakash S, Scotet V, Reddy DN, Le Maréchal C, Ratan Chandak G, Chen JM, Férec C. Genetic analysis of the glycoprotein 2 gene in patients with chronic pancreatitis. Pancreas 2010; 39:353-8. [PMID: 20335779 DOI: 10.1097/mpa.0b013e3181bb9620] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVES The aim of this study was to evaluate whether variations in the glycoprotein 2 gene (GP2) may potentially affect the risk of chronic pancreatitis. METHODS Six hundred sixty-one French white patients (idiopathic chronic pancreatitis, n = 590; familial chronic pancreatitis, n = 42; hereditary pancreatitis, n = 29), 445 Dravidian patients from India (tropical calcific pancreatitis, n = 306; idiopathic chronic pancreatitis, n = 139), and 962 unrelated healthy subjects (French white, n = 500; Dravidian, n = 462) participated in this case-control association study. The entire coding sequence of the GP2 gene was searched for conventional genetic variations by direct sequencing, whereas all 12 exons of the GP2 gene were screened for copy number variations by quantitative fluorescent multiplex-polymerase chain reaction. RESULTS Only 3 rare missense mutations (p.A137T, p.E250D, and p.V432M; only p.E250D was not detected in any control subjects) and 3 common synonymous polymorphisms (c.348C>T, c.714G>C, and c.1275A>G) were identified. The c.348C>T and c.1275A>G variations were found to be contradictorily associated with the disease (ranging from protective effects to disease-predisposing effects) in the French white and Indian populations. CONCLUSION The paucity of patient-specific missense mutations and contradictory findings with respect to 2 common polymorphisms in the 2 contrasting populations suggest that the GP2 gene is unlikely to play a major role in the etiology of chronic pancreatitis.
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Affiliation(s)
- Emmanuelle Masson
- Institut National de la Santé et de la Recherche Médicale (INSERM), U613, 29218 Brest, France
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Bahi-Buisson N, Girard B, Gautier A, Nectoux J, Fichou Y, Saillour Y, Poirier K, Chelly J, Bienvenu T. Epileptic encephalopathy in a girl with an interstitial deletion of Xp22 comprising promoter and exon 1 of the CDKL5 gene. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:202-7. [PMID: 19455595 DOI: 10.1002/ajmg.b.30974] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We report a 2-year-old girl with early onset seizures variant of Rett syndrome with a deletion at Xp22 detected by multiplex ligation-dependent probe amplification (MLPA) technique. This patient presented with tonic seizures at 7 days of life. Subsequently, she developed infantile spasms at three months and finally refractory myoclonic epilepsy. She demonstrated severe encephalopathy with hypotonia, deceleration of head growth, with eye gaze but limited eye pursuit, no language, limited hand use, and intermittent hand stereotypies. This combination of clinical features, suggestive of early onset variant of Rett syndrome led us to screen the CDKL5 gene. In a first step, screening of the whole coding sequence of the CDKL5 gene revealed no point mutations. In a second step, we searched gross rearrangements by MLPA and identified a microdeletion affecting both the promoter and exon 1 in CDKL5. Subsequent analysis on a Nimblegen HD2 microarray confirmed a deletion of approximately 300 kb at Xp22, including the BEND2, SCML2, and CDKL5 genes. In conclusion, our report suggests that searching for large rearrangements in CDKL5 should be considered in girls with early onset seizures and Rett-like features.
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Affiliation(s)
- Nadia Bahi-Buisson
- Service de Neurologie Pédiatrique, Département de Pédiatrie, Hôpital Necker Enfants Malades, AP-HP, Paris, France
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Chauvin A, Chen JM, Quemener S, Masson E, Kehrer-Sawatzki H, Ohmle B, Cooper DN, Le Marechal C, Ferec C. Elucidation of the complex structure and origin of the human trypsinogen locus triplication. Hum Mol Genet 2009; 18:3605-14. [DOI: 10.1093/hmg/ddp308] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Elce A, Boccia A, Cardillo G, Giordano S, Tomaiuolo R, Paolella G, Castaldo G. Three novel CFTR polymorphic repeats improve segregation analysis for cystic fibrosis. Clin Chem 2009; 55:1372-9. [PMID: 19443567 DOI: 10.1373/clinchem.2008.119545] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Molecular diagnosis for cystic fibrosis (CF) is based on the direct identification of mutations in the CFTR gene [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] (detection rate about 90% with scanning procedures) and on segregation analysis of intragenic polymorphisms for carrier and prenatal diagnosis in about 20% of CF families in which 1 or both causal mutations are unknown. METHODS We identified 3 novel intragenic polymorphic repeats (IVS3polyA, IVS4polyA, and IVS10CA repeats) in the CFTR gene and developed and validated a procedure based on the PCR followed by capillary electrophoresis for large-scale analysis of these polymorphisms and the 4 previously identified microsatellites (IVS1CA, IVS8CA, IVS17bTA, and IVS17bCA repeats) in a single run. We validated the procedure for both single- and 2-cell samples (for a possible use in preimplantation diagnosis), and on a large number of CF patients bearing different genotypes and non-CF controls. RESULTS The allelic distribution and heterozygosity results suggest that the 3 novel polymorphisms strongly contribute to carrier and prenatal diagnosis of CF in families in which 1 or both causal mutations have not been identified. At least 1 of the 4 previously identified microsatellites was informative in 78 of 100 unrelated CF families; at least 1 of all 7 polymorphisms was informative in 98 of the families. Finally, the analysis of haplotypes for the 7 polymorphisms revealed that most CF mutations are associated with different haplotypes, suggesting multiple slippage events but a single origin for most CFTR mutations. CONCLUSIONS The analysis of the 7 polymorphisms is a rapid and efficient tool for routine carrier, prenatal, and preimplantation diagnosis of CF.
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Affiliation(s)
- Ausilia Elce
- Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy
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Hantash FM, Rebuyon A, Peng M, Redman JB, Sun W, Strom CM. Apparent homozygosity of a novel frame shift mutation in the CFTR gene because of a large deletion. J Mol Diagn 2009; 11:253-6. [PMID: 19324987 DOI: 10.2353/jmoldx.2009.080117] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Patients develop cystic fibrosis because of a variety of homozygous recessive mutations, including single nucleotide polymorphisms, insertions, and deletions, in the cystic fibrosis transmembrane regulator (CFTR) gene, or because of compound heterozygosity for two mutations in the CFTR gene. A false determination of homozygosity for a particular CFTR mutation could negatively affect both carrier screens for a patient's family as well as researchers' ability to study the physiological implications of a particular mutation. We argued previously that homozygosity for rare or novel mutations in the CFTR gene could result from a mutation on one allele and the presence of a large deletion encompassing the same sequence region on the second allele. We present here a patient with classic cystic fibrosis who has a novel microdeletion in exon 7 on one allele and a large deletion encompassing exon 7 on the second allele. These data highlight the need to prevent misdiagnosis of homozygous mutations, which can lead to misinterpretation of mutation penetrance and its effects on protein function.
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Affiliation(s)
- Feras M Hantash
- Department of Molecular Genetics, Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92690, USA.
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Anwar S, Riazuddin S, Ahmed ZM, Tasneem S, Ateeq-ul-Jaleel, Khan SY, Griffith AJ, Friedman TB, Riazuddin S. SLC26A4 mutation spectrum associated with DFNB4 deafness and Pendred's syndrome in Pakistanis. J Hum Genet 2009; 54:266-70. [DOI: 10.1038/jhg.2009.21] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Dorfman R, Nalpathamkalam T, Taylor C, Gonska T, Keenan K, Yuan XW, Corey M, Tsui LC, Zielenski J, Durie P. Do common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene? Clin Genet 2009; 77:464-73. [PMID: 20059485 DOI: 10.1111/j.1399-0004.2009.01351.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computational methods are used to predict the molecular consequences of amino-acid substitutions on the basis of evolutionary conservation or protein structure, but their utility in clinical diagnosis or prediction of disease outcome has not been well validated. We evaluated three popular computer programs, namely, PANTHER, SIFT and PolyPhen, by comparing the predicted clinical outcomes for a group of known CFTR missense mutations against the diagnosis of cystic fibrosis (CF) and clinical manifestations in cohorts of subjects with CF-disease and CFTR-related disorders carrying these mutations. Owing to poor specificity, none of tools reliably distinguished between individual mutations that confer CF disease from mutations found in subjects with a CFTR-related disorder or no disease. Prediction scores for CFTR mutations derived from PANTHER showed a significant overall statistical correlation with the spectrum of disease severity associated with mutations in the CFTR gene. In contrast, PolyPhen- and SIFT-derived scores only showed significant differences between CF-causing and non-CF variants. Current computational methods are not recommended for establishing or excluding a CF diagnosis, notably as a newborn screening strategy or in patients with equivocal test results.
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Affiliation(s)
- R Dorfman
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Canada
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Srikanta D, Sen SK, Huang CT, Conlin EM, Rhodes RM, Batzer MA. An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair. Genomics 2008; 93:205-12. [PMID: 18951971 DOI: 10.1016/j.ygeno.2008.09.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 09/15/2008] [Accepted: 09/26/2008] [Indexed: 11/18/2022]
Abstract
The Alu family is a highly successful group of non-LTR retrotransposons ubiquitously found in primate genomes. Similar to the L1 retrotransposon family, Alu elements integrate primarily through an endonuclease-dependent mechanism termed target site-primed reverse transcription (TPRT). Recent studies have suggested that, in addition to TPRT, L1 elements occasionally utilize an alternative endonuclease-independent pathway for genomic integration. To determine whether an analogous mechanism exists for Alu elements, we have analyzed three publicly available primate genomes (human, chimpanzee and rhesus macaque) for endonuclease-independent recently integrated or lineage specific Alu insertions. We recovered twenty-three examples of such insertions and show that these insertions are recognizably different from classical TPRT-mediated Alu element integration. We suggest a role for this process in DNA double-strand break repair and present evidence to suggest its association with intra-chromosomal translocations, in-vitro RNA recombination (IVRR), and synthesis-dependent strand annealing (SDSA).
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Affiliation(s)
- Deepa Srikanta
- Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, Baton Rouge, LA 70803, USA
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Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice. J Cyst Fibros 2008; 7:179-96. [PMID: 18456578 DOI: 10.1016/j.jcf.2008.03.009] [Citation(s) in RCA: 384] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2007] [Accepted: 03/14/2008] [Indexed: 02/06/2023]
Abstract
It is often challenging for the clinician interested in cystic fibrosis (CF) to interpret molecular genetic results, and to integrate them in the diagnostic process. The limitations of genotyping technology, the choice of mutations to be tested, and the clinical context in which the test is administered can all influence how genetic information is interpreted. This paper describes the conclusions of a consensus conference to address the use and interpretation of CF mutation analysis in clinical settings. Although the diagnosis of CF is usually straightforward, care needs to be exercised in the use and interpretation of genetic tests: genotype information is not the final arbiter of a clinical diagnosis of CF or CF transmembrane conductance regulator (CFTR) protein related disorders. The diagnosis of these conditions is primarily based on the clinical presentation, and is supported by evaluation of CFTR function (sweat testing, nasal potential difference) and genetic analysis. None of these features are sufficient on their own to make a diagnosis of CF or CFTR-related disorders. Broad genotype/phenotype associations are useful in epidemiological studies, but CFTR genotype does not accurately predict individual outcome. The use of CFTR genotype for prediction of prognosis in people with CF at the time of their diagnosis is not recommended. The importance of communication between clinicians and medical genetic laboratories is emphasized. The results of testing and their implications should be reported in a manner understandable to the clinicians caring for CF patients.
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Tomaiuolo R, Sangiuolo F, Bombieri C, Bonizzato A, Cardillo G, Raia V, D'Apice M, Bettin M, Pignatti P, Castaldo G, Novelli G. Epidemiology and a novel procedure for large scale analysis of CFTR rearrangements in classic and atypical CF patients: A multicentric Italian study. J Cyst Fibros 2008; 7:347-51. [DOI: 10.1016/j.jcf.2007.12.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 12/07/2007] [Accepted: 12/15/2007] [Indexed: 01/17/2023]
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Dequeker E, Stuhrmann M, Morris MA, Casals T, Castellani C, Claustres M, Cuppens H, des Georges M, Ferec C, Macek M, Pignatti PF, Scheffer H, Schwartz M, Witt M, Schwarz M, Girodon E. Best practice guidelines for molecular genetic diagnosis of cystic fibrosis and CFTR-related disorders--updated European recommendations. Eur J Hum Genet 2008. [PMID: 18685558 DOI: 10.1038/+ejhg.2008.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The increasing number of laboratories offering molecular genetic analysis of the CFTR gene and the growing use of commercial kits strengthen the need for an update of previous best practice guidelines (published in 2000). The importance of organizing regional or national laboratory networks, to provide both primary and comprehensive CFTR mutation screening, is stressed. Current guidelines focus on strategies for dealing with increasingly complex situations of CFTR testing. Diagnostic flow charts now include testing in CFTR-related disorders and in fetal bowel anomalies. Emphasis is also placed on the need to consider ethnic or geographic origins of patients and individuals, on basic principles of risk calculation and on the importance of providing accurate laboratory reports. Finally, classification of CFTR mutations is reviewed, with regard to their relevance to pathogenicity and to genetic counselling.
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Affiliation(s)
- Els Dequeker
- Center for Human Genetics, Campus Gasthuisberg, KULeuven, Belgium
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Distribution of CFTR mutations in Saguenay- Lac-Saint-Jean: proposal of a panel of mutations for population screening. Genet Med 2008; 10:201-6. [PMID: 18344710 DOI: 10.1097/gim.0b013e318164cb1c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Saguenay-Lac-Saint-Jean is a region located in the northeastern part of the Province of Quebec, Canada, and is characterized by a founder effect. In this region, it has been documented that the incidence of cystic fibrosis reached 1/902 live births between 1975 and 1988, three times higher than the average incidence of 1/2500 live births reported in other Caucasian populations. This corresponds to a carrier rate of 1/15. METHODS Using genotyping data from the Canadian Consortium for Cystic Fibrosis Genetic Studies, this article describes the cystic fibrosis transmembrane conductance regulator profile of the cystic fibrosis population living in the Saguenay-Lac-Saint-Jean region and compares it with cystic fibrosis populations living in three other regions of the Province of Quebec. RESULTS Significant differences in allelic frequencies of common mutations (as DeltaF508, 621 + 1G>T and A455E), and in percentage of covered allele with three or six mutations, were found in Saguenay-Lac-Saint-Jean compared to other regions. Based on this result, two mutation panels exceeding 90% sensitivity threshold are now proposed for cystic fibrosis carrier screening in this region. CONCLUSION The implementation of the proposed carrier screening program could diminish the incidence of this disease in this region and allow future parents to make informed decisions about family planning.
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