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Banjar H, Qeretli R, Ramadan A, Al-Ibraheem A, Bnatig F. The first report on CFTR mutations of meconium ileus in cystic fibrosis population in Saudi Arabia: A single center review. INTERNATIONAL JOURNAL OF PEDIATRICS AND ADOLESCENT MEDICINE 2021; 9:32-35. [PMID: 35573065 PMCID: PMC9072234 DOI: 10.1016/j.ijpam.2021.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 03/16/2021] [Indexed: 11/26/2022] Open
Abstract
Introduction Meconium ileus (MI) is one of the most common causes of intestinal obstruction in newborns. It is the earliest clinical manifestation of cystic fibrosis (CF). MI is suspected if a baby fails to pass meconium shortly after birth and develops symptoms of bowel obstruction, such as distention of the abdomen or vomiting. MI can lead to bowel perforation, a twisting of the bowel, or inflammation and infection of the abdominal cavity. Objectives To find the incidence and prevalence of meconium ileus in cystic fibrosis patients and to report on the most common gene mutation of MI in CF patients. Methodology Retrospective review of the medical documentations of all MI patients during the period of 1989–2018. Results A total of 40 CF confirmed patients were presented with MI. Twenty-nine patients (71%) are alive and 11 patients (29%) died or lost to follow-up. The following CFTR mutations were found: Eight patients (20%) with c.2988+1G>A; Intron 18. Seven patients (17.5%) with c.1418delG; Exon 11. Five patients (12.5%) with c.579+1G>T; Intron 5. Four patients (10%) with c.1911delG; Exon 14. Four patients (10%) with c.1521_1523delCTT; Exon 11. Four patients (10%) with c.416A>T; Exon 13. Three patients (7.5%) with c.2421A>G; Exon 14. Two patients (5%) with c.3908A>C; Exon 21. One patient (2.5%) with c.3889dupT; Exon 24. One patient (2.5%) with c.1657C>T; Exon 12. One patient (2.5%) with c.2547C>A; Exon 14a. Eighteen patients (45%) were presented with vomiting, 38 patients (95%) had postnatal radiological findings, 7 patients (17.5%) had electrolytes imbalance. Five patients (12.5%) had cholestasis and 4 patients (10%) developed chronic liver disease. Thirty-five patients (79.5%) underwent surgical repair and 9 patients (20.5%) were treated medically. Mean age of operation was 2.25 (2) days. Of 9 patients, 6 (66.6%) were treated with gastrograffin enema, 2 patients (22.2%) with oral N-acetylcysteine and 1 patient (11.1%) with saline rectal wash. Thirteen patients (31.5%) required TPN. Five patients had recurrent operation. Conclusion CF and meconium ileus are commonly present in CF patients in Saudi Arabia. Prognosis is similar to other CFs without MI, if treated early. Thirty percent of our CF/MI patients have intronic mutations.
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Next-Generation Sequencing for Molecular Diagnosis of Cystic Fibrosis in a Brazilian Cohort. DISEASE MARKERS 2021; 2021:9812074. [PMID: 33613790 PMCID: PMC7878085 DOI: 10.1155/2021/9812074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/23/2020] [Accepted: 01/27/2021] [Indexed: 12/05/2022]
Abstract
Cystic fibrosis (CF), an autosomal recessive genetic disease, is recognized as one of the most prevalent diseases in Caucasian populations. Epidemiological data show that the incidence of CF varies between countries and ethnic groups in the same region. CF occurs due to pathogenic variants in the gene encoding cystic fibrosis transmembrane conductance regulator (CFTR), located on chromosome 7q31.2. To date, more than 2,000 variants have been registered in the CFTR database. The study of these variants leads to the diagnosis and the possibility of a specific treatment for each patient through precision medicine. In this study, complete screening of CFTR was performed through next-generation sequencing (NGS) to gain insight into the variants circulating in the population of Rio de Janeiro and to provide patient access to treatment through genotype-specific therapies. Samples from 93 patients with an inconclusive molecular diagnosis were subjected to full-length screening of CFTR using an Illumina NGS HiSeq platform. Among these patients, 46 had two pathogenic variants, whereas 12 had only one CFTR variant. Twenty-four variants were not part of our routine screening. Of these 24 variants, V938Gfs∗37 had not been described in the CF databases previously. This research achieved a molecular diagnosis of the patients with CF and identification of possible molecular candidates for genotype-specific treatments.
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Banjar HH, Tuleimat L, El Seoudi AAA, Mogarri I, Alhaider S, Nizami IY, AlMaghamsi T, Alkaf SA, Moghrabi N. Genotype patterns for mutations of the cystic fibrosis transmembrane conductance regulator gene: a retrospective descriptive study from Saudi Arabia. Ann Saudi Med 2020; 40:15-24. [PMID: 32026723 PMCID: PMC7012030 DOI: 10.5144/0256-4947.2020.15] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 07/20/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Cystic fibrosis (CF) occurs in populations in Saudi Arabia and the Gulf area. Approximately 2000 known variants have been identified for the CF transmembrane conductance regulator (CTFR) gene. Screening for ten of the most common variants can detect 80% of alleles. OBJECTIVE Determine the pattern of CFTR variants in the CF population of Saudi Arabia. DESIGN A retrospective, descriptive. SETTING Tertiary care center. PATIENTS AND METHODS We examined the medical records of 396 confirmed CF patients of all age groups that were positive for a CFTR variant from the period of 1 January 1998 to 1 December 2017. MAIN OUTCOME MEASURES Zygosity, morbidity and mortality patterns of different types of CFTR variants. SAMPLE SIZE 312 families that included 396 patients. RESULTS Of 48 variants identified, 6 were novel, having not been described in the medical literature. A homozygous state was found in 283 families (90.7%) and compound heterozygosity in 23 (7.4%). Six families were heterozygous (1.9%). Median age (interquartile range) was 10.2 months (4.4 months to 5.7 years) at diagnosis and 9.7 (5.4-16.5) years at follow up. Of 396 patients, 378 patients (95.5%) survived and 18 (4.5%) died. The ten most common variants identified in descending frequency were: p.Gly473GlufsX54 in 98 alleles (16%), p.Ile1234Val in 66 alleles (11%), F508del in 64 alleles (11%), 711+1G>T in 62 alleles (10%), 3120+1G>A in 62 alleles (11%), p.His139Leuin 38 alleles (6.4%), p.Gln637Hisfs in 30 alleles (5.2%), p.Ser549Arg in 27 alleles (4.5%), p.Asn1303Lys in 14 alleles (2.3%), delExon19-21in 10 alleles (1.6%). This analysis identified 79.2% of our CFTR variants. CONCLUSION CFTR mutational patterns in our CF population are characterized by a high allelic heterogeneity. The high prevalence of homozygous variants reflects the high level of consanguinity between parents. LIMITATIONS Our CFTR screening reflected only about 80% of CF patients in Saudi Arabia. CONFLICT OF INTEREST None.
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Affiliation(s)
- Hanaa Hasan Banjar
- From the Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lin Tuleimat
- From the Department of Medicine, Al Faisal University, Riyadh, Saudi Arabia
| | | | - Ibrahim Mogarri
- From the Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sami Alhaider
- From the Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Imran Yaqoob Nizami
- From the Organ Transplant Center, King Faisal Specialist and Research Center, Riyadh, Saudi Arabia
| | - Talal AlMaghamsi
- From the Department of Pediatrics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sara Andulrahman Alkaf
- From the Biostatistic Epidemiology and Scientific Computing Department, King Faisal Center for Research and Islamic Studies, Riyadh, Saudi Arabia
| | - Nabil Moghrabi
- From the Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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Banjar H, Al-Mogarri I, Nizami I, Al-Haider S, AlMaghamsi T, Alkaf S, Al-Enazi A, Moghrabi N. Geographic distribution of cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations in Saudi Arabia. Int J Pediatr Adolesc Med 2019; 8:25-28. [PMID: 33718573 PMCID: PMC7922840 DOI: 10.1016/j.ijpam.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/18/2019] [Accepted: 12/03/2019] [Indexed: 01/17/2023]
Abstract
Introduction Cystic fibrosis (CF) has been reported before in Saudi Arabia and the Gulf area. It has been found that screening for 10 most common cystic fibrosis transmembrane conductance regulator (CFTR) mutations can detect 80% of positive CFTR cases. Objectives To determine the geographic distribution of the most common CFTR variants in 5 regions of Saudi Arabia. Methodology A retrospective chart review of all CFTR variants conducted from January 1, 1992 to December 1, 2017. Results The ten most common CFTR mutations in the Saudi population were as follows: p.Gly473GlufsX54 (17%), p.Phe508del (12%), p.Ile1234Val (12%), 3120+1G > A (11%), 711+1G > T (9%), p.His139Leu (6%), p.Gln637Hisfs (5%), p.Ser549Arg (3%), p.N1303K (3%), and delExon19-21 (2%) along with other variants 79 (20%). In terms of the highest frequency, the c.2988+1G > A (3120+1G > A) variant was found in the eastern province (7.3%) of Saudi Arabia, the c.1418delG (p.Gly473GlufsX54) variant in the northern province (6.8%), the c.579+1G > T (711+1G > T) variant in the southern province (4.8%), the c.3700A > G (p.Ile1234Val) variant in the central province (4.8%), and c.1521_1523delCTT (p.Phe508del) variant in the western province (4.3%). Conclusion The eastern and the northern provinces have the highest prevalence of CF, with the c.2988+1G > A (3120+1G > A) and c.1418delG (p.Gly473GlufsX54) variants showing the highest distribution in the Saudi CF population, which may reflect the effect of consanguinity within the same tribe. Proper family screening and counseling should be emphasized.
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Affiliation(s)
- Hanaa Banjar
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Ibrahim Al-Mogarri
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Imran Nizami
- Organ Transplant Center, (King Faisal Specialist Hospital and Research Center), Riyadh, Saudi Arabia
| | - Sami Al-Haider
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Talal AlMaghamsi
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Jeddah, Saudi Arabia
| | - Sara Alkaf
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Abdulaziz Al-Enazi
- Department of Pediatrics, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Nabil Moghrabi
- Department of Genetics, Molecular Diagnostic Laboratory, The Research Center, KFSHRC, Riyadh, Saudi Arabia
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Khan H, Mew N, Kaufman S, Yazigi N, Fishbein T, Khan K. Unusual Cystic Fibrosis Transmembrane Conductance Regulator Mutations and Liver Disease: A Case Series and Review of the Literature. Transplant Proc 2019; 51:790-793. [DOI: 10.1016/j.transproceed.2018.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/27/2018] [Accepted: 11/15/2018] [Indexed: 12/18/2022]
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Fernandez Fernandez E, De Santi C, De Rose V, Greene CM. CFTR dysfunction in cystic fibrosis and chronic obstructive pulmonary disease. Expert Rev Respir Med 2018; 12:483-492. [PMID: 29750581 DOI: 10.1080/17476348.2018.1475235] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Obstructive lung diseases such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are causes of high morbidity and mortality worldwide. CF is a multiorgan genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and is characterized by progressive chronic obstructive lung disease. Most cases of COPD are a result of noxious particles, mainly cigarette smoke but also other environmental pollutants. Areas covered: Although the pathogenesis and pathophysiology of CF and COPD differ, they do share key phenotypic features and because of these similarities there is great interest in exploring common mechanisms and/or factors affected by CFTR mutations and environmental insults involved in COPD. Various molecular, cellular and clinical studies have confirmed that CFTR protein dysfunction is common in both the CF and COPD airways. This review provides an update of our understanding of the role of dysfunctional CFTR in both respiratory diseases. Expert commentary: Drugs developed for people with CF to improve mutant CFTR function and enhance CFTR ion channel activity might also be beneficial in patients with COPD. A move toward personalized therapy using, for example, microRNA modulators in conjunction with CFTR potentiators or correctors, could enhance treatment of both diseases.
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Affiliation(s)
- Elena Fernandez Fernandez
- a Lung Biology Group, Department of Clinical Microbiology , RCSI Education & Research Centre, Beaumont Hospital , Dublin 9 , Ireland
| | - Chiara De Santi
- a Lung Biology Group, Department of Clinical Microbiology , RCSI Education & Research Centre, Beaumont Hospital , Dublin 9 , Ireland
| | - Virginia De Rose
- b Department of Clinical and Biological Sciences , University of Torino , Torino , Italy
| | - Catherine M Greene
- a Lung Biology Group, Department of Clinical Microbiology , RCSI Education & Research Centre, Beaumont Hospital , Dublin 9 , Ireland
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Santos-Carballal B, Fernández Fernández E, Goycoolea FM. Chitosan in Non-Viral Gene Delivery: Role of Structure, Characterization Methods, and Insights in Cancer and Rare Diseases Therapies. Polymers (Basel) 2018; 10:E444. [PMID: 30966479 PMCID: PMC6415274 DOI: 10.3390/polym10040444] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/04/2018] [Accepted: 04/11/2018] [Indexed: 12/23/2022] Open
Abstract
Non-viral gene delivery vectors have lagged far behind viral ones in the current pipeline of clinical trials of gene therapy nanomedicines. Even when non-viral nanovectors pose less safety risks than do viruses, their efficacy is much lower. Since the early studies to deliver pDNA, chitosan has been regarded as a highly attractive biopolymer to deliver nucleic acids intracellularly and induce a transgenic response resulting in either upregulation of protein expression (for pDNA, mRNA) or its downregulation (for siRNA or microRNA). This is explained as the consequence of a multi-step process involving condensation of nucleic acids, protection against degradation, stabilization in physiological conditions, cellular internalization, release from the endolysosome ("proton sponge" effect), unpacking and enabling the trafficking of pDNA to the nucleus or the siRNA to the RNA interference silencing complex (RISC). Given the multiple steps and complexity involved in the gene transfection process, there is a dearth of understanding of the role of chitosan's structural features (Mw and degree of acetylation, DA%) on each step that dictates the net transfection efficiency and its kinetics. The use of fully characterized chitosan samples along with the utilization of complementary biophysical and biological techniques is key to bridging this gap of knowledge and identifying the optimal chitosans for delivering a specific gene. Other aspects such as cell type and administration route are also at play. At the same time, the role of chitosan structural features on the morphology, size and surface composition of synthetic virus-like particles has barely been addressed. The ongoing revolution brought about by the recent discovery of CRISPR-Cas9 technology will undoubtedly be a game changer in this field in the short term. In the field of rare diseases, gene therapy is perhaps where the greatest potential lies and we anticipate that chitosans will be key players in the translation of research to the clinic.
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Affiliation(s)
| | - Elena Fernández Fernández
- Lung Biology Group, Department Clinical Microbiology, RCSI, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland.
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Regan JF, Kamitaki N, Legler T, Cooper S, Klitgord N, Karlin-Neumann G, Wong C, Hodges S, Koehler R, Tzonev S, McCarroll SA. A rapid molecular approach for chromosomal phasing. PLoS One 2015; 10:e0118270. [PMID: 25739099 PMCID: PMC4349636 DOI: 10.1371/journal.pone.0118270] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Determining the chromosomal phase of pairs of sequence variants - the arrangement of specific alleles as haplotypes - is a routine challenge in molecular genetics. Here we describe Drop-Phase, a molecular method for quickly ascertaining the phase of pairs of DNA sequence variants (separated by 1-200 kb) without cloning or manual single-molecule dilution. In each Drop-Phase reaction, genomic DNA segments are isolated in tens of thousands of nanoliter-sized droplets together with allele-specific fluorescence probes, in a single reaction well. Physically linked alleles partition into the same droplets, revealing their chromosomal phase in the co-distribution of fluorophores across droplets. We demonstrated the accuracy of this method by phasing members of trios (revealing 100% concordance with inheritance information), and demonstrate a common clinical application by phasing CFTR alleles at genomic distances of 11-116 kb in the genomes of cystic fibrosis patients. Drop-Phase is rapid (requiring less than 4 hours), scalable (to hundreds of samples), and effective at long genomic distances (200 kb).
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Affiliation(s)
- John F. Regan
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
- * E-mail: (JFR); (SAM)
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Cambridge, Massachusetts, United States of America
| | - Tina Legler
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Samantha Cooper
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Niels Klitgord
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - George Karlin-Neumann
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Catherine Wong
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shawn Hodges
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Ryan Koehler
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Svilen Tzonev
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, United States of America
| | - Steven A. McCarroll
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Cambridge, Massachusetts, United States of America
- * E-mail: (JFR); (SAM)
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Martinez B, Heller M, Gaitch N, Hubert D, Burgel PR, Levy P, Girodon E, Bienvenu T. p.Arg75Gln, a CFTR variant involved in the risk of CFTR-related disorders? J Hum Genet 2014; 59:206-10. [DOI: 10.1038/jhg.2014.2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/02/2013] [Accepted: 12/05/2013] [Indexed: 01/08/2023]
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Cystic fibrosis: insight into CFTR pathophysiology and pharmacotherapy. Clin Biochem 2012; 45:1132-44. [PMID: 22698459 DOI: 10.1016/j.clinbiochem.2012.05.034] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Revised: 05/15/2012] [Accepted: 05/28/2012] [Indexed: 12/14/2022]
Abstract
Cystic fibrosis is the most common life-threatening recessively inherited disease in Caucasians. Due to early provision of care in specialized reference centers and more comprehensive care, survival has improved over time. Despite great advances in supportive care and in our understanding of its pathophysiology, there is still no cure for the disease. Therapeutic strategies aimed at rescuing the abnormal protein are either being sought after or under investigation. This review highlights salient insights into pathophysiology and candidate molecules suitable for CFTR pharmacotherapy. Clinical trials using Ataluren, VX-809 and ivacaftor have provided encouraging data. Preclinical data with inhibitors of phosphodiesterase type 5, such as sildenafil and analogs, have highlighted their potential for CFTR pharmacotherapy. Because sildenafil and analogs are in clinical use for other clinical applications, research on this class of drugs might speed up the development of new therapies for CF.
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Ivacaftor potentiation of multiple CFTR channels with gating mutations. J Cyst Fibros 2012; 11:237-45. [DOI: 10.1016/j.jcf.2011.12.005] [Citation(s) in RCA: 312] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 12/21/2011] [Accepted: 12/27/2011] [Indexed: 01/09/2023]
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Schneider A, LaRusch J, Sun X, Aloe A, Lamb J, Hawes R, Cotton P, Brand RE, Anderson MA, Money ME, Banks PA, Lewis MD, Baillie J, Sherman S, DiSario J, Burton FR, Gardner TB, Amann ST, Gelrud A, George R, Kassabian S, Martinson J, Slivka A, Yadav D, Oruc N, Barmada MM, Frizzell R, Whitcomb DC, Whitcomb DC. Combined bicarbonate conductance-impairing variants in CFTR and SPINK1 variants are associated with chronic pancreatitis in patients without cystic fibrosis. Gastroenterology 2011; 140:162-71. [PMID: 20977904 PMCID: PMC3171690 DOI: 10.1053/j.gastro.2010.10.045] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 09/14/2010] [Accepted: 10/15/2010] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Idiopathic chronic pancreatitis (ICP) is a complex inflammatory disorder associated with multiple genetic and environmental factors. In individuals without cystic fibrosis (CF), variants of CFTR that inhibit bicarbonate conductance but maintain chloride conductance might selectively impair secretion of pancreatic juice, leading to trypsin activation and pancreatitis. We investigated whether sequence variants in the gene encoding the pancreatic secretory trypsin inhibitor SPINK1 further increase the risk of pancreatitis in these patients. METHODS We screened patients and controls for variants in SPINK1 associated with risk of chronic pancreatitis and in all 27 exons of CFTR. The final study group included 53 patients with sporadic ICP, 27 probands with familial ICP, 150 unrelated controls, 375 additional controls for limited genotyping. CFTR wild-type and p.R75Q were cloned and expressed in HEK293 cells, and relative conductances of HCO(3)(-) and Cl(-) were measured. RESULTS SPINK1 variants were identified in 36% of subjects and 3% of controls (odds ratio [OR], 18.1). One variant of CFTR not associated with CF, p.R75Q, was found in 16% of subjects and 5.3% of controls (OR, 3.4). Coinheritance of CFTR p.R75Q and SPINK1 variants occurred in 8.75% of patients and 0.38% of controls (OR, 25.1). Patch-clamp recordings of cells that expressed CFTR p.R75Q showed normal chloride currents but significantly reduced bicarbonate currents (P = .0001). CONCLUSIONS The CFTR variant p.R75Q causes a selective defect in bicarbonate conductance and increases risk of pancreatitis. Coinheritance of p.R75Q or CF causing CFTR variants with SPINK1 variants significantly increases the risk of ICP.
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Affiliation(s)
| | - Jessica LaRusch
- Department of Medicine, University of Pittsburgh, Pittsburgh PA
| | - Xiumei Sun
- Department of Cell Biology and Physiology, University of Pittsburgh, Pittsburgh PA
| | - Amy Aloe
- Department of Medicine, University of Pittsburgh, Pittsburgh PA
| | - Janette Lamb
- Department of Medicine, University of Pittsburgh, Pittsburgh PA
| | - Robert Hawes
- Digestive Disease Center, Medical University of South Carolina, Charleston, SC
| | - Peter Cotton
- Digestive Disease Center, Medical University of South Carolina, Charleston, SC
| | - Randall E. Brand
- Department of Medicine, Evanston Northwestern Healthcare, Chicago IL
| | | | | | - Peter A. Banks
- Division of Gastroenterology, Brigham and Women’s Hospital, Boston MD
| | - Michele D. Lewis
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL
| | - John Baillie
- Department of Medicine, Duke University Medical Center, Durham NC
| | - Stuart Sherman
- Department of Medicine, Indiana University Medical Center, Indianapolis, IN
| | - James DiSario
- Monterey Bay Gastroenterology Consultants, Monterey, CA
| | - Frank R. Burton
- Department of Internal Medicine, St. Louis University School of Medicine, St Louis, MO
| | | | | | - Andres Gelrud
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH
| | - Ryan George
- Department of Medicine, University of Pittsburgh, Pittsburgh PA
| | | | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh PA
| | - Adam Slivka
- Department of Medicine, University of Pittsburgh, Pittsburgh PA
| | - Dhiraj Yadav
- Department of Medicine, University of Pittsburgh, Pittsburgh PA
| | - Nevin Oruc
- Department of Medicine, University of Pittsburgh, Pittsburgh PA
| | | | - Raymond Frizzell
- Department of Cell Biology and Physiology, University of Pittsburgh, Pittsburgh PA
| | - David C. Whitcomb
- Department of Medicine, University of Pittsburgh, Pittsburgh PA, Department of Cell Biology and Physiology, University of Pittsburgh, Pittsburgh PA, Department of Human Genetics, University of Pittsburgh, Pittsburgh PA
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Watihayati MS, Fatemeh H, Marini M, Atif AB, Zahiruddin WM, Sasongko TH, Tang TH, Zabidi-Hussin ZAMH, Nishio H, Zilfalil BA. Combination of SMN2 copy number and NAIP deletion predicts disease severity in spinal muscular atrophy. Brain Dev 2009; 31:42-5. [PMID: 18842367 DOI: 10.1016/j.braindev.2008.08.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 08/04/2008] [Accepted: 08/22/2008] [Indexed: 11/19/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by mutations in the SMN1 gene. The SMN2 gene is highly homologous to SMN1 and has been reported to be correlated with severity of the disease. The clinical presentation of SMA varies from severe to mild, with three clinical subtypes (type I, type II, and type III) that are assigned according to age of onset and severity of the disease. Here, we aim to investigate the potential association between the number of copies of SMN2 and the deletion in the NAIP gene with the clinical severity of SMA in patients of Malaysian origin. Forty-two SMA patients (14 of type I, 20 type II, and 8 type III) carrying deletions of the SMN1 gene were enrolled in this study. SMN2 copy number was determined by fluorescence-based quantitative polymerase chain reaction assay. Twenty-nine percent of type I patients carried one copy of SMN2, while the remaining 71% carried two copies. Among the type II and type III SMA patients, 29% of cases carried two copies of the gene, while 71% carried three or four copies of SMN2. Deletion analysis of NAIP showed that 50% of type I SMA patients had a homozygous deletion of exon 5 of this gene and that only 10% of type II SMA cases carried a homozygous deletion, while all type III patients carried intact copies of the NAIP gene. We conclude that there exists a close relationship between SMN2 copy number and SMA disease severity, suggesting that the determination of SMN2 copy number may be a good predictor of SMA disease type. Furthermore, NAIP gene deletion was found to be associated with SMA severity. In conclusion, combining the analysis of deletion of NAIP with the assessment of SMN2 copy number increases the value of this tool in predicting the severity of SMA.
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Affiliation(s)
- Mohd Shamshudin Watihayati
- Human Genome Center, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kota Bharu, Kelantan, Malaysia
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Loumi O, Ferec C, Mercier B, Creff J, Fercot B, Denine R, Grangaud JP. CFTR mutations in the Algerian population. J Cyst Fibros 2008; 7:54-9. [PMID: 17572159 DOI: 10.1016/j.jcf.2007.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 04/19/2007] [Accepted: 04/24/2007] [Indexed: 10/23/2022]
Abstract
The nature and frequency of the major CFTR mutations in the North African population remain unclear, although a small number of CFTR mutation detection studies have been done in Algeria and Tunisia, showing largely European mutations such as F508del, G542X and N1303K, albeit at different frequencies, which presumably emerged via population admixture with Caucasians. Some unique mutations were identified in these populations. This is the first study that includes a genetic and clinical evaluation of CF patients living in Algeria. In order to offer an effective diagnostic service and to make accurate risk estimates, we decided to identify the CFTR mutations in 81 Algerian patients. We carried out D-HPLC, chemical-clamp denaturing gradient gel electrophoresis, multiplex amplification analysis of the CFTR gene and automated direct DNA sequencing. We identified 15 different mutations which account for 58.5% of the CF chromosomes. We used a quantitative PCR technique (quantitative multiplex PCR short fragment fluorescence analysis) to screen for deletion/duplication in the 27 exons of the gene. Taking advantage of the homogeneity of the sample, we report clinical features of homozygous CF patients. As CFTR mutations have been detected in males with infertility, 46 unrelated Algerian individuals with obstructive azoospermia were also investigated.
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Affiliation(s)
- O Loumi
- Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Bab-Ezzouar Alger, Algérie.
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15
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Lee P, Waalen J, Crain K, Smargon A, Beutler E. Human chitotriosidase polymorphisms G354R and A442V associated with reduced enzyme activity. Blood Cells Mol Dis 2007; 39:353-60. [PMID: 17693102 PMCID: PMC2696477 DOI: 10.1016/j.bcmd.2007.06.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Accepted: 06/06/2007] [Indexed: 10/23/2022]
Abstract
A common polymorphism in the chitotriosidase gene (CHIT1) exists in which a 24 bp duplication in exon 10 results in aberrant splicing and deletion of 87 nucleotides. In this study, the gene frequency was found to be 0.56 (n=2054) in subjects of Asian ancestry, 0.17 (n=984) in subjects of European ancestry and 0.07 (n=536) in subjects of African ancestry. Notably, the median enzyme activity in wild-type subjects (TT) was much higher in subjects of European ancestry (2.69 mU/ml, n=202 subjects), than subjects of African (2.57 mU/ml, n=230 subjects) (P<0.0001) and Asian ancestry (0.86 mU/ml, n=114 subjects) (P<0.0001). The question of why chitotriosidase deficiency exists at such a high frequency is a challenging one. We postulated that if there was a selective advantage for chitotriosidase deficiency then there would be polymorphisms that would be associated with reduced enzyme activity independent of the 24 bp duplication. We found that the G102S and the A442G polymorphisms found occurring in subjects of all ancestries were not significantly associated with a reduction of enzyme activity. In contrast, the G354R (P<0.0001) and the A442V (P=0.0013) polymorphisms occurring predominantly in subjects of African ancestry were significantly associated with reduced chitotriosidase activity. We also investigated the possibility that chitotriosidase deficiency was associated with tuberculosis or with atopy, including allergic rhinitis, contact dermatitis, food or drug allergies and asthma.
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Affiliation(s)
- Pauline Lee
- The Scripps Research Institute, Department of Molecular and Experimental Medicine, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Sontag MK, Corey M, Hokanson JE, Marshall JA, Sommer SS, Zerbe GO, Accurso FJ. Genetic and physiologic correlates of longitudinal immunoreactive trypsinogen decline in infants with cystic fibrosis identified through newborn screening. J Pediatr 2006; 149:650-657. [PMID: 17095337 DOI: 10.1016/j.jpeds.2006.07.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 05/23/2006] [Accepted: 07/12/2006] [Indexed: 10/23/2022]
Abstract
OBJECTIVES To characterize the time course and physiologic significance of decline in serum immunoreactive trypsinogen (IRT) levels in infants with cystic fibrosis (CF) by mode of diagnosis and genotype, and to examine IRT heritability. STUDY DESIGN We studied longitudinal IRT measurements in 317 children with CF. We developed statistical models to describe IRT decline. Pancreatic disease severity (Mild or Severe) was assigned using CF genotype and was confirmed in 47 infants through fat malabsorption studies. RESULTS Infants with severe disease exhibited IRT decline with non-detectable levels typically seen by 5 years of age. Infants with mild disease exhibited a decline in the first 2 years, asymptomatically approaching a level greater than published norms. IRT and fecal fat were inversely correlated. IRT values in infants with meconium ileus (MI) were significantly lower than newborn-screened infants at birth. The high proportion of shared variation in predicted IRT values among sibling pairs with severe disease suggests that IRT is heritable. CONCLUSIONS IRT declines characteristically in infants with CF. Lower IRT values in newborns with MI suggest increased pancreatic injury. Furthermore, IRT is heritable among patients with severe disease suggesting genetic modifiers of early CF pancreatic injury. This study demonstrates heritability of a statistically modeled quantitative phenotype.
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Affiliation(s)
- Marci K Sontag
- Department of Preventive Medicine and Biometrics, University of Colorado Health Sciences Center, Denver, Colorado, USA.
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17
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Sklan EH, Podoly E, Soreq H. RACK1 has the nerve to act: structure meets function in the nervous system. Prog Neurobiol 2006; 78:117-34. [PMID: 16457939 DOI: 10.1016/j.pneurobio.2005.12.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2005] [Revised: 11/20/2005] [Accepted: 12/07/2005] [Indexed: 11/26/2022]
Abstract
The receptor for activated protein kinase C 1 (RACK1) is an intracellular adaptor protein. Accumulating evidence attributes to this member of the tryptophan-aspartate (WD) repeat family the role of regulating several major nervous system pathways. Structurally, RACK1 is a seven-bladed-beta-propeller, interacting with diverse proteins having distinct structural folds. When bound to the IP3 receptor, RACK1 regulates intracellular Ca2+ levels, potentially contributing to processes such as learning, memory and synaptic plasticity. By binding to the NMDA receptor, it dictates neuronal excitation and sensitivity to ethanol. When bound to the stress-induced acetylcholinesterase variant AChE-R, RACK1 is implicated in stress responses and behavior, compatible with reports of RACK1 modulations in brain ageing and in various neurodegenerative diseases. This review sheds new light on both the virtues and the variety of neuronal RACK1 interactions and their physiological consequences.
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Affiliation(s)
- Ella H Sklan
- The Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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18
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Divac A, Nikolic A, Mitic-Milikic M, Nagorni-Obradovic L, Petrovic-Stanojevic N, Dopudja-Pantic V, Nadaskic R, Savic A, Radojkovic D. High frequency of the R75Q CFTR variation in patients with chronic obstructive pulmonary disease. J Cyst Fibros 2005; 3:189-91. [PMID: 15463907 DOI: 10.1016/j.jcf.2004.05.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2004] [Accepted: 05/17/2004] [Indexed: 02/02/2023]
Abstract
We performed the complete screening of the CFTR gene in a group of 31 patients with COPD in order to investigate the impact of mutations and polymorphisms in the CFTR gene. The cumulative frequency of CFTR mutations (17.74%) was significantly higher than in our general population (P < 0.0001). The R75Q was significantly overrepresented in COPD patients (8.06%; P = 0.002). In all patients carrying the R75Q chronic bronchitis was a dominant symptom of COPD, and all were homozygous for the V470 allele. These findings suggest that R75Q mutation could be characteristic CFTR variant for COPD patients.
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Affiliation(s)
- Aleksandra Divac
- Institute of Molecular Genetics and Genetic Engineering, Vojvode Stepe 444A, 11000 Belgrade, Serbia and Montenegro
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De Angioletti M, Lacerra G, Sabato V, Carestia C. Beta+45 G --> C: a novel silent beta-thalassaemia mutation, the first in the Kozak sequence. Br J Haematol 2004; 124:224-31. [PMID: 14687034 DOI: 10.1046/j.1365-2141.2003.04754.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A family from the Southeast of Italy was found to have a novel beta-globin mutant, beta+45 G-->C, with the features of a silent beta-thalassaemia mutation. It was asymptomatic in two heterozygotes, but its interaction with the severe thalassaemia mutation beta-IVS-II-654 C-->T worsened the haematological and biosynthetic phenotype in two compound heterozygotes; moreover, another compound heterozygote, who was also heterozygote for the alphaalphaalpha(anti3.7), suffered from thalassaemia intermedia. The mutation was found associated in cis with the IVS-II-754 T-->C substitution, which did not lead to abnormally spliced mRNA. Furthermore, the amount of beta+45 mRNA was the same as the betaA mRNA in the reticulocytes of the carriers. In vitro transcription/translation experiments demonstrated that the beta+45 G-->C decreased the efficiency of translation of the beta-globin chain by about 30%: this slight impairment was consistent with the observed clinical phenotype. The beta+45 G-->C is the first mutation found in the Kozak sequence (GACACCATGG) of the beta-globin gene and the first one at the position -6 upstream the ATG. The Kozak consensus sequence plays a major role in the initiation of translation process. The present finding supports the hypothesis that the G in position -6 is important in this process.
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Affiliation(s)
- Maria De Angioletti
- Istituto di Genetica e Biofisica Adriano Buzzati Traverso, CNR Via G. Marconi 10-12, 80125 Naples, Italy
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20
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Bernacki SH, Farkas DH, Shi W, Chan V, Liu Y, Beck JC, Bailey KS, Pratt VM, Monaghan KG, Matteson KJ, Schaefer FV, Friez M, Shrimpton AE, Stenzel TT. Bioelectronic Sensor Technology for Detection of Cystic Fibrosis and Hereditary Hemochromatosis Mutations. Arch Pathol Lab Med 2003; 127:1565-72. [PMID: 14632577 DOI: 10.5858/2003-127-1565-bstfdo] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Context.—Bioelectronic sensors, which combine microchip and biological components, are an emerging technology in clinical diagnostic testing. An electronic detection platform using DNA biochip technology (eSensor) is under development for molecular diagnostic applications. Owing to the novelty of these devices, demonstrations of their successful use in practical diagnostic applications are limited.
Objective.—To assess the performance of the eSensor bioelectronic method in the validation of 6 Epstein-Barr virus–transformed blood lymphocyte cell lines with clinically important mutations for use as sources of genetic material for positive controls in clinical molecular genetic testing. Two cell lines carry mutations in the CFTR gene (cystic fibrosis), and 4 carry mutations in the HFE gene (hereditary hemochromatosis).
Design.—Samples from each cell line were sent for genotype determination to 6 different molecular genetic testing facilities, including the laboratory developing the DNA biochips. In addition to the bioelectronic method, at least 3 different molecular diagnostic methods were used in the analysis of each cell line. Detailed data were collected from the DNA biochip output, and the genetic results were compared with those obtained using the more established methods.
Results.—We report the successful use of 2 applications of the bioelectronic platform, one for detection of CFTR mutations and the other for detection of HFE mutations. In all cases, the results obtained with the DNA biochip were in concordance with those reported for the other methods. Electronic signal output from the DNA biochips clearly differentiated between mutated and wild-type alleles. This is the first report of the use of the cystic fibrosis detection platform.
Conclusions.—Bioelectronic sensors for the detection of disease-causing mutations performed well when used in a “real-life” situation, in this case, a validation study of positive control blood lymphocyte cell lines with mutations of public health importance. This study illustrates the practical potential of emerging bioelectronic DNA detection technologies for use in current molecular diagnostic applications.
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Affiliation(s)
- Susan H Bernacki
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
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Durno C, Corey M, Zielenski J, Tullis E, Tsui LC, Durie P. Genotype and phenotype correlations in patients with cystic fibrosis and pancreatitis. Gastroenterology 2002; 123:1857-64. [PMID: 12454843 DOI: 10.1053/gast.2002.37042] [Citation(s) in RCA: 149] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Pancreatitis is known to occur in some patients with cystic fibrosis (CF), but the prevalence, natural history, and genotypic basis are unclear. We examined a well-defined cohort of patients with CF to answer these questions. METHODS Patients with CF were identified from a computerized database (1966-1996). Chart audit identified all patients with CF and pancreatitis. RESULTS Among 1075 patients with CF, 937 (87%) were pancreatic insufficient at diagnosis, 28 (3%) were pancreatic sufficient but developed pancreatic insufficiency after diagnosis, and 110 (10%) have remained pancreatic sufficient. No patients with pancreatic insufficiency developed pancreatitis. Nineteen patients (17.3%) with pancreatic sufficiency experienced one or more attacks of pancreatitis. The mean age at diagnosis of pancreatitis was 22.7 +/- 10.3 years (range, 10-35 years), and pancreatitis was recognized before the diagnosis of CF in 6 patients (32%). The diagnosis of CF in pancreatic-sufficient patients, with and without pancreatitis, was established at a significantly older age than in those with pancreatic insufficiency (P < 0.0001). Genotyped patients with pancreatic insufficiency carried 2 severe mutant alleles. All genotyped patients with pancreatic sufficiency and pancreatitis carried at least one mild mutation. No specific genotype was predictive of pancreatitis. CONCLUSIONS Patients with CF with pancreatic sufficiency carry at least one mild mutant allele and are at a significant risk of developing pancreatitis. Symptoms of pancreatitis may precede the diagnosis of CF. Pancreatitis is associated with an otherwise mild CF phenotype.
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Affiliation(s)
- Carol Durno
- Programmes in Integrative Biology, The Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
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23
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Kilinç MO, Ninis VN, Dağli E, Demirkol M, Ozkinay F, Arikan Z, Coğulu O, Hüner G, Karakoç F, Tolun A. Highest heterogeneity for cystic fibrosis: 36 mutations account for 75% of all CF chromosomes in Turkish patients. AMERICAN JOURNAL OF MEDICAL GENETICS 2002; 113:250-7. [PMID: 12439892 DOI: 10.1002/ajmg.10721] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We analyzed the CFTR locus in 83 Turkish cystic fibrosis patients to identify mutations, haplotypes, and the carrier frequency in the population. We detected 36 different mutations in 125 (75%) of the total 166 CF chromosomes. Seven novel mutations were identified: four missense (K68E, Q493P, E608G, and V1147I), two splice-site (406 -3T > C and 3849 +5G > A), and one deletion (CFTRdele17b,18). The data showed that the Turkish population has the highest genetic heterogeneity at the CFTR locus reported so far. The results of this thorough molecular analysis at the CFTR locus of a population not of European descent shows that CF is not uncommon in all such populations. The large number of mutations present, as well as the high heterogeneity in haplotypes associated with the mutations suggests that most of the mutations have persisted for a long time in the population. Consistently, the carrier frequency is assessed to be high, indicating that the disease in the population is ancient.
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Affiliation(s)
- Mehmet Okyay Kilinç
- Department of Molecular Biology and Genetics, Boğaziçi University, Bebek 80815 Istanbul, Turkey
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24
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A common polymorphism in the annexin V Kozak sequence (−1C>T) increases translation efficiency and plasma levels of annexin V, and decreases the risk of myocardial infarction in young patients. Blood 2002. [DOI: 10.1182/blood.v100.6.2081] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractAnnexin V has phospholipid-binding capacity and plays a potent antithrombotic role. Recently, a C to T transition has been described in the Kozak region of this gene, affecting the nucleotide preceding the initiation ATG codon. We have developed a simple method to detect this genetic change, showing by analysis of 580 Mediterranean white subjects that the −1C to T transition (−1C>T) is a common polymorphism (allele frequency, 0.121). This polymorphism is in linkage disequilibrium with a new C>G polymorphism located 27 bp downstream in intron 2. We show that −1C/C carriers presented significantly lower plasma levels of annexin V than −1C/T subjects (0.45 ± 0.20 ng/mL versus 0.73 ± 0.28 ng/mL, respectively;P = .02). In vitro transcription/translation experiments support that the −1T allele increases translation efficiency. The clinical relevance of the −1C>T change was investigated in consecutive patients with nontraumatic spontaneous intracranial hemorrhage (n = 225), deep venous thrombosis (n = 151), and coronary heart disease (n = 101). Finally, we also studied 166 survivors of an acute myocardial infarction occurring at age of 45 or less. This polymorphism seems to have a minor effect in bleeding disorders, but to play a protective role against early myocardial infarction, reducing by 2-fold the risk of developing the disease (P = .006; odds ratio, 0.51; 95% confidence interval, 0.30-0.85).
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25
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A common polymorphism in the annexin V Kozak sequence (−1C>T) increases translation efficiency and plasma levels of annexin V, and decreases the risk of myocardial infarction in young patients. Blood 2002. [DOI: 10.1182/blood.v100.6.2081.h81802002081_2081_2086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Annexin V has phospholipid-binding capacity and plays a potent antithrombotic role. Recently, a C to T transition has been described in the Kozak region of this gene, affecting the nucleotide preceding the initiation ATG codon. We have developed a simple method to detect this genetic change, showing by analysis of 580 Mediterranean white subjects that the −1C to T transition (−1C>T) is a common polymorphism (allele frequency, 0.121). This polymorphism is in linkage disequilibrium with a new C>G polymorphism located 27 bp downstream in intron 2. We show that −1C/C carriers presented significantly lower plasma levels of annexin V than −1C/T subjects (0.45 ± 0.20 ng/mL versus 0.73 ± 0.28 ng/mL, respectively;P = .02). In vitro transcription/translation experiments support that the −1T allele increases translation efficiency. The clinical relevance of the −1C>T change was investigated in consecutive patients with nontraumatic spontaneous intracranial hemorrhage (n = 225), deep venous thrombosis (n = 151), and coronary heart disease (n = 101). Finally, we also studied 166 survivors of an acute myocardial infarction occurring at age of 45 or less. This polymorphism seems to have a minor effect in bleeding disorders, but to play a protective role against early myocardial infarction, reducing by 2-fold the risk of developing the disease (P = .006; odds ratio, 0.51; 95% confidence interval, 0.30-0.85).
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26
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Orgad S, Neumann S, Loewenthal R, Netanelov-Shapira I, Gazit E. Prevalence of cystic fibrosis mutations in Israeli Jews. GENETIC TESTING 2001; 5:47-52. [PMID: 11336401 DOI: 10.1089/109065701750168725] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The aim of this study was to evaluate the screening policies of cystic fibrosis (CF) in the Jewish population. The prevalence of mutations that account for CF in Israel have been defined in the past by determining the frequency of CF mutations in affected individuals. This study is a population-based study and is, therefore, different from previous patient-based studies. We found that the CF mutations D1152H, W1089X, and 405 + IG-->A were present in some ethnic groups in which no CF patients carrying these mutations were reported. These facts necessitate a reevaluation of the screening policy regarding the ethnic groups in Israel. We studied 9,430 healthy Jewish Israeli individuals of 36 countries of origin. The prevalence of CF mutations was 1:19, 1:19, 1:28, and 1:42 for the Ashkenazi, Sephardi, North African, and Eastern Jews, respectively. CF mutations were identified in 374 (4.0%) individuals. These included 173 (46.3%) carriers of the W1282X mutation; 110 (29.4%) found to carry delF508; 23 (6.1%) who carried G542X; 22 (5.9%) who carried 3849 + 10Kb (C-->T; 20 (5.3%) who carried D1152H; 10 (2.7%) who carried N1303K; 11 (2.9%) who carried 405 + IG-->A; 4 (1.1%) who carried W1089X; and one (0.3%) who carried S549R. No carriers were detected for the 1717-1G-->A, G85E, and T360K mutations, which were tested for in 7,383, 1,558, and 41 individuals, respectively.
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Affiliation(s)
- S Orgad
- Transplantation Division, Biomolecular Section, CF Screening Unit, Sheba Medical Center, Tel Hashomer, Israel.
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Wong LJ, Wang J, Zhang YH, Hsu E, Heim RA, Bowman CM, Woo MS. Improved detection of CFTR mutations in Southern California Hispanic CF patients. Hum Mutat 2001; 18:296-307. [PMID: 11668613 DOI: 10.1002/humu.1191] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), a common autosomal recessive disease in Caucasians. The broad mutation spectrum varies among different patient groups. Current molecular diagnoses are designed to detect 80-97% of CF chromosomes in Caucasians and Ashkenazi Jews but have a much lower detection rate in Hispanic CF patients. Grebe et al. [1994] reported a 58% detection rate in Hispanic patients. Since then, there has been no large-scale, complete mutational analysis of Hispanic CF patients. In this study, the mutations in 62 Hispanic patients from southern California were investigated. The entire coding and flanking intronic regions of the CFTR gene were analyzed by temporal temperature gradient gel electrophoresis (TTGE) followed by sequencing to identify the mutations. Eleven novel mutations were discovered in this patient group: 3876delA, 406-1G>A, 935delA, 663delT, 3271delGG, 2105-2117del13insAGAAA, 3199del6, Q179K, 2108delA, 3171delC, and 3500-2A>T. Among the mutations, seven were out-of-frame insertions and deletions that result in truncated proteins, two were splice-site mutations, one was an in-frame 6 bp deletion, and one was a missense mutation that involved the non-conservative change of glutamine-179 to lysine. All patients presented severe classical clinical course with pancreatic insufficiency and poor growth, consistent with the nature of truncation mutation. The results indicate that TTGE screening following the analysis of recurrent mutations will substantially improve the mutation detection rate for Hispanic CF patients from southern California.
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Affiliation(s)
- L J Wong
- Institute for Molecular and Human Genetics, Georgetown University Medical Center, Washington, DC, USA.
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28
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Daudin M, Bieth E, Bujan L, Massat G, Pontonnier F, Mieusset R. Congenital bilateral absence of the vas deferens: clinical characteristics, biological parameters, cystic fibrosis transmembrane conductance regulator gene mutations, and implications for genetic counseling. Fertil Steril 2000; 74:1164-74. [PMID: 11119745 DOI: 10.1016/s0015-0282(00)01625-3] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
OBJECTIVE To evaluate relationships between the phenotypic and genotypic characteristics of patients with congenital bilateral absence of the vas deferens (CBAVD). DESIGN Retrospective study. SETTING A university hospital urology-andrology department. PATIENT(S) Forty-one men with CBAVD. INTERVENTION(S) CBAVD was diagnosed during surgical and/or ultrasound exploration of the vasa deferentia (VD) (n = 39), or on the basis of impalpable scrotal VD (n = 2). MAIN OUTCOME MEASURE(S) History, clinical and seminal characteristics, and cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations including IVS-8 polyT analysis. RESULT(S) A palpable scrotal vas deferens was present as a fibrous cord or nonpermeable duct in 13% of patients undergoing surgical exploration. Seminal vesicles were bilaterally absent in 28% of patients. No CFTR gene mutation or 5T allele was detected in 24.5% of the patients. Two CBAVD patients with renal agenesis carried a CFTR gene mutation (DeltaF508/5T-9T and R117G/7T-9T). CBAVD patients who have both a semen volume of < or =1.0 mL and a semen pH of < 7.0 have a significantly higher risk of severe CFTR gene mutation (OR = 9.12 [95% CI = 1.81-49.50]). CONCLUSION(S) A palpable scrotal vas deferens was found in 13% of CBAVD patients. Semen volume of < or =1.0 mL and semen pH of < 7.0 in CBAVD patients were associated with a higher risk of severe CFTR gene mutations. Patients with CBAVD and renal agenesis should be screened for CFTR gene mutations before assisted reproductive techniques are used.
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Affiliation(s)
- M Daudin
- CECOS Midi-Pyrénées, Toulouse, France.
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29
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Wolf MT, Lorenz B, Winterpacht A, Drechsler M, Schumacher V, Royer-Pokora B, Blankenagel A, Zabel B, Wildhardt G. Ten novel mutations found in Aniridia. Hum Mutat 2000; 12:304-13. [PMID: 9792406 DOI: 10.1002/(sici)1098-1004(1998)12:5<304::aid-humu3>3.0.co;2-d] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Aniridia (AN) is a sight-threatening congenital ocular disorder characterized by iris hypoplasia, corneal pannus, foveal and optic nerve hypoplasia, cataract formation, and glaucoma. In two-thirds of the patients, AN is inherited in an autosomal dominant fashion with almost complete penetrance but variable expression. The remaining cases are sporadic. Aniridia has been shown to be associated with mutations in the PAX6 gene, located on chromosome 11p13, telomeric to the Wilms' tumor predisposition gene (WT1). This paper describes 14 mutations in the PAX6 gene in patients with AN. Among these 14 mutations, 10 have been unpublished until now. They result most probably in haploinsufficiency and consequently in a reduced protein level of functional PAX6 protein. The mutations reported here are scattered all over the gene, including the paired-box, the glycine-rich region, the homeobox, and the proline-serine-threonine (PST)-rich region.
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Affiliation(s)
- M T Wolf
- University Children's Hospital, Mainz, Germany
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Friedman KJ, Heim RA, Knowles MR, Silverman LM. Rapid characterization of the variable length polythymidine tract in the cystic fibrosis (CFTR) gene: association of the 5T allele with selected CFTR mutations and its incidence in atypical sinopulmonary disease. Hum Mutat 2000; 10:108-15. [PMID: 9259194 DOI: 10.1002/(sici)1098-1004(1997)10:2<108::aid-humu3>3.0.co;2-g] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The CFTR intron 8 variable length polythymidine tract modulates the cystic fibrosis (CF) phenotype associated with the mutation R117H. To explore whether other mutations reside on multiple intron 8 backgrounds with discernible impacts on phenotype, we developed an allele-specific PCR assay to characterize this locus. Our approach types samples rapidly without the use or radioisotopes. Polythymidine alleles were identified for mutations either associated with a wide range of clinical phenotypes (R117H, R347P, G85E, D1152H, R334W, 2789 + 5 G > A, 3849 + 10kb C > T), and/or located at hypermutable CpG loci (R117H, 3845 + 10kb C > T, R553X, R334W, S945L and R75Q). R117H was detected in cis with each of three alleles (5T, 7T, 9T) at the intron 8 locus. The novel R117H-9T association was detected in a 10-month African-American male with borderline-to-mildly elevated sweat chloride values (approximately 50-66 mEq/L). All other mutations studied were associated with 7T except 3849 + 10kb C > T, which was detected on both 7T and 9T backgrounds, but not 5T. Three individuals with a delta F508/3849 + 10kb C > T genotype were 9T,9T and had pancreatic sufficiency and normal sweat chloride values, whereas 15 others who carried 3849 + 10kb C > T on a 7T background had variable pancreatic function (sufficient, n = 12, insufficient, n = 3), and variable sweat chloride values (normal, n = 12, elevated, n = 3). Surprisingly, when not associated with known CFTR mutations, 5T was detected with elevated frequency among individuals with sinopulmonary disease of ill-defined etiology, but with some characteristics of variant CF. In summary, the 5T allele was not found in cis with CF-causing mutations besides R117H, but an elevated 5T allele frequency in variant CF patients suggests 5T may be associated with disease in some situations.
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Affiliation(s)
- K J Friedman
- University of North Carolina, Chapel Hill 27154, USA.
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31
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Zielenski J, Patrizio P, Markiewicz D, Asch RH, Tsui LC. Identification of two mutations (S50Y and 4173delC) in the CFTR gene from patients with congenital bilateral absence of vas deferens (CBAVD). Hum Mutat 2000; 9:183-4. [PMID: 9067761 DOI: 10.1002/(sici)1098-1004(1997)9:2<183::aid-humu13>3.0.co;2-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- J Zielenski
- Department of Genetics, Hospital for Sick Children, Toronto, Canada
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Haber PS, Norris MD, Apte MV, Rodgers SC, Norton ID, Pirola RC, Roberts-Thomson IC, Wilson JS. Alcoholic Pancreatitis and Polymorphisms of the Variable Length Polythymidine Tract in the Cystic Fibrosis Gene. Alcohol Clin Exp Res 1999. [PMID: 10195826 DOI: 10.1111/j.1530-0277.1999.tb04145.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Lafayette D, Abuelo D, Passero MA, Tantravahi U. Attitudes toward cystic fibrosis carrier and prenatal testing and utilization of carrier testing among relatives of individuals with cystic fibrosis. J Genet Couns 1999; 8:17-36. [PMID: 11657177 DOI: 10.1023/a:1022830519602] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Jarvi K, McCallum S, Zielenski J, Durie P, Tullis E, Wilchanski M, Margolis M, Asch M, Ginzburg B, Martin S, Buckspan MB, Tsui LC. Heterogeneity of reproductive tract abnormalities in men with absence of the vas deferens: role of cystic fibrosis transmembrane conductance regulator gene mutations. Fertil Steril 1998; 70:724-8. [PMID: 9797105 DOI: 10.1016/s0015-0282(98)00247-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To determine if the types of reproductive tract abnormalities linked to absence of the vas deferens varies with the cystic fibrosis transmembrane conductance regulator (CFTR) genotype. DESIGN Prospective data gathering. SETTING University infertility clinic. PATIENT(S) Forty-six infertile men with absence of the scrotal vas deferens and no signs of cystic fibrosis. INTERVENTION(S) All had blood taken for CFTR gene analysis, 33 had scrotal ultrasounds, and 25 had transrectal ultrasounds. MAIN OUTCOME MEASURE(S) The frequency of testicular, seminal vesicle, and ampullae of the vas deferens malformations was compared between subgroups of men with two, one, or no CFTR gene mutations. RESULT(S) None (0 of 21) of the men with at least one CFTR gene mutations had normal ampullae of the vas or seminal vesicles bilaterally. Two (50%) of 4 men with no CFTR gene mutations had normal ampullae of the vas deferens bilaterally, and 50% had normal bilateral seminal vesicles (statistically significantly different). There was no correlation between testicular malformations and CFTR genotype. CONCLUSION(S) This study indicates that the severity of the malformations in the testis is unrelated to the CFTR genotype, whereas the frequency and severity of wolffian duct malformations are related directly to the CFTR genotype.
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Affiliation(s)
- K Jarvi
- Department of Surgery, Mount Sinai Hospital, Toronto, Ontario, Canada
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Cohn JA, Friedman KJ, Noone PG, Knowles MR, Silverman LM, Jowell PS. Relation between mutations of the cystic fibrosis gene and idiopathic pancreatitis. N Engl J Med 1998; 339:653-8. [PMID: 9725922 DOI: 10.1056/nejm199809033391002] [Citation(s) in RCA: 545] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND It is unknown whether genetic factors predispose patients to idiopathic pancreatitis. In patients with cystic fibrosis, mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene typically cause pulmonary and pancreatic insufficiency while rarely causing pancreatitis. We examined whether idiopathic pancreatitis is associated with CFTR mutations in persons who do not have lung disease of cystic fibrosis. METHODS We studied 27 patients (mean age at diagnosis, 36 years), 22 of whom were female, who had been referred for an evaluation of idiopathic pancreatitis. DNA was tested for 17 CFTR mutations and for the 5T allele in intron 8 of the CFTR gene. The 5T allele reduces the level of functional CFTR and is associated with an inherited form of infertility in males. Patients with two abnormal CFTR alleles were further evaluated for unrecognized cystic fibrosis-related lung disease, and both base-line and CFTR-mediated ion transport were measured in the nasal mucosa. RESULTS Ten patients with idiopathic chronic pancreatitis (37 percent) had at least one abnormal CFTR allele. Eight CFTR mutations were detected (prevalence ratio, 11:1; 95 percent confidence interval, 5 to 23; P<0.001). In three patients both alleles were affected (prevalence ratio, 80:1; 95 percent confidence interval, 17 to 379; P<0.001). These three patients did not have lung disease typical of cystic fibrosis on the basis of sweat testing, spirometry, or base-line nasal potential-difference measurements. Nonetheless, each had abnormal nasal cyclic AMP-mediated chloride transport. CONCLUSION In a group of patients referred for evaluation of idiopathic pancreatitis, there was a strong association between mutations in the CFTR gene and pancreatitis. The abnormal CFTR genotypes in these patients with pancreatitis resemble those associated with male infertility.
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Affiliation(s)
- J A Cohn
- Department of Medicine, Veterans Affairs and Duke University Medical Centers, Durham, NC 27710, USA
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Affiliation(s)
- M J Schwarz
- Regional Molecular Genetics Laboratory, Royal Manchester Children's Hospital, UK
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Petreska L, Koceva S, Plaseska D, Chernick M, Gordova-Muratovska A, Fustic S, Nestorov R, Efremov GD. Molecular basis of cystic fibrosis in the Republic of Macedonia. Clin Genet 1998; 54:203-9. [PMID: 9788722 DOI: 10.1111/j.1399-0004.1998.tb04285.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eighty-three cystic fibrosis (CF) patients and their families, belonging to various ethnic groups living in the Republic of Macedonia were studied for molecular defects in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, and for the associated extragenic marker loci XV-2c and KM19. The DNA methodology used included characterization of CFTR mutations in 19 exons (and flanking sequences) of the gene and analysis of distribution of the XV-2c/KM19 haplotypes among normal (N) and CF chromosomes by polymerase chain reaction (PCR) amplification followed by dot blot hybridization, restriction digestion, single-strand conformational polymorphism, constant denaturing gel electrophoresis, denaturing gradient gel electrophoresis, and sequencing. We identified 58.4% (97/166) of the CF chromosomes. Nine different CFTR gene mutations, including three novel ones, were found. Eight known and one new CFTR intragene polymorphisms were also characterized. The haplotype analysis of the XV-2c/TaqI and KM19/PstI polymorphic loci have shown that haplotype C is the most frequently found haplotype among the non-deltaF508 CF chromosomes from Macedonia (36.5%). The results demonstrate the broad heterogeneity of CF origin in this part of the Balkan Peninsula.
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Affiliation(s)
- L Petreska
- Research Center for Genetic Engineering and Biotechnology, Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
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Abstract
Some genes that contain premature nonsense codons express alternatively-spliced mRNA that has skipped the exon containing the nonsense codon. This paradoxical association of translation signals (nonsense codons) and RNA splicing has inspired numerous explanations. The first is based on the fact that premature nonsense codons often reduce mRNA abundance. The reduction in abundance of full-length mRNA then allows more efficient amplification during PCR of normal, minor, exon-deleted products. This mechanism has been demonstrated to explain an extensive correlation between nonsense codons and exon-skipping for the hamster Hprt gene. The second explanation is that the mutation producing an in-frame nonsense codon has an effect on exon definition. This has been demonstrated for the Mup and hamster Hprt gene by virtue of the fact that missense mutations at the same sites also are associated with the same exon-deleted mRNA. The third general explanation is that a hypothetical process takes place in the nucleus that recognizes nonsense codons, termed 'nuclear scanning', which then has an effect on mRNA splicing. Definitive evidence for nuclear scanning is lacking. My analysis of both nonsense and missense mutations associated with exon skipping in a large number of genes revealed that both types of mutations frequently introduce a T into a purine-rich DNA sequence and are often within 30 base pairs of the nearest exon boundary. This is intriguing given that purine-rich splicing enhancers are known to be inhibited by the introduction of a T. Almost all mutations associated with exon skipping occur in purine-rich or A/C-rich sequences, also characteristics of splicing enhancers. I conclude that most cases of exon skipping associated with premature termination codons may be adequately explained either by a structural effect on exon definition or by nonquantitative methods to measure mRNA, rather than an effect on a putative nuclear scanning mechanism.
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Affiliation(s)
- C R Valentine
- Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, Jefferson, AR 72079-9502, USA.
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39
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Feldmann D, Sardet A, Cougoureux E, Plouvier E, Fontaine JL, Tournier G, Aymard P. Identification of three novel mutations in the CFTR gene, R117P, deltaD192, and 3121-1G-->A in four French patients. Hum Mutat 1998; Suppl 1:S78-80. [PMID: 9452048 DOI: 10.1002/humu.1380110127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- D Feldmann
- Laboratoire de Biochimie, Service de Gastro-Entérologie Pédiatrique, Hôpital Armand Trousseau, Paris, France
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40
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Gilfillan A, Warner JP, Kirk JM, Marshall T, Greening A, Ho LP, Hargreave T, Stack B, McIntyre D, Davidson R, Dean JC, Middleton W, Brock DJ. P67L: a cystic fibrosis allele with mild effects found at high frequency in the Scottish population. J Med Genet 1998; 35:122-5. [PMID: 9507391 PMCID: PMC1051215 DOI: 10.1136/jmg.35.2.122] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Only three mutant cystic fibrosis (CF) alleles have to date been established as conferring a dominant mild effect on affected subjects who are compound heterozygotes. We now add a fourth, P67L, which occurs on about 1.4% of Scottish CF chromosomes. Among 13 patients (12 unrelated) with this allele, the average age at diagnosis was 22.5 +/- 11.3 years. None of the cases had consistently raised sweat chloride concentrations, the average value being 57 +/- 9 mmol/l; 77% of the patients were pancreatic sufficient. When compared to three other established mild CF alleles, R117H, A455E, and 3849 + 10kb C-T, a compound heterozygote for P67L has minimal disease and clinical suspicions are unlikely to be confirmed other than by DNA typing.
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Affiliation(s)
- A Gilfillan
- Human Genetics Unit, University of Edinburgh, Western General Hospital, UK
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41
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Xiong X, Bragin A, Widdicombe JH, Cohn J, Skach WR. Structural cues involved in endoplasmic reticulum degradation of G85E and G91R mutant cystic fibrosis transmembrane conductance regulator. J Clin Invest 1997; 100:1079-88. [PMID: 9276724 PMCID: PMC508282 DOI: 10.1172/jci119618] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Abnormal folding of mutant cystic fibrosis transmembrane conductance regulator (CFTR) and subsequent degradation in the endoplasmic reticulum is the basis for most cases of cystic fibrosis. Structural differences between wild-type (WT) and mutant proteins, however, remain unknown. Here we examine the intracellular trafficking, degradation, and transmembrane topology of two mutant CFTR proteins, G85E and G91R, each of which contains an additional charged residue within the first putative transmembrane helix (TM1). In microinjected Xenopus laevis oocytes, these mutations markedly disrupted CFTR plasma membrane chloride channel activity. G85E and G91R mutants (but not a conservative mutant, G91A) failed to acquire complex N-linked carbohydrates, and were rapidly degraded before reaching the Golgi complex thus exhibiting a trafficking phenotype similar to DeltaF508 CFTR. Topologic analysis revealed that neither G85E nor G91R mutations disrupted CFTR NH2 terminus transmembrane topology. Instead, WT as well as mutant TM1 spanned the membrane in the predicted C-trans (type II) orientation, and residues 85E and 91R were localized within or adjacent to the plane of the lipid bilayer. To understand how these charged residues might provide structural cues for ER degradation, we examined the stability of WT, G85E, and G91R CFTR proteins truncated at codons 188, 393, 589, or 836 (after TM2, TM6, the first nucleotide binding domain, or the R domain, respectively). These results indicated that G85E and G91R mutations affected CFTR folding, not by gross disruption of transmembrane assembly, but rather through insertion of a charged residue within the plane of the bilayer, which in turn influenced higher order tertiary structure.
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Affiliation(s)
- X Xiong
- Department of Molecular and Cellular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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43
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Kerem E, Nissim-Rafinia M, Argaman Z, Augarten A, Bentur L, Klar A, Yahav Y, Szeinberg A, Hiba O, Branski D, Corey M, Kerem B. A missense cystic fibrosis transmembrane conductance regulator mutation with variable phenotype. Pediatrics 1997; 100:E5. [PMID: 9271620 DOI: 10.1542/peds.100.3.e5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE Cystic fibrosis (CF) has variable clinical presentation. Disease severity is partially associated with the type of mutation. The aim of this study was to report genotype-phenotype analysis of the G85E mutation. PATIENTS The phenotype of 12 patients (8 were from the same extended family, and 5 of them were siblings from 2 families) carrying at least one copy of the G85E mutation was evaluated and compared with the phenotype of 40 patients carrying the two severe mutations, W1282X and/or DeltaF508 (group 1), and with 20 patients carrying the splicing mutation, 3849+10kb C->T, which was found to be associated with milder disease (group 2). RESULTS A high phenotypic variability was found among the patients carrying the G85E mutation. This high variability was found among patients carrying the same genotype and among siblings. All the studied chromosomes carrying the G85E mutation had the 7T variant in the polythymidine tract at the branch/acceptor site in intron 8. Of the G85E patients, 25% had pancreatic sufficiency and none had meconium ileus, compared with 0% and 32%, respectively, of patients from group 1, and 80% and 0%, respectively, from group 2. Two patients carrying the G85E mutation had sweat chloride levels <60 mmol/L whereas all the others had typically elevated levels >80 mmol/L. Compared with group 2, patients carrying the G85E mutation were diagnosed at an earlier age and had higher sweat chloride levels, with mean values similar to group 1 but significantly more variable. Forced expiratory volume in 1 second (FEV1) was similar in the three groups, with no differences in the slope or in age-adjusted mean values of FEV1. The levels of transcripts lacking exon 9 transcribed from the G85E allele measured in 3 patients were 55%, 49%, and 35% and their FEV1 values were 82%, 83%, and 50% predicated, respectively. CONCLUSIONS The G85E mutation shows variable clinical presentation in all clinical parameters. This variability could be seen among patients carrying on the other chromosome the same CFTR mutation, and also among siblings. This variability is not associated with the level of exon 9 skipping. Thus, the G85E mutation cannot be classified either as a severe or as a mild mutation.
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Affiliation(s)
- E Kerem
- Department of Pediatrics, Cystic Fibrosis (CF) Clinic, Shaare Zedek Medical Center, Jerusalem, Israel
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McAndrew PE, Parsons DW, Simard LR, Rochette C, Ray PN, Mendell JR, Prior TW, Burghes AH. Identification of proximal spinal muscular atrophy carriers and patients by analysis of SMNT and SMNC gene copy number. Am J Hum Genet 1997; 60:1411-22. [PMID: 9199562 PMCID: PMC1716150 DOI: 10.1086/515465] [Citation(s) in RCA: 403] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The survival motor neuron (SMN) transcript is encoded by two genes, SMNT and SMNC. The autosomal recessive proximal spinal muscular atrophy that maps to 5q12 is caused by mutations in the SMNT gene. The SMNT gene can be distinguished from the SMNC gene by base-pair changes in exons 7 and 8. SMNT exon 7 is not detected in approximately 95% of SMA cases due to either deletion or sequence-conversion events. Small mutations in SMNT now have been identified in some of the remaining nondeletion patients. However, there is no reliable quantitative assay for SMNT, to distinguish SMA compound heterozygotes from non-5q SMA-like cases (phenocopies) and to accurately determine carrier status. We have developed a quantitative PCR assay for the determination of SMNT and SMNC gene-copy number. This report demonstrates how risk estimates for the diagnosis and detection of SMA carriers can be modified by the accurate determination of SMNT copy number.
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Affiliation(s)
- P E McAndrew
- Department of Pathology, Ohio State University, Columbus 43210, USA
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45
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Strasberg PM, Noreau D, McGlynn-Steele L, Koultchitski G, Ray PN. PCR-Based Test for Two Cystic Fibrosis Mutations (A455E, 711+1 G→T) Common Among French Canadians. Clin Chem 1997. [DOI: 10.1093/clinchem/43.6.1083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Paula M Strasberg
- Dept. of Paediatr. Lab. Med., Div. of Genetics, Rm. 3420, Hospital for Sick Children, 555 University Ave., Toronto, ON M5G 1X8
- Dept. of Clin. Biochem., Faculty of Med., Univ. of Toronto, Toronto, ON M5G 1L5
| | - Danielle Noreau
- Dept. of Paediatr. Lab. Med., Div. of Genetics, Rm. 3420, Hospital for Sick Children, 555 University Ave., Toronto, ON M5G 1X8
| | - Leslie McGlynn-Steele
- Dept. of Paediatr. Lab. Med., Div. of Genetics, Rm. 3420, Hospital for Sick Children, 555 University Ave., Toronto, ON M5G 1X8
| | - Galina Koultchitski
- Dept. of Paediatr. Lab. Med., Div. of Genetics, Rm. 3420, Hospital for Sick Children, 555 University Ave., Toronto, ON M5G 1X8
| | - Peter N Ray
- Dept. of Paediatr. Lab. Med., Div. of Genetics, Rm. 3420, Hospital for Sick Children, 555 University Ave., Toronto, ON M5G 1X8
- Dept. of Mol. and Med. Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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46
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De Braekeleer M, Simard F, Aubin G. Little phenotypic variability in three CF sibs compound heterozygous for the 621 + 1G-->T and the 711 + 1G-->T mutations. Clin Genet 1997; 51:214-6. [PMID: 9137890 DOI: 10.1111/j.1399-0004.1997.tb02456.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We describe a family in which three sibs are compound heterozygotes for two rather rare CFTR splice-site mutations, the 621 + 1G-->T and the 711 + 1G-->T mutations. Little phenotypic variation was observed between sibs, of whom two are deceased. Their disease is characterized by pancreatic insufficiency, a severe pulmonary involvement and major growth retardation.
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Affiliation(s)
- M De Braekeleer
- Département des Sciences Humaines, Université du Uuébec à Chicoutimi, Canada
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47
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Ostedgaard LS, Rich DP, DeBerg LG, Welsh MJ. Association of domains within the cystic fibrosis transmembrane conductance regulator. Biochemistry 1997; 36:1287-94. [PMID: 9063876 DOI: 10.1021/bi962174s] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a Cl- channel composed of two membrane-spanning domains (MSD), two nucleotide-binding domains (NBD), and an R domain. To understand how these domains interact, we expressed various constructs of CFTR containing membrane-spanning and/or cytosolic domains either separately or together. We then tested for functional association of these domains using the SPQ halide-efflux assay or physical association using coimmunoprecipitation experiments. Coexpression of the amino-terminal half (MSD1, NBD1, and the R domain) and the carboxy-terminal half (MSD2 and NBD2) of CFTR generated functional Cl- channel activity whereas expression of either alone did not give a signal with the SPQ assay. This result suggests that the two halves associate in the membrane. Using domain-specific antibodies, we found that either half of CFTR could coimmunoprecipitate the other, suggesting a physical association. Coimmunoprecipitation persisted between halves missing the NBDs, the R domain, or the amino-terminal tail. Moreover, constructs from MSD1 containing only the first and second transmembrane sequences and intervening extracellular loop were sufficient for interaction with MSD2. These data suggest that interactions between the two membrane-spanning domains of CFTR may mediate association between the two halves of the protein.
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Affiliation(s)
- L S Ostedgaard
- Department of Internal Medicine, Howard Hughes Medical Institute, University of Iowa College of Medicine, Iowa City 52242, USA
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48
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Xie J, Drumm ML, Zhao J, Ma J, Davis PB. Human epithelial cystic fibrosis transmembrane conductance regulator without exon 5 maintains partial chloride channel function in intracellular membranes. Biophys J 1996; 71:3148-56. [PMID: 8968585 PMCID: PMC1233803 DOI: 10.1016/s0006-3495(96)79508-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The cardiac isoform of the cystic fibrosis transmembrane conductance regulator (CFTR) is a splice variant of the epithelial CFTR, with lacks 30 amino acids encoded by exon 5 in the first intracellular loop. For examination of the role of exon 5 in CFTR channel function, a CFTR deletion mutant, in which exon 5 was removed from the human epithelial CFTR, was constructed. The wild type and delta exon5 CFTR were expressed in a human embryonic kidney cell line (293 HEK). Fully mature glycosylated CFTR (approximately 170 kDa) was immunoprecipitated from cells transfected with wild type CFTR cDNA, whereas cells transfected with delta exon5 CFTR express only a core-glycosylated from (approximately 140 kDa). The Western blot test performed on subcellular membrane fractions showed that delta exon5 CFTR was located in the intracellular membranes. Neither incubation at lower temperature (26 degrees C) nor stimulation of 293 HEK cells with forskolin or CPT-cAMP caused improvement in glycosylation and processing of delta exon5 CFTR proteins, indicating that the human epithelial CFTR lacking exon5 did not process properly in 293 HEK cells. On incorporation of intracellular membrane vesicles containing the delta exon5 CFTR proteins into the lipid bilayer membrane, functional phosphorylation- and ATP-dependent chloride channels were identified. CFTR channels with an 8-pS full-conductance state were observed in 14% of the experiments. The channel had an average open probability (Po) of 0.098 +/- 0.022, significantly less than that of the wild type CFTR (Po = 0.318 +/- 0.028). More frequently, the delta exon5 CFTR formed chloride channels with lower conductance states of approximately 2-3 and approximately 4-6 pS. These subconductance states were also observed with wild type CFTR but to a much lesser extent. Average Po for the 2-3-pS subconductance state, estimated from the area under the curve on an amplitude histogram, was 0.461 +/- 0.194 for delta exon5 CFTR and 0.332 +/- 0.142 for wild type (p = 0.073). The data obtained indicate that deleting 30 amino acids from the first intracellular loop of CFTR affects both processing and function of the CFTR chloride channel.
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Affiliation(s)
- J Xie
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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49
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Chenal V, Souque P, Markovits A, Griffais R. Choosing highly specific primers for the polymerase chain reaction using the octomer frequency disparity method: application to Chlamydia trachomatis. Gene 1996; 176:97-101. [PMID: 8918239 DOI: 10.1016/0378-1119(96)00226-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The eight-nucleotide sequence (octomer) at the 3' end of PCR primers is important to PCR specificity. We describe a correlation between the specificity of PCR primers used with human DNA and the frequency of the 3' octomer in a human database. We therefore applied a methodology (OFD) based on octomer frequency disparity to identify 16 PCR targets in the chromosome of the intracellular bacterium, Chlamydia trachomatis (Ct). In addition, the 16 sets of primers were tested with a standard procedure. All the primer pairs were highly specific for Ct and did not lead to non-specific amplification when used with human DNA. This work shows that the choice of specific PCR primers is possible using a method based on the statistical representativeness of octomers in genomes.
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Affiliation(s)
- V Chenal
- Laboratoire des Rickettsiales et des Chlamydiales, Institut Pasteur, Paris, France
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Vazquez C, Antiñolo G, Casals T, Dapena J, Elorz J, Seculi JL, Sirvent J, Cabanas R, Soler C, Estivill X. Thirteen cystic fibrosis patients, 12 compound heterozygous and one homozygous for the missense mutation G85E: a pancreatic sufficiency/insufficiency mutation with variable clinical presentation. J Med Genet 1996; 33:820-2. [PMID: 8933333 PMCID: PMC1050759 DOI: 10.1136/jmg.33.10.820] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
To study the severity of mutation G85E, located in the first membrane spanning domain of the CFTR gene, we studied the clinical features of 13 Spanish patients with cystic fibrosis (CF) carrying this mutation. G85E accounts for about 1% of Spanish CF alleles. One patient was homozygous G85E/G85E and the rest were compound heterozygotes for G85E and other mutations (delta F508 nine patients, delta I507 two patients, and 712-1G > T one patient). The characteristics of the pooled G85E/any mutation group were compared with those of 30 delta F508 homozygotes. Mean age at diagnosis and percentage of ideal height for age were higher in the G85E/any mutation group (4.2 (SD 4.7) v 2.4 (SD 2.3), p < 0.05, and 102.8 (SD 4.7) v 97.8 (SD 4.1), p < 0.01), both probably related to the greater prevalence of pancreatic sufficiency (70% v 0%, p < 0.01). The G85E homozygote was pancreatic sufficient. Sweat sodium levels were slightly higher, and salt loss related problems more frequent, in the G85E/any group. Two of the G85E patients died of respiratory failure aged 6 and 14 years. Striking discordance in the phenotype was observed in two pairs of sibs, one of them dizygotic twins, suggesting that factors, genetic and environmental, other than CFTR genotype are important in determining CF phenotype.
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Affiliation(s)
- C Vazquez
- Cystic Fibrosis Unit, Hospital Infantil de Cruces, Pais Vasco, Spain
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