Chantal Farra

TNF Polymorphisms in Patients with Behçet Disease: A Meta-analysis

BACKGROUND AND AIMS Polymorphisms in the tumor necrosis factor (TNF) gene at the locations -308, -238, -863, -857 and -1031 have been studied in various ethnic groups for possible association with Behçets disease. The aim of this meta-analysis is to examine the association between polymorphism in the TNF gene at the locations -308, -238, -863, -857 and -1031 and Behçets disease. METHODS A literature review was performed using MEDLINE, EMBASE and the Cochrane Central Register of Controlled Trials for original studies published in English up to October 31, 2009 and that examined the association of the TNF-alpha promoter polymorphisms with Behçets disease. All pooled odds ratios (OR) were derived from random-effects model with its 95% confidence intervals (CI). We assessed statistical heterogeneity among studies using Cochrane Q test and by calculating I(2). The Cochrane collaborations software program, RevMan 5 was used to prepare and complete this review. RESULTS The literature search resulted in 13 studies. Ten studies met the included criteria and thus were selected. Overall, -1031C (OR = 1.35, 95% CI = 1.09-1.68), -238A (OR = 1.51, 95% CI = 1.12-2.04) and -857T (OR = 0.76, 95% CI = 0.58-0.98) had a significant association with Behcets disease. The pooled estimates for the other polymorphisms were not statistically significantly associated with Behcets disease; -308A and -863A. CONCLUSIONS Behcets disease was associated with the -1031C, -238A and the -857T promoter polymorphisms in various ethnic groups.

Validation of a reverse-hybridization StripAssay for the simultaneous analysis of common α-thalassemia point mutations and deletions

Abstract Background: α-Thalassemia is a worldwide disease and considered to be a major public health problem in countries within the so-called thalassemia belt. The complex genetics of α-thalassemias requires diagnostic methods with the capacity to screen rapidly and accurately for common causative mutations. Methods: We developed and validated a reverse-hybridization assay (Alpha-Globin StripAssay) for the rapid and simultaneous detection of 21 α-globin mutations: two single gene deletions (–α3.7; –α4.2), five double gene deletions [--MED; --SEA; --THAI; --FIL; –(α)20.5], αααanti-3.7 gene triplication, two point mutations in the α1 gene (cd 14 G>A; Hb Adana) and 11 point mutations in the α2 gene (initiation cd T>C; cd 19 –G; IVS1 –5nt; cd 59 G>A; Hb Quong Sze; Hb Constant Spring; Hb Icaria; Hb Pakse; Hb Koya Dora; polyA-1; polyA-2). Results: Reliable genotyping of recombinant mutant clones and reference DNA samples was achieved by means of two corresponding test strips presenting parallel arrays of allele-specific oligonucleotides. The entire procedure from blood sampling to the identification of mutations required less than 6 h, and hybridization/detection was manual or automated. The diagnostic potential of this Alpha-Globin StripAssay was carefully evaluated on 272 pre-typed samples in a multicenter validation study. In 96.14% of the cases, StripAssay typing was completely concordant with the reference methods. Conclusions: The Alpha-Globin StripAssay proved to be a fast, easy-to-perform and reliable screening method to identify >90% of α-globin mutations in endemic areas worldwide. Clin Chem Lab Med 2007;45:605–10.

Clinical and molecular analysis in families with autosomal recessive osteogenesis imperfecta identifies mutations in five genes and suggests genotype-phenotype correlations

Autosomal recessive osteogenesis imperfecta (AR‐OI) is an inherited condition which in recent years has been shown with increasing genetic and clinical heterogeneity. In this article, we performed clinical assessment and sought mutations in patients from 10 unrelated families with AR‐OI, one of whom was presented with the additional features of Bruck syndrome (BS). Pathogenic changes were identified in five different genes: three families had mutations in FKBP10, three in SERPINF1, two in LEPRE1, one in CRTAP, and one in PPIB. With the exception of a FKBP10 mutation in the BS case, all changes are novel. Of note, insertion of an AluYb8 repetitive element was detected in exon 6 of SERPINF1. Since the studied patients had variable manifestations and some distinctive features, genotype/phenotype correlations are suggested.

Mutational spectrum of cystic fibrosis in the Lebanese population

BACKGROUND Cystic fibrosis (CF) is the most common autosomal recessive disease in Caucasians; it is however, considered to be rare in the Arab populations. Reports of the cystic fibrosis transmembrane regulator (CFTR) mutations from Arabs, especially from the Lebanese population, are limited. METHODS Twenty-two unrelated Lebanese families, with at least one child with CF, were studied. DNA extracts from blood samples of patients and parents were screened for CFTR gene mutations. RESULTS Eleven different mutations were identified. Of the 44 alleles studied, the most common mutations were: F508del (34%), N1303K (27%), W1282X (7%), and S4X (7%). Five mutations - not previously reported in the Lebanese population - were identified; these are: S549N, G542X, 2043delG, 4016insG, and R117H-7T. CONCLUSIONS The most common CFTR mutations in addition to five mutations not previously described in the Lebanese population were identified. Identification of CFTR mutations in the Lebanese population is important for molecular investigations and genetic counseling.

Acceptance of preimplantation genetic diagnosis for β-thalassemia in Lebanese women with previously affected children

The aim of the study was to assess the rate of acceptance of preimplantation genetic diagnosis (PGD) as an alternative to prenatal diagnosis in Lebanese women with previously affected children with homozygous β‐thalassemia.

Validation of a semiconductor next‐generation sequencing assay for the clinical genetic screening of CFTR

Genetic testing for cystic fibrosis and CFTR‐related disorders mostly relies on laborious molecular tools that use Sanger sequencing to scan for mutations in the CFTR gene. We have explored a more efficient genetic screening strategy based on next‐generation sequencing (NGS) of the CFTR gene. We validated this approach in a cohort of 177 patients with previously known CFTR mutations and polymorphisms. Genomic DNA was amplified using the Ion AmpliSeq™ CFTR panel. The DNA libraries were pooled, barcoded, and sequenced using an Ion Torrent PGM sequencer. The combination of different robust bioinformatics tools allowed us to detect previously known pathogenic mutations and polymorphisms in the 177 samples, without detecting spurious pathogenic calls. In summary, the assay achieves a sensitivity of 94.45% (95% CI: 92% to 96.9%), with a specificity of detecting nonvariant sites from the CFTR reference sequence of 100% (95% CI: 100% to 100%), a positive predictive value of 100% (95% CI: 100% to 100%), and a negative predictive value of 99.99% (95% CI: 99.99% to 100%). In addition, we describe the observed allelic frequencies of 94 unique definitely and likely pathogenic, uncertain, and neutral CFTR variants, some of them not previously annotated in the public databases. Strikingly, a seven exon spanning deletion as well as several more technically challenging variants such as pathogenic poly‐thymidine‐guanine and poly‐thymidine (poly‐TG‐T) tracts were also detected. Targeted NGS is ready to substitute classical molecular methods to perform genetic testing on the CFTR gene.

A patient with duplication (7)(p22.1pter) characterized by array-CGH†

Approximately 40 patients with terminal duplication of the distal short arm of chromosome 7 have been reported, the smallest being dup(7)(p21). We report here on a patient with a smaller duplication, dup(7)(p22.1), detected on G‐banding and characterized by array‐CGH. We establish phenotype–karyotype correlations with the reported patients with other 7p duplications.

Genetics of autoimmune thyroid disease in the Lebanese population.

This study aims to investigate the association of human leukocyte antigen (HLA) class II genes and cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) with autoimmune thyroid diseases in the Lebanese population. A total of 128 patients with autoimmune thyroid disease (55 with Graves’ disease (GD) and 73 with Hashimoto’s thyroiditis (HT)) were typed for HLA DQA1 (0301 and 0501) and DQB1 (0201, 0302, and 0303) and for 49A/G CTLA-4 using PCR-based sequence-specific priming methods. A total of 186 matched controls were typed for the same alleles and compared to the diseased population. Results showed no significant differences in HLA DQB1*0201 or DQB1*0301 allelic frequencies or CTLA-4 polymorphisms between patients and controls. For GD, there was a weak association with HLA DQB1*0302 [34.6% (19 of 55) vs. 21.5% (40 of 186), P = 0.048, odds ratio (OR) = 1.926, confidence interval (CI) = 0.999–3.715] and HLA DQB1*0302-DQA1*0501 haplotype [56.36% (31 of 55) vs. 40.8% (76 of 186), P = 0.042, OR = 1.870, CI = 1.018–3.433]. For HT, the frequencies of DQB1*0302-DQA1*0501 haplotype [28.8% (21of 73) vs. 14.5% (27 of 186), P = 0.008, OR = 2.378, CI = 1.241–4.558] and DQB1*0302-DQA1*0301 haplotype [60.2% (44 of 73) vs. 38.7% (72 of 186), P = 0.002, OR = 2.402, CI = 1.381–4.180] were significantly higher in patients. On the other hand, weak association was found between HT and DQA1*0301 allele [32.9% (24 of 73) vs. 20.9% (39 of 186), P = 0.044, OR = 1.846, CI = 1.011–3.373]. Findings show that DQB1*0302-DQA1*0501 and DQB1*0302-DQA1*0301 haplotypes may play a role in the pathogenesis of HT in the Lebanese population. For the 49A/G CTLA-4 polymorphism, no significant difference was found between patients and controls.

Goldenhar syndrome associated with prenatal maternal Fluoxetine ingestion: Cause or coincidence?

Goldenhar syndrome, also known as oculo-auriculo-vertebral spectrum, is a complex, heterogeneous condition characterized by abnormal prenatal development of facial structures. We present the occurrence of Goldenhar syndrome in an infant born to a woman with a history of prenatal Fluoxetine ingestion throughout her pregnancy. Because this is the first reported case associating maternal Fluoxetine intake with fetal craniofacial malformations, a potential mechanism of injury is discussed. The propositus, a male born from nonconsanguinous parents, had facial asymmetry with right microtia and mandibular hypoplasia; he also had bilateral hypoplastic macula, scoliotic deformity of the thoracic spine, and ventricular septal defect. The mother was under treatment with Fluoxetine 20 mg/day prior to conception and maintained the same dosage throughout her pregnancy. The drug is a selective serotonin re-uptake inhibitor, the most widely prescribed for the treatment of depression. The occurrence of developmental aberrations may be caused by a profound serotonin receptor suppressive state in utero leading to aberrant clinical manifestations of the first and second branchial arches. Despite the very many limitations of case reporting of teratogenic events, it remains an important source of information on which more advanced research is based.

Genotype/Phenotype Correlation in Primary Congenital Glaucoma Patients in the Lebanese Population: A Pilot Study

Abstract Background: The incidence of primary congenital glaucoma (PCG) varies among geographic regions and ethnic groups. The frequency of PCG in Lebanon and identification of disease-causing mutations have not been studied previously. Purpose: To investigate the role of Cytochrome P1B1 (CYP1B1) gene and Myocillin (MYOC) gene mutations in PCG in the Lebanese population and study possible genotype/phenotype correlations. Methods: Patients with unilateral or bilateral PCG diagnosed at the American University of Beirut Medical Center and their first-degree relatives (parents and siblings) were screened for CYP1B1 and MYOC mutations. Demographic and phenotypic characteristics were recorded. Phenotypic characteristics pertaining to disease severity and outcomes were compared. Results: Eighteen Lebanese families (66 subjects) with at least one member affected with PCG were included in this study. Mutations in the CYP1B1 gene were detected in 6 families (33%). Five previously described mutations (p.R444Q; p.E229K; p.R469W; p.G61E; p.M1T) and one new single nucleotide deletion were identified (1793delC). Patients in whom CYP1B1 mutations were detected tended to have a more severe phenotype as evidenced by earlier age at diagnosis, higher rate of bilateral disease, and higher number of glaucoma surgeries than those in whom no CYP1B1 mutations were present. MYOC gene mutations were not detected in any patients. Conclusion: The rate of CYP1B1 mutations in Lebanese patients with PCG is lower than that reported in other Arab and Middle Eastern populations and suggests other genes are responsible for PCG in the remainder.