CFTR pathogenic variants spectrum in a cohort of Mexican patients with cystic fibrosis.

Background: Molecular diagnosis of cystic fibrosis (CF) is challenging in Mexico due to the population's high genetic heterogeneity. To date, 46 pathogenic variants (PVs) have been reported, yielding a detection rate of 77%. We updated the spectrum and frequency of PVs responsible for this disease in mexican patients. Methods: We extracted genomic DNA from peripheral blood lymphocytes obtained from 297 CF patients and their parents. First, we analyzed the five most frequent PVs in the Mexican population using PCR-mediated site-directed mutagenesis. In patients with at least one identified allele, CFTR sequencing was performed using next-generation sequencing tools and multiplex ligation-dependent probe amplification. For variants not previously classified as pathogenic, we used a combination of in silico prediction, CFTR modeling, and clinical characteristics to determine a genotype-phenotype correlation. Results: We identified 95 PVs, increasing the detection rate to 87.04%. The most frequent variants were p.(PheF508del) (42.7%), followed by p.(Gly542*) (5.6%), p.(Ser945Leu) (2.9%), p.(Trp1204*) and p.(Ser549Asn) (2.5%), and CFTRdel25-26 and p.(Asn386Ilefs*3) (2.3%). The remaining variants had frequencies of <2.0%, and some were exclusive to one family. We identified 10 novel PVs localized in different exons (frequency range: 0.1-0.8%), all of which produced structural changes, deletions, or duplications in different domains of the protein, resulting in dysfunctional ion flow. The use of different in silico software and American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) criteria allowed us to assume that all of these PVs were pathogenic, causing a severe phenotype. Conclusions: In a highly heterogeneous population, combinations of different tools are needed to identify the variants responsible for CF and enable the establishment of appropriate strategies for CF diagnosis, prevention, and treatment.

Next-generation sequencing for identifying a novel/de novo pathogenic variant in a Mexican patient with cystic fibrosis: a case report.

BACKGROUND: Mexico is among the countries showing the highest heterogeneity of CFTR variants. However, no de novo variants have previously been reported in Mexican patients with cystic fibrosis (CF). CASE PRESENTATION: Here, we report the first case of a novel/de novo variant in a Mexican patient with CF. Our patient was an 8-year-old male who had exhibited the clinical onset of CF at one month of age, with steatorrhea, malabsorption, poor weight gain, anemia, and recurrent respiratory tract infections. Complete sequencing of the CFTR gene by next generation sequencing (NGS) revealed two different variants in trans, including the previously reported CF-causing variant c.3266G > A (p.Trp1089*, W1089*), that was inherited from the mother, and the novel/de novo CFTR variant c.1762G > T (p.Glu588*). CONCLUSION: Our results demonstrate the efficiency of targeted NGS for making a rapid and precise diagnosis in patients with clinically suspected CF. This method can enable the provision of accurate genetic counselling, and improve our understanding of the molecular basis of genetic diseases.

Influence of SNPs in Genes that Modulate Lung Disease Severity in a Group of Mexican Patients with Cystic Fibrosis.

BACKGROUND: The variation in cystic fibrosis (CF) lung disease not always is explained by the CFTR genotype, so it has become apparent that modifier genes must play a considerable role in the phenotypic heterogeneity of CF, so we investigated the association of allelic variants in modifier genes that modulate the severity of lung function in a group of Mexican patients diagnosed with CF. METHODS: We included 140 CF patients classified according to lung phenotype and analyzed 17 single nucleotide polymorphisms (SNPs) by TaqMan® allelic discrimination. RESULTS: We demonstrated that patients with GG or GC genotype of the allelic variant rs11003125 (MBL2-550) of the MBL2 gene exhibit most of the lung manifestations at an earlier age; and the rs1042713 allelic variant of ADRB2 gene, showed statistical difference only with the age of first spirometry. When we used the dominant model, the MBL2 allele rs11003125 (MBL2-550; p = 0.022, Odds Ratio (OR) 2.87, 95% CI 1.14-7.27) was significantly associated with CF patients as risk factor, and the ADRB2 allele rs1042713 (p.Arg16Gly; p = 0.005, Odds Ratio (OR) 0.37, 95% CI 0.19-0.75) was significantly associated with CF patients as protect factor. CONCLUSIONS: Our findings suggest that the MBL2 and ADRB2 genes exerts an important genetic influence on the lung disease in our patients. Taking into account our results, we insist on not leaving aside this type of studies, since having techniques such as GWAS or WES will be able to advance in achieving a better quality of life for CF patients with severe lung disease.

[Genotype-phenotype correlation in a sample of Mexican patients with cystic fibrosis]. / Correlación genotipo-fenotipo en una muestra de pacientes mexicanos con fibrosis quística.

INTRODUCTION: Cystic fibrosis is a lethal autosomal recessive disease, commonly seen in Caucasian population. The World Health Organization (WHO) estimated that in Mexico, the incidence is approximately 1 per 8,500 live births. Defects in CFTR (cystic fibrosis transmembrane conductance regulator) protein are responsible for alterations in the transport of chloride in the apical membrane of exocrine epithelial cells. This results to a lot of variability in the clinical manifestations, which range from a very serious disease that compromises the life of the patient, to only primary infertility due to absence of CBAVD. The study of the CFTR gene, responsible for this entity, has led to understand the correlation between the molecular defects in this gene and the clinical expression of the patients. Most reports show that only pancreatic function in CF patients directly correlated with genotype and not with other clinical features such as lung disease. OBJECTIVE: In this work we analyzed the genotype-phenotype correlation in a cohort of Mexican patients with CF. MATERIAL AND METHODS: We included 230 patients with CF, stratified based on the genotype and pancreatic disease. Both ratings were correlated with clinical parameters as in sweat chloride levels, lung disease, pancreatic insufficiency or sufficiency (IP and SP) and colonization by Pseudomonas aeruginosa (P. aeruginosa). RESULTS AND DISCUSSION: Our data suggest a strong correlation between the severity of mutations and pancreatic function. Related to this, significant differences were observed in sweat chloride levels, lung disease, colonization by P. aeruginosa, and the age of onset of symptoms, and diagnosis among patients with IP and SP (p < 0.001). The close correlation between IP, both with mutations that eliminate the function of CFTR gene, as with the presence of more serious clinical picture, suggests that IP could be used as an indicator of the severity of CF patients especially in those without characterized mutations yet.

Clinical disease caused by Klebsiella in 2 unrelated patients with interleukin 12 receptor beta1 deficiency.

Patients with interleukin 12 (IL-12)p40 or IL-12 receptor ß1 (IL12Rß1) deficiencies are prone to develop infections caused by mycobacteria and salmonella; other infections have only been rarely observed. In this report we describe 2 unrelated patients with complete autosomal recessive IL12Rß1 deficiency who suffered from sepsis attributable to Klebsiella pneumoniae. A Mexican boy suffered from disseminated bacille Calmette-Guérin disease and infections caused by K pneumoniae and Candida albicans and had a fatal outcome. A Turkish girl living in France suffered from disseminated Nocardia nova infection and K pneumoniae sepsis. Therefore, Klebsiella infections should be considered in patients with IL12Rß1 deficiency. Conversely, IL12Rß1 deficiency should be considered in patients with unexplained klebsiellosis.

CFTR allelic heterogeneity in Mexican patients with cystic fibrosis: implications for molecular screening.

INTRODUCTION: Cystic fibrosis, the most common autosomal recessive disorder, is caused by defects in the CF transmembrane conductance regulator gene (CFTR) that encodes a chloride channel. To date, over 1,800 mutations have been described related to the causative gene of CF, showing a variable frequency among populations. In a previous extensive analysis of the CFTR locus in 97 Mexican patients, 34 different mutations (75% of CF alleles) were found using several strategies for mutation screening; however, 63% had at least an uncharacterized allele. Despite the combined technologies used, there are still a great number of unknown mutations in the Mexican population. OBJECTIVE: Screening of the CFTR gene to provide additional evidence of the mutational wide spectrum responsible for CF in Mexican patients. MATERIAL AND METHODS: In this study, the number of unrelated CF patients was increased to 230, 133 new cases and the 97 previously reported to include 63% with at least an uncharacterized allele. Additional tools were used to improve the detection rate of CF mutations, such as a commercial kit for 36 mutations plus a single chain conformational polymorphism method and DNA sequencing. RESULTS: By using a combination of these strategies we characterized 77.7% of all the CF alleles, resulting in a total of 46 different mutations detected, including the identification of 12 additional mutations (p.R334W, p.A455E, c.3120+1G > A, c.3272-26A > G, c.711+1G > T, p.Q552X, p.W1282X, c.IVS8-5T, p.R1162X and p.R347P, p.D1152H and p.T1036N). Although these 12 mutations have been reported in other populations, they have not yet been reported in Mexican patients. This report shows that Mexico has one of the widest spectra of CFTR mutations worldwide. The knowledge of the ethnic and geographic distribution of CFTR mutations in this population will allow the development of more effective methods for diagnosis and treatment.

Sweat conductivity and chloride titration for cystic fibrosis diagnosis in 3834 subjects.

Sweat test is the standard for cystic fibrosis (CF) diagnosis. Conductivity is an alternative method not yet approved, in spite of its good correlation with chloride concentration. The aim was to assess the capacity of sweat conductivity to discriminate between CF and non-CF subjects. Automated measurements of conductivity and chloride concentration were carried out on the same sweat samples from subjects with clinical suspicion of CF. Sweat samples from 3,834 subjects, median age 1.8 years (range 1 month-54 years) were analysed, and those with chloride titration >60 mmol/l were considered as CF patients (n=294). Conductivity median values in CF and non-CF subjects were 111 mmol/l (82-148) and 36 mmol/l (12-89), respectively. The Spearman correlation between chloride titration and conductivity was r=0.60 (P<0.001). The receiver operating characteristics (ROC) curve showed very high agreement between two methods. The best conductivity cut-off value to diagnose CF was > or =90 mmol/l (sensitivity 99.7%, specificity 100%, positive and negative predictive values of 100% and 99.97%, respectively, and kappa=0.998). Likewise, the best conductivity cut-off value to exclude CF was <75 mmol/l. The sweat conductivity method showed good correlation with chloride titration, and accurately discriminated between subjects with and without CF. In accordance with this, CF diagnosis might be confirmed for conductivity values > or =90 mmol/l and excluded for <75 mmol/l. Values between 75 and 89 mmol/l should correspond to an equivocal range. However, more studies are needed to confirm the role of conductivity in definitive CF diagnosis.