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Kozawa Y, Yamamoto A, Nakakuki M, Fujiki K, Kondo S, Okada T, Fukuyasu T, Yamaguchi M, Taniguchi I, Nomura N, Liu L, Higuchi M, Niwa E, Sohma Y, Naruse S, Takeyama Y, Ishiguro H. Clinical and genetic features of cystic fibrosis in Japan. J Hum Genet 2023; 68:671-680. [PMID: 37217688 DOI: 10.1038/s10038-023-01160-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/28/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by pathogenic variants in CF transmembrane conductance regulator (CFTR). While CF is the most common hereditary disease in Caucasians, it is rare in East Asia. In the present study, we have examined clinical features and the spectrum of CFTR variants of CF patients in Japan. Clinical data of 132 CF patients were obtained from the national epidemiological survey since 1994 and CF registry. From 2007 to 2022, 46 patients with definite CF were analyzed for CFTR variants. All exons, their boundaries, and part of promoter region of CFTR were sequenced and the presence of large deletion and duplications were examined by multiplex ligation-dependent probe amplification. CF patients in Japan were found to have chronic sinopulmonary disease (85.6%), exocrine pancreatic insufficiency (66.7%), meconium ileus (35.6%), electrolyte imbalance (21.2%), CF-associated liver disease (14.4%), and CF-related diabetes (6.1%). The median survival age was 25.0 years. The mean BMI percentile was 30.3%ile in definite CF patients aged < 18 years whose CFTR genotypes were known. In 70 CF alleles of East Asia/Japan origin, CFTR-dele16-17a-17b was detected in 24 alleles, the other variants were novel or very rare, and no pathogenic variants were detected in 8 alleles. In 22 CF alleles of Europe origin, F508del was detected in 11 alleles. In summary, clinical phenotype of Japanese CF patients is similar to European patients, but the prognosis is worse. The spectrum of CFTR variants in Japanese CF alleles is entirely different from that in European CF alleles.
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Affiliation(s)
- Yuka Kozawa
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akiko Yamamoto
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miyuki Nakakuki
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kotoyo Fujiki
- Department of Nutrition, Nagoya University of Arts and Sciences, Nisshin, Japan
| | - Shiho Kondo
- Department of Health and Nutrition, Nagoya Women's University, Nagoya, Japan
| | - Takuto Okada
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomoya Fukuyasu
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Food and Nutrition, Tsu City College, Tsu, Japan
| | - Makoto Yamaguchi
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Itsuka Taniguchi
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nao Nomura
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Libin Liu
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mayuko Higuchi
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Erina Niwa
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiro Sohma
- Division of Molecular Therapy, Department of Pharmaceutical Sciences, School of Pharmacy and Center for Basic Medical Research, International University of Health and Welfare, Otawara, Japan
| | | | - Yoshifumi Takeyama
- Department of Surgery, Kindai University School of Medicine, Osakasayama, Japan
| | - Hiroshi Ishiguro
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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Lee M, Roos P, Sharma N, Atalar M, Evans TA, Pellicore MJ, Davis E, Lam ATN, Stanley SE, Khalil SE, Solomon GM, Walker D, Raraigh KS, Vecchio-Pagan B, Armanios M, Cutting GR. Systematic Computational Identification of Variants That Activate Exonic and Intronic Cryptic Splice Sites. Am J Hum Genet 2017; 100:751-765. [PMID: 28475858 DOI: 10.1016/j.ajhg.2017.04.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/30/2017] [Indexed: 12/30/2022] Open
Abstract
We developed a variant-annotation method that combines sequence-based machine-learning classification with a context-dependent algorithm for selecting splice variants. Our approach is distinctive in that it compares the splice potential of a sequence bearing a variant with the splice potential of the reference sequence. After training, classification accurately identified 168 of 180 (93.3%) canonical splice sites of five genes. The combined method, CryptSplice, identified and correctly predicted the effect of 18 of 21 (86%) known splice-altering variants in CFTR, a well-studied gene whose loss-of-function variants cause cystic fibrosis (CF). Among 1,423 unannotated CFTR disease-associated variants, the method identified 32 potential exonic cryptic splice variants, two of which were experimentally evaluated and confirmed. After complete CFTR sequencing, the method found three cryptic intronic splice variants (one known and two experimentally verified) that completed the molecular diagnosis of CF in 6 of 14 individuals. CryptSplice interrogation of sequence data from six individuals with X-linked dyskeratosis congenita caused by an unknown disease-causing variant in DKC1 identified two splice-altering variants that were experimentally verified. To assess the extent to which disease-associated variants might activate cryptic splicing, we selected 458 pathogenic variants and 348 variants of uncertain significance (VUSs) classified as high confidence from ClinVar. Splice-site activation was predicted for 129 (28%) of the pathogenic variants and 75 (22%) of the VUSs. Our findings suggest that cryptic splice-site activation is more common than previously thought and should be routinely considered for all variants within the transcribed regions of genes.
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Affiliation(s)
- Melissa Lee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Neeraj Sharma
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Melis Atalar
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taylor A Evans
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Matthew J Pellicore
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emily Davis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anh-Thu N Lam
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Susan E Stanley
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sara E Khalil
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - George M Solomon
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - Doug Walker
- Pediatric Pulmonary Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Karen S Raraigh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Briana Vecchio-Pagan
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mary Armanios
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Garry R Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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McKiernan PJ, Greene CM. High-throughput profiling for discovery of non-coding RNA biomarkers of lung disease. Expert Rev Mol Diagn 2015; 16:173-85. [PMID: 26581119 DOI: 10.1586/14737159.2016.1122526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In respiratory medicine there is a need for clinical biomarkers for diagnosis, prognosis and assessment of response to therapy. Noncoding RNA (ncRNA) is expressed in all human cells; two major classes--long ncRNA and microRNA--are detectable extracellularly in the circulation and other biofluids. Altered ncRNA expression is associated with lung disease; collectively this indicates that ncRNA represents a potential biomarker class. This article presents and compares existing platforms for detection and quantification of ncRNA, specifically hybridization, qRT-PCR and RNA sequencing, and outlines methods for data interpretation and normalization. Each approach has merits and shortcomings, which can affect the choice of method when embarking on a biomarker study. Biomarker properties and pre-analytical considerations for ncRNA profiling are also presented. Since a variety of profiling approaches are available, careful study and experimental design are important. Finally, challenges and goals for reliable, standardized high-throughput ncRNA profiling in biofluids as lung disease biomarkers are reviewed.
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Affiliation(s)
- Paul J McKiernan
- a Respiratory Research, Department of Medicine, The Royal College of Surgeons in Ireland, Education and Research Centre , Beaumont Hospital , Dublin , Ireland
| | - Catherine M Greene
- a Respiratory Research, Department of Medicine, The Royal College of Surgeons in Ireland, Education and Research Centre , Beaumont Hospital , Dublin , Ireland
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McKiernan PJ, Molloy K, Cryan SA, McElvaney NG, Greene CM. Long noncoding RNA are aberrantly expressed in vivo in the cystic fibrosis bronchial epithelium. Int J Biochem Cell Biol 2014; 52:184-91. [PMID: 24631641 DOI: 10.1016/j.biocel.2014.02.022] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/24/2014] [Accepted: 02/28/2014] [Indexed: 12/12/2022]
Abstract
Long non-coding RNAs (lncRNAs) have emerged recently as key regulatory molecules with diverse roles at almost every level of the regulation of gene expression. The roles of these RNAs in the pathogenesis of cystic fibrosis (CF); a lethal multisystem, autosomal recessive disorder have yet to be explored. Our aim was to examine the expression profile of lncRNA, in the airway epithelium of people with CF. We examined the expression of 30,586 lncRNAs by microarray (Human LncRNA Array v3.0, Arraystar, Inc.), in vivo in bronchial cells isolated from endobronchial brushings obtained from CF and non-CF individuals. In total, we identified 1,063 lncRNAs with differential expression between CF and non-CF individuals (fold change ≥3, p≤0.001). The microarray also contained probes for ∼26,109 protein coding transcripts, of which 720 were differentially expressed between CF and non-CF brush samples (fold change ≥3, p≤0.001). Confirmation of a selection of differentially expressed coding mRNA and lncRNA transcripts such as XIST and TLR8 was achieved using qRT-PCR. Gene ontology bioinformatics analysis highlighted that many processes over-represented in the CF bronchial epithelium are related to inflammation. These data show a significantly altered lncRNA and mRNA expression profile in CF bronchial cells in vivo. Dysregulation of some of these lncRNAs may play important roles in the chronic infection and inflammation that exists in the lungs of people with CF.
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Affiliation(s)
- Paul J McKiernan
- Respiratory Research Division, Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Kevin Molloy
- Respiratory Research Division, Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Sally A Cryan
- School of Pharmacy, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Noel G McElvaney
- Respiratory Research Division, Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland
| | - Catherine M Greene
- Respiratory Research Division, Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin 9, Ireland.
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Lin JH, Collaco JM, Paranjape SM. Cystic fibrosis in a Hispanic adolescent. Pediatr Pulmonol 2014; 49:E40-1. [PMID: 23401342 PMCID: PMC4052445 DOI: 10.1002/ppul.22758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 01/04/2013] [Indexed: 11/10/2022]
Abstract
We describe the presentation of a Hispanic adolescent with chronic respiratory symptoms and poor growth that led to a diagnosis of cystic fibrosis (CF) based on an indeterminate sweat chloride result and DNA sequence analysis that revealed a single new frameshift mutation, Nt3878insATCAG, which results in a premature stop codon in exon 20 of the CFTR gene. This case, highlighted by the identification of a deleterious, disease-causing mutation, illustrates the importance of maintaining both a high clinical suspicion for CF and low threshold for obtaining genetic testing in a non-Caucasian Hispanic adolescent with a characteristic clinical presentation.
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Affiliation(s)
- Jenny H Lin
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
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McKiernan PJ, Cunningham O, Greene CM, Cryan SA. Targeting miRNA-based medicines to cystic fibrosis airway epithelial cells using nanotechnology. Int J Nanomedicine 2013; 8:3907-15. [PMID: 24143095 PMCID: PMC3798151 DOI: 10.2147/ijn.s47551] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cystic fibrosis (CF) is an inherited disorder characterized by chronic airway inflammation. microRNAs (miRNAs) are endogenous small RNAs which act on messenger (m) RNA at a post transcriptional level, and there is a growing understanding that altered expression of miRNA is involved in the CF phenotype. Modulation of miRNA by replacement using miRNA mimics (premiRs) presents a new therapeutic paradigm for CF, but effective and safe methods of delivery to the CF epithelium are limiting clinical translation. Herein, polymeric nanoparticles are investigated for delivery of miRNA mimics into CF airway epithelial cells, using miR-126 as a proof-of-concept premiR cargo to determine efficiency. Two polymers, polyethyleneimine (PEI) and chitosan, were used to prepare miRNA nanomedicines, characterized for their size, surface (zeta) potential, and RNA complexation efficiency, and screened for delivery and cytotoxicity in CFBE41o- (human F508del cystic fibrosis transmembrane conductance regulator bronchial epithelial) cells using a novel high content analysis method. RNA extraction was carried out 24 hours post transfection, and miR-126 and TOM1 (target of Myb1) expression (a validated miR-126 target) was assessed. Manufacture was optimized to produce small nanoparticles that effectively complexed miRNA. Using high content analysis, PEI-based nanoparticles were more effective than chitosan-based nanoparticles in facilitating uptake of miRNA into CFBE41o- cells and this was confirmed in miR-126 assays. PEI-premiR-126 nanoparticles at low nitrogen/phosphate (N/P) ratios resulted in significant knockdown of TOM1 in CFBE41o- cells, with the most significant reduction of 66% in TOM1 expression elicited at an N/P ratio of 1:1 while chitosan-based miR-126 nanomedicines failed to facilitate statistically significant knockdown of TOM1 and both nanoparticles appeared relatively nontoxic. miRNA nanomedicine uptake can be qualitatively and quantitatively assessed rapidly by high content analysis and is highly polymer-dependent but, interestingly, there is not a direct correlation between the levels of miRNA uptake and the downstream gene knockdown. Polymeric nanoparticles can deliver premiRs effectively to CFBEs in order to modulate gene expression but must be tailored specifically for miRNA delivery.
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Affiliation(s)
- Paul J McKiernan
- Respiratory Research Division, Department of Medicine, Royal College of Surgeons in Ireland Education and Research Centre, Beaumont Hospital, Dublin, Ireland
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Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet 2013; 45:1160-7. [PMID: 23974870 PMCID: PMC3874936 DOI: 10.1038/ng.2745] [Citation(s) in RCA: 428] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 07/30/2013] [Indexed: 12/16/2022]
Abstract
Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation to clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 cystic fibrosis patients in registries and clinics in North America and Europe. Among these patients, 159 CFTR variants had an allele frequency of ≥0.01%. These variants were evaluated for both clinical severity and functional consequence with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of cystic fibrosis patients enabled assignment of 12 of the remaining 32 variants as neutral while the other 20 variants remained indeterminate. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically-relevant genomic variation.
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Raynal C, Baux D, Theze C, Bareil C, Taulan M, Roux AF, Claustres M, Tuffery-Giraud S, des Georges M. A classification model relative to splicing for variants of unknown clinical significance: application to the CFTR gene. Hum Mutat 2013; 34:774-84. [PMID: 23381846 DOI: 10.1002/humu.22291] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/29/2013] [Indexed: 12/24/2022]
Abstract
Molecular diagnosis of cystic fibrosis and cystic fibrosis transmembrane regulator (CFTR)-related disorders led to the worldwide identification of nearly 1,900 sequence variations in the CFTR gene that consist mainly of private point mutations and small insertions/deletions. Establishing their effect on the function of the encoded protein and therefore their involvement in the disease is still challenging and directly impacts genetic counseling. In this context, we built a decision tree following the international guidelines for the classification of variants of unknown clinical significance (VUCS) in the CFTR gene specifically focused on their consequences on splicing. We applied general and specific criteria, including comprehensive review of literature and databases, familial genetics data, and thorough in silico studies. This model was tested on 15 intronic and exonic VUCS identified in our cohort. Six variants were classified as probably nonpathogenic considering their impact on splicing and eight as probably pathogenic, which include two apparent missense mutations. We assessed the validity of our method by performing minigenes studies and confirmed that 93% (14/15) were correctly classified. We provide in this study a high-performance method that can play a full role in interpreting the results of molecular diagnosis in emergency context, when functional studies are not achievable.
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Affiliation(s)
- Caroline Raynal
- CHU Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Génétique Moléculaire, Montpellier, France.
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Wambach JA, Wegner DJ, DePass K, Heins H, Druley TE, Mitra RD, An P, Zhang Q, Nogee LM, Cole FS, Hamvas A. Single ABCA3 mutations increase risk for neonatal respiratory distress syndrome. Pediatrics 2012; 130:e1575-82. [PMID: 23166334 PMCID: PMC3507255 DOI: 10.1542/peds.2012-0918] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Neonatal respiratory distress syndrome (RDS) due to pulmonary surfactant deficiency is heritable, but common variants do not fully explain disease heritability. METHODS Using next-generation, pooled sequencing of race-stratified DNA samples from infants ≥34 weeks' gestation with and without RDS (n = 513) and from a Missouri population-based cohort (n = 1066), we scanned all exons of 5 surfactant-associated genes and used in silico algorithms to identify functional mutations. We validated each mutation with an independent genotyping platform and compared race-stratified, collapsed frequencies of rare mutations by gene to investigate disease associations and estimate attributable risk. RESULTS Single ABCA3 mutations were overrepresented among European-descent RDS infants (14.3% of RDS vs 3.7% of non-RDS; P = .002) but were not statistically overrepresented among African-descent RDS infants (4.5% of RDS vs 1.5% of non-RDS; P = .23). In the Missouri population-based cohort, 3.6% of European-descent and 1.5% of African-descent infants carried a single ABCA3 mutation. We found no mutations among the RDS infants and no evidence of contribution to population-based disease burden for SFTPC, CHPT1, LPCAT1, or PCYT1B. CONCLUSIONS In contrast to lethal neonatal RDS resulting from homozygous or compound heterozygous ABCA3 mutations, single ABCA3 mutations are overrepresented among European-descent infants ≥34 weeks' gestation with RDS and account for ~10.9% of the attributable risk among term and late preterm infants. Although ABCA3 mutations are individually rare, they are collectively common among European- and African-descent individuals in the general population.
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Affiliation(s)
| | | | | | | | - Todd E. Druley
- Division of Hematology and Oncology, the Edward Mallinckrodt Department of Pediatrics,,Center for Genome Sciences and Systems Biology, Department of Genetics
| | - Robi D. Mitra
- Center for Genome Sciences and Systems Biology, Department of Genetics
| | - Ping An
- Division of Statistical Genomics, Washington University School of Medicine, St Louis, Missouri; and
| | - Qunyuan Zhang
- Division of Statistical Genomics, Washington University School of Medicine, St Louis, Missouri; and
| | - Lawrence M. Nogee
- Division of Neonatal–Perinatal Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Nakakuki M, Fujiki K, Yamamoto A, Ko SBH, Yi L, Ishiguro M, Yamaguchi M, Kondo S, Maruyama S, Yanagimoto K, Naruse S, Ishiguro H. Detection of a large heterozygous deletion and a splicing defect in the CFTR transcripts from nasal swab of a Japanese case of cystic fibrosis. J Hum Genet 2012; 57:427-33. [PMID: 22572733 DOI: 10.1038/jhg.2012.46] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in CFTR (CF transmembrane conductance regulator). Although CF is the most common hereditary disease in Caucasians, it is rare in Asian populations. Common disease-causing mutations of CFTR in Caucasians are rarely identified in Japanese patients with CF. In the present study, CFTR transcripts from nasal swab were analyzed in a Japanese boy, in addition to conventional PCR and direct sequence of all exons, their boundaries and promoter region of the CFTR gene. The boy was diagnosed with CF by chronic respiratory infection and the elevated sweat chloride level. None of the disease-causing mutations of CFTR was detected by the conventional analysis. Cloning and sequence of the CFTR transcripts revealed a heterozygous deletion spanning exons 16, 17a and 17b. The deletion was confirmed by multiplex ligation-dependent probe amplification and the direct sequence of the junction fragment obtained from the genomic DNA by primer walking, which revealed the mutation c.2908+1085_3367+260del7201. We also identified a splicing defect: deletion/skipping of exon 1 in the CFTR transcript from the other allele. The analysis of CFTR transcripts from nasal swab is recommended in the genetic analysis of CF in Japanese.
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Affiliation(s)
- Miyuki Nakakuki
- Department of Human Nutrition, Nagoya University Graduate School of Medicine, Research Center of Health, Physical Fitness and Sports, Nagoya University, Nagoya, Japan
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