Detection of Large Rearrangements in the Cystic Fibrosis Transmembrane Conductance Regulator Gene by Multiplex Ligation-Dependent Probe Amplification Assay When Sequencing Fails to Detect Two Disease-Causing Mutations

Svensson, Annika; Chou, Lan Szu; Miller, Christine; Robles, J.; Swensen, Jeffrey; Voelkerding, Karl V.; Mao, Rong; Lyon, Elaine

doi:10.1089/gtmb.2009.0099

Cited by 13 publications

(9 citation statements)

References 17 publications

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“…DNA samples with no detectable pathogenic mutation as revealed by Sanger sequencing, were tested for deletions or duplications using SALSA MLPA probemix P091-D1 CFTR assay (MRC-Holland, Amsterdam, Netherlands). The assay was performed according to the manufacturer’s recommendation which targets all 27 exons and the promoter region of the CFTR gene [ 14 ]. All amplified products were loaded into ABI 3130 XL Genetic analyzer (Applied Biosystems, Foster City, USA) and peaks were sized using ROX 500 (Applied Biosystems, Foster City, USA).…”

Section: Methodsmentioning

confidence: 99%

Distribution of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Mutations in a Cohort of Patients Residing in Palestine

et al. 2015

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Cystic fibrosis (CF) is an autosomal recessive inherited life-threatening disorder that causes severe damage to the lungs and the digestive system. In Palestine, mutations in the Cystic Fibrosis Transmembrane Conductance Regulator gene (CFTR) that contributes to the clinical presentation of CF are ill defined. A cohort of thirty three clinically diagnosed CF patients from twenty one different Palestinian families residing in the central and southern part of Palestine were incorporated in this study. Sweat chloride testing was performed using the Sweat Chek Conductivity Analyzer (ELITECH Group, France) to confirm the clinical diagnosis of CF. In addition, nucleic acid from the patients’ blood samples was extracted and the CFTR mutation profiles were assessed by direct sequencing of the CFTR 27 exons and the intron-exon boundaries. For patient’s DNA samples where no homozygous or two heterozygous CFTR mutations were identified by exon sequencing, DNA samples were tested for deletions or duplications using SALSA MLPA probemix P091-D1 CFTR assay. Sweat chloride testing confirmed the clinical diagnosis of CF in those patients. All patients had NaCl conductivity >60mmol/l. In addition, nine different CFTR mutations were identified in all 21 different families evaluated. These mutations were c.1393-1G>A, F508del, W1282X, G85E, c.313delA, N1303K, deletion exons 17a-17b-18, deletion exons 17a-17b and Q1100P. c.1393-1G>A was shown to be the most frequent occurring mutation among tested families. We have profiled the underling mutations in the CFTR gene of a cohort of 21 different families affected by CF. Unlike other studies from the Arab countries where F508del was reported to be the most common mutation, in southern/central Palestine, the c.1393-1G>A appeared to be the most common. Further studies are needed per sample size and geographic distribution to account for other possible CFTR genetic alterations and their frequencies. Genotype/phenotype assessments are also recommended and finally carrier frequency should be ascertained.

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Section: Methodsmentioning

confidence: 99%

Distribution of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Mutations in a Cohort of Patients Residing in Palestine

et al. 2015

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“…The CFTR gene encodes the CFTR protein that functions as a Cl-selective anion channel gated by cycles of ATP binding and hydrolysis at its nucleotide-binding domains [ 5 ]. Regarding CFTR gene mutations, to date, there are 1908 identified mutations, of which 982 are missense or nonsense [ 6 ], while the deletions and duplications of complete exons account for 1–2% of all mutations [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Current Status of Genetic Diagnosis Laboratories and Frequency of Genetic Variants Associated with Cystic Fibrosis through a Newborn-Screening Program in Turkey

Bozdoğan

Mujde

Boğa

et al. 2021

Genes

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Background: Cystic fibrosis (CF) is the most common worldwide, life-shortening multisystem hereditary disease, with an autosomal recessive inheritance pattern caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The national newborn screening (NBS) program for CF has been initiated in Turkey since 2015. If the immunoreactive trypsinogen (IRT) is elevated (higher than 70 μg/L in the second control) and confirmed by sweat test or clinical findings, genetic testing is performed. The aims of this study are to emphasize the effect of NBS on the status of genetic diagnosis centers with the increasing numbers of molecular testing methods, and to determine the numbers and types of CFTR mutations in Turkey. Methods: The next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA) results of 1595 newborns, who were referred to Cukurova University Adana Genetic Diseases Diagnosis and Treatment Center (AGENTEM) for molecular genetic testing, were evaluated with positive CF NBS program results since 2017. Results: According to the results; 560 (35.1%) of the 1595 patients carried at least 1 (one) CF-related variant, while 1035 patients (64.9%) had no mutation. Compound heterozygosity for two mutations was the most common in patients, while two detected variants were homozygote in 14 patients. A total of 161 variants were detected in 561 patients with mutations. Fifteen novel variants that have not been previously reported were found. Moreover, p.L997F was identified as the most frequent pathogenic mutation that might affect the IRT measurements used for the NBS. The distribution of mutation frequencies in our study showed a difference from those previously reported; for example, the well-known p.F508del was the third most common (n = 42 alleles), rather than the first. The most striking finding is that 313 cases had a pathogenic variant together with the V470M variant, which might have a cumulative effect on CF perpetuation. Conclusion: This study is the first to determine the mutational spectrum of CFTR in correlation with the NBS program in the Turkish population. NBS for CF raises issues regarding screening in diverse populations, both medical and non-medical benefits, and carrier identification. Through the lens of NBS, we focused on the integrated diagnostic algorithms and their effect on the results of genetic testing.

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“…Direct gene sequencing [17,18] and search for CFTR genomic rearrangements [19,20] are needed to detect other possible regionally prevalent mutations and rare (private) mutations not found with mutation-specific tests. This would allow us to improve diagnostic confirmation, carrier analysis and genetic counselling, and assist in the future development of a newborn screening program and cost-effective tests.…”

Section: Discussionmentioning

confidence: 99%

Cystic fibrosis in Chilean patients: Analysis of 36 common CFTR gene mutations

Lay-Son

Puga

Astudillo

et al. 2011

Journal of Cystic Fibrosis

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Detection of Large Rearrangements in the Cystic Fibrosis Transmembrane Conductance Regulator Gene by Multiplex Ligation-Dependent Probe Amplification Assay When Sequencing Fails to Detect Two Disease-Causing Mutations

Abstract: The MLPA assay for detection of large rearrangements may be valuable in individuals with positive SC levels where one or no mutations have been identified by sequencing.

Cited by 13 publications

References 17 publications

Distribution of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Mutations in a Cohort of Patients Residing in Palestine

Distribution of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Mutations in a Cohort of Patients Residing in Palestine

Current Status of Genetic Diagnosis Laboratories and Frequency of Genetic Variants Associated with Cystic Fibrosis through a Newborn-Screening Program in Turkey

Cystic fibrosis in Chilean patients: Analysis of 36 common CFTR gene mutations

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