Family history predictors of BRCA1/BRCA2 mutation status among Tunisian breast/ovarian cancer families.

BACKGROUND: With the increasing request for BRCA1/BRCA2 mutation tests, several risk models have been developed to predict the presence of mutation in these genes; in this study, we have developed an efficient BRCA genetic testing strategy. METHOD: As first step, to identify predictor variables associated with BRCA status, we have undertaken a cumulative mutation analysis including data from three Tunisian studies. Then, we have developed a logistic regression model for predicting the likelihood of harboring a BRCA mutation. Using receiver operating characteristic curves (ROC), an effective evaluation was performed. A total of 92 Tunisian families were included. Overall, 27 women were positive for BRCA1/BRCA2 deleterious mutations. RESULTS: Tow recurrent mutations (c.211dupA and c.5266dupC) explained 76 % of BRCA1-related families and three recurrent mutations (c.1310_1313del, c.1542_1547delAAGA and c.7887_7888insA) explained 90 % of BRCA2-related families. Early age at diagnosis of breast cancer, ovarian cancer, bilateral breast cancer were associated with BRCA1, whereas male breast cancer and four or more breast cancer cases in the family were associated with BRCA2. The area under the receiver operating characteristic curve of the risk score was 0.802 (95 % confidence interval = 0.0699-0. 905). CONCLUSION: Logistic regression reported particular profiles related to BRCA germline mutation carriers in our population, as well as an efficient prediction model that may be a useful tool for increasing the cost-effectiveness of genetic testing strategy.

Estimating the Total Pathogenic Allele Frequency of Autosomal Recessive Disorders in Case of Consanguinity.

OBJECTIVE: Estimating the total allele frequency of all pathogenic alleles of an autosomal recessive disease is not possible if only mutational data of a sample of affected individuals are available. However, if the affected individuals come from a population where consanguinity is not uncommon, this total allele frequency can be estimated by additionally using the positive individual inbreeding coefficients or an estimate of the population inbreeding coefficient. In this paper, we propose two estimators. METHODS/RESULTS: We propose to estimate the total allele frequency by a conditional maximum likelihood estimator if a part of the affected individuals in the sample comes from consanguineous marriages with known inbreeding coefficients. A simulation study shows that this estimator is unbiased and robust. We propose a second estimator which is based on an estimate of the population inbreeding coefficient. The method is applied to mutational data and individual inbreeding coefficients of Tunisian patients with congenital adrenal hyperplasia. CONCLUSION: Additionally using individual inbreeding coefficients or an estimate of the population inbreeding coefficient makes it possible to estimate the total allele frequency. Since consanguinity is commonly practiced in many parts of the world, the estimators proposed in the paper are of practical importance.

The relationship between telomere length and clinicopathologic characteristics in colorectal cancers among Tunisian patients.

Alterations in telomere dynamics have emerged as having a causative role in carcinogenesis. Both the telomere attrition contribute to tumor initiation via increasing chromosomal instability and that the telomere elongation induces cell immortalization and leads to tumor progression. The objectives of this study are to investigate the dynamics of telomere length in colorectal cancer (CRC) and the clinicopathological parameters implicated. We measured the relative telomere length (RTL) in cancerous tissues and in corresponding peripheral blood leukocytes (PBL) using quantitative PCR (Q-PCR) from 94 patients with CRC. Telomere length correlated significantly in cancer tissues and corresponding PBL (r = 0.705). Overall, cancer tissue had shorter telomeres than PBL (p = 0.033). In both cancer tissue and PBL, the RTL was significantly correlated with age groups (p = 0.008 and p = 0.012, respectively). The RTL in cancer tissue was significantly longer in rectal tumors (p = 0.04) and in the late stage of tumors (p = 0.01). In PBL, the RTL was significantly correlated with the macroscopic aspect of tumors (p = 0.02). In addition, the telomere-length ratio of cancer to corresponding PBL increased significantly with late-stage groups. Shortening of the telomere was detected in 44.7%, elongation in 36.2%, and telomeres were unchanged in 19.1% of 94 tumors. Telomere shortening occurred more frequently in the early stage of tumors (p = 0.01). This study suggests that the telomere length in PBL is affected by the macroscopic aspect of tumors and that telomere length in cancer tissues is a marker for progression of CRC and depends on tumor-origin site.

CONSANGUINITY AND HOMOZYGOSITY AMONG TUNISIAN PATIENTS WITH AN AUTOSOMAL RECESSIVE DISORDER.

Consanguineous unions are a deeply rooted social practice among traditional societies. Despite their presumed social advantages, they can result in several health conditions. The aim of this study was: i) to compare consanguinity levels between Tunisian patients affected with autosomal recessive disorders (ARDs) and those with a chromosomal abnormality; and ii) to gain more insight into the mutational status of patients affected with ARDs. Data were collected from 290 files of patients affected by one of five ARDs confirmed by molecular analysis and 248 files of patients with confirmed Down syndrome. Information on the disease, mutation defining the disease, parents' relatedness and geographical origin was gathered. Consanguinity was found among 58% of the ARD patients and among 22% of Down syndrome patients, and a homozygous status was found in 90% of the patients born to related parents and in 70% of patients born to unrelated parents. Also, children from unrelated parents from the same geographical background were found to be more frequently affected by homozygous mutations than those from unrelated parents from different geographical backgrounds. The present study shows how marriage practices affect patterns of genetic variations and how they can lead to homogenization in the genetic pool.

RGS6: a novel gene associated with congenital cataract, mental retardation, and microcephaly in a Tunisian family.

PURPOSE: The object of this study is to identify the underlying genetic defect in a consanguineous Tunisian family affected with autosomal recessive congenital cataract associated with mental retardation and microcephaly. METHODS: A whole-genome scan was performed with polymorphic microsatellites in the axiom data for the screened members. Homozygous regions were analyzed with integrated Systems Tool for Eye gene Discovery (iSyTE), to identify candidate genes with lens-enriched expression that were potentially associated with cataract. Then we screened for mutations by direct sequencing. Structure and function of the mutant gene were analyzed by bioinformatics analysis. RESULTS: Using whole-genome scanning, we identified six runs of homozygosity shared among affected members of the studied family. Analysis of these regions by iSyTE allowed us to select 3 genes (RGS6, PCNX, and P4HA1) according to their expression in 3 critical stages of lens development. Upon screening for mutations by sequencing analysis, we found a novel mutation in RGS6, the splice-acceptor variant c.1369-1G>C that was not previously reported in congenital cataract phenotypes. CONCLUSIONS: Our study identified a new gene to be included in the large spectrum of cataract-associated genes. Importantly, the study demonstrated that, in addition to lens-enriched genes that exhibit high expression levels, genes identified by iSyTE that are highly lens-enriched but have lower absolute expression may also represent candidates for potential function in the lens.

High-resolution melting (HRM) assay for the detection of recurrent BRCA1/BRCA2 germline mutations in Tunisian breast/ovarian cancer families.

Germline deleterious mutations in the BRCA1/BRCA2 genes are associated with an increased risk for the development of breast and ovarian cancer. Given the large size of these genes the detection of such mutations represents a considerable technical challenge. Therefore, the development of cost-effective and rapid methods to identify these mutations became a necessity. High resolution melting analysis (HRM) is a rapid and efficient technique extensively employed as high-throughput mutation scanning method. The purpose of our study was to assess the specificity and sensitivity of HRM for BRCA1 and BRCA2 genes scanning. As a first step we estimate the ability of HRM for detection mutations in a set of 21 heterozygous samples harboring 8 different known BRCA1/BRCA2 variations, all samples had been preliminarily investigated by direct sequencing, and then we performed a blinded analysis by HRM in a set of 68 further sporadic samples of unknown genotype. All tested heterozygous BRCA1/BRCA2 variants were easily identified. However the HRM assay revealed further alteration that we initially had not searched (one unclassified variant). Furthermore, sequencing confirmed all the HRM detected mutations in the set of unknown samples, including homozygous changes, indicating that in this cohort, with the optimized assays, the mutations detections sensitivity and specificity were 100 %. HRM is a simple, rapid and efficient scanning method for known and unknown BRCA1/BRCA2 germline mutations. Consequently the method will allow for the economical screening of recurrent mutations in Tunisian population.

Prevalence of Bardet-Biedl syndrome in Tunisia.

Bardet-Biedl syndrome (BBS, OMIM 209900) is a ciliopathy causing multivisceral abnormalities. This disease is mainly characterized by obesity, post-axial polydactyly, hypogenitalism, intellectual disabilities, pigmentary retinopathy, and renal deficiency. The prevalence of BBS has been estimated in different populations, ranging from 1 in 160,000 in European populations to 1 in 13,000 in Bedouins from Kuwait. In the present report, we present the first epidemiological study of Bardet-Biedl syndrome in Tunisia. From 1984 to 2009, 46 Tunisian families, including 67 affected members, were diagnosed as BBS. The patients' ages ranged between 6 months and 37 years, with median age of 10.4 years. High level of consanguinity was noted in our cohort (93.47%). The overall minimum prevalence in our population was estimated to be approximately 1 in 156,000 individuals. Our study reflects the actual frequency of BBS in North Africa and showed that this disease seems uncommon.

[Linkage analysis of six Algerian families with autosomal recessive non specific mental retardation]. / Analyse génétique de six familles Algériennes avec retard mental non spécifique autosomique récessif.

BACKGROUND: Mental retardation is one of the most frequent major handicap, with a 1-3 % frequency in the general population. The recent progress of molecular biology and cytogenetic allowed to identify new genes for non syndromic autosomal recessive mental retardation. AIM: To seek a genetic linkage to the loci implied in the nonspecific mental retardation transmitted into autosomal recessive (ARNSMR) in Algerian families with several affected members and to make the Genetic analysis of ARNSMR for 4 known loci: 3p25-pter; 4q24- q25, 19p13.12 and 1p21.1-p13. METHODS: The study concerned 34 individuals including 15 patients, belonging to six consanguineous Algerian families. Genotyping was made using polymorphic microsatellite markers and the analysis carried out thanks to the program Gene Mapper software. Statistical analyses were validated using the Fast Link programme of the Easy linkage software (V4:00 betas). RESULTS: The study carried out made it possible to exclude linkage of all loci for 3 families, nevertheless the linkage of one family to the locus 1p21.1-p13.3 remains possible. CONCLUSION: The absence of linkage of 4 Algerian families with autosomal recessive mental retardation to 3 well known loci, confirms the genetic heterogeneity of mental retardation. We have to pursue research of candidate genes by whole genome scan.

Non-syndromic autosomal recessive mental retardation in Tunisian families : exclusion of GRIK2 and TUSC3 genes.

BACKGROUND: Mental retardation is one of the most frequent major handicap, with a 1-3 % frequency in the general population, it appear a major problem of public health. The recent progress of molecular biology and cytogenetic allowed to identify new genes for non syndromic autosomal recessive mental retardation (NSAR-MR). AIM: Genetic analysis of NSAR-MR: the GRIK2 gene (6q16.3-q21) and the TUSC3 gene (8p22). METHODS: Four Tunisian families with NSAR-MR were included in this study. Genotyping was made using polymorphic microsatellite markers and statistical analysis was validated using the Fast Link programme of the Easy linkage software (V4:00beta). RESULTS: Genotyping and linkage analysis excluded linkage of the GRIK2 gene and TUSC3 gene. CONCLUSION: Our results confirm the extreme genetic heterogeneity of NSAR-MR.

Absence of PITX3 mutation in a Tunisian family with congenital cataract and mental retardation.

PURPOSE: The PITX3 (pituitary homeobox 3) gene encodes for a homeobox bicoid-like transcription factor. When one allele is mutated, it leads to dominant cataract and anterior segment mesenchymal dysgenesis in humans. When both copies are mutated, homozygous mutation contributes to microphtalmia with brain malformations. In the current study, a family with autosomal recessive congenital cataract (ARCC) associated with mental retardation (MR) was examined to identify PITX3 mutations. METHODS: Sequencing of the PITX3 gene was performed on two affected and three unaffected members of the studied Tunisian family. The results were analyzed with Sequencing Analysis 5.2 and SeqScape. RESULTS: No mutation in the four exons of PITX3 was revealed. Two substitution polymorphisms, c.439C>T and c.930C>A, were detected in exons 3 and 4, respectively. These alterations did not segregate with the disease. CONCLUSIONS: Although PITX3 was shown to be essential to normal embryonic eye and brain development in vertebrates, we report the absence of PITX3 mutations in a family presenting congenital cataract and mental retardation.

Tunisia: communities and community genetics.

The population of Tunisia rose from 2.7 millions before the Second World War to 10,074,951 in 2005. Modern Tunisians are the descendents of indigenous Berbers and of people from various civilizations that were assimilated into the population over the centuries. Since its independence in 1956, Tunisia has enjoyed a stable political regime. The social landscape has also changed, based on the declaration of the Code of Personal Status, and on the nationwide education and economic progress. Consanguineous marriages are prevalent, with the same distribution between maternal and paternal relatives' offspring. Large and consanguineous families contributed to the description of a number of new autosomal recessive conditions and to identify new loci and genes. Genetic disorders are common in Tunisia, where most people are receptive to health guidelines. Selective abortion of an affected fetus is legal in Tunisia. Contraception is encouraged. This paper reviews common genetic disorders in the country. In spite of the high quality of health care services provided in Tunisia and the progress made in genetic research in the country, genetic services still remain insufficient and do not cover all parts of the country. At present, genetic counseling and prenatal diagnosis seems to be the method of choice to prevent genetic diseases in Tunisia, and such services should be developed as a priority despite the financial costs of such a program.