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IntroductionBladder cancer (BC) is a highly prevalent malignancy worldwide and particularly in Lebanon. Several studies have reported genetic risk factors in GSTM1 and NAT2, as well as many modifiable and non-modifiable risk factors, associated with BC.MethodsThis is a retrospective study that includes 51 Lebanese patients with BC. Peripheral blood samples were collected from patients and DNA extraction was performed using the standard salting-out method. Whole exome sequencing (WES) was performed and was followed by a thorough analysis of GSTM1, NAT2 and a panel of 127 genes known to be implicated in different hereditary cancers, for the detection of pathogenic germline mutations in the studied individuals.ResultsOur cohort included 42 men (82.4%) and 9 women (17.6%), with a mean age at diagnosis equal to 67 years. Of all participants, 10.8% had a family member diagnosed with BC and 17.3% with other cancer types. Our WES analysis allowed the detection of a high-risk variant found in APC (rs1801155) and a variant in BRIP1 (rs28903098) that are frequent in our cohort and more prevalent in our Lebanese in-house database compared to other international databases. Furthermore, two actionable variants, one in PALB2 (rs864622498) and another in ERCC2 (rs121913016) were detected in 2 different individuals from our cohort, paving the way to personalized therapies in these patients. A variant in NAT2 (rs1799931), shown to be associated with BC in other populations, was detected in 4 patients from our cohort.ConclusionThis is the first study in Lebanon and one of very few international studies carried out by NGS in patients with BC. Further studies in larger cohorts are required to confirm our findings in the Lebanese population.

Introduction/Background* Borderline ovarian tumors (BOT) are low malignant potential lesions with a good prognosis that represent around 15% of all epithelial tumors of the ovary. In addition to that, 30% of patients with BOT are less than 40 years old which makes the preservation of fertility a key point in management. Molecular studies in ovarian cancer have shown a correlation between the genetic profile of the tumor and the patient‘s prognosis Methodology We report the case of a 25-year-old patient, G0P0A0, diagnosed with a mucinous borderline right ovarian tumor back in 2005. In 2009, during a routine control ultrasound, another ovarian cyst was identified on the right side. She was operated again of a cystectomy and peritoneal staging and histopathology confirmed the mucinous nature of the tumor. FIGO stage was IA in both cases. The two blocs of tumors underwent a full exome sequencing technique in order to identify possible key mutations. Result(s)* Both tumors had variations of EGFR, FGFR3, BRCA1, STK11, NTKR1 and PIK3CA genes. However, the first tumor also had a KRAS mutation that wasn’t found in the second lesion four years later. KRAS variants have been shown to be present in low grade ovarian cancer and well-differentiated tumors. Conclusion* Borderline tumors often recurs in form of borderline tumor but the genetic profile should not be the same as the primary tumor, as shown in our case report. Loss of KRAS could explain the recurrence of the disease. Seeing that the molecular profile of the tumor is in constant change, a continuity in the spectrum normal-benign-borderline-malignant could be hypothesized.

Among all cancer types, pulmonary cancer has the highest mortality rate. Tobacco consumption remains the major risk factor for the development of lung cancer. However, many studies revealed a correlation between inherited genetic variants and predisposition to lung cancer, especially in nonsmokers. To date, genetic testing for the detection of germline mutations is not yet recommended in patients with lung cancer and testing is focused on somatic alterations given their implication in the treatment choice. Understanding the impact of genetic predisposition on the occurrence of lung cancer is essential to enable the introduction of accurate guidelines and recommendations that might reduce mortality. In this review paper, we describe familial lung cancer, and expose germline mutations that are linked to this type of cancer. We also report pathogenic genetic variants linked to syndromes associated with lung cancer.

Intellectual disability (ID) is a neurodevelopmental disorder characterized by limitations in both intellectual and behavioral functioning. It can occur in non-syndromic and syndromic forms involving multiple organs. While the majority of genetic variants linked to ID are de novo, inherited variants are also detected in some forms. Here, we report a consanguineous Lebanese family presenting with an autosomal recessive syndromic ID characterized by neurodevelopmental delay, mild dysmorphic features, hearing impairment and endocrine dysfunction. Whole exome sequencing enabled the detection of the homozygous nonsense mutation in BOD1, p.R151X, in the proband. BOD1 is required for chromosomes biorientation during cell division. It also contributes to the regulation of cell survival and to the modulation of fatty acid metabolism. Another nonsense mutation in BOD1 was linked to ID in a consanguineous Iranian family. This is the second report of BOD1 mutations in humans and the first in a syndromic ID including gonadal dysfunction and high-frequency hearing impairment. Our findings confirm the involvement of BOD1 in cognitive functioning and expand the clinical spectrum of BOD1 deficiency.

International audience; Background:The past few decades have witnessed a tremendous development in the field of genetics. Theimplementation of next generation sequencing (NGS) technologies revolutionized the field of molecular biologyand made the genetic information accessible at a large scale. However, connecting a rare genetic variation to acomplex phenotype remains challenging. Indeed, identifying the cause of a genetic disease requires amultidisciplinary approach, starting with the establishment of a clear phenotype with a detailed family history andending, in some cases, with functional assays that are crucial for the validation of the pathogenicity of a mutation.Methods:Two hundred Lebanese patients, presenting a wide spectrum of genetic disorders (neurodevelopmental,neuromuscular or metabolic disorders, etc.), sporadic or inherited, dominant or recessive, were referred, over thelast three and a half years, to the Medical Genetics Unit (UGM) of Saint Joseph University (USJ). In order to identify the genetic basis of these diseases, Whole Exome Sequencing (WES), followed by a targeted analysis, was performed for each case. In order to improve the genetic diagnostic yield, WES data, generated during the first 2 years of this study, were reanalyzed for all patients who were left undiagnosed at the genetic level. Reanalysis was based on updated bioinformatics tools and novel gene discoveries.Results:Our initial analysis allowed us to identify the specific genetic mutation causing the disease in 49.5% of the cases, in line with other international studies. Repeated WES analysis enabled us to increase the diagnostics yield to 56%.Conclusion:The present article reports the detailed results of both analysis and pinpoints the contribution of WES data reanalysis to an efficient genetic diagnosis. Lessons learned from WES reanalysis and interpretation are also shared.

The expanded use of NGS tests in genetic diagnosis enables the massive generation of data related to each individual, among which some findings are of medical value. Over the last three and a half years, 280 unrelated Lebanese patients, presenting a wide spectrum of genetic disorders were referred to our center for genetic evaluation by WES. Molecular diagnosis was established in 56% of the cases, as was previously reported. The current study evaluates secondary findings in these patients in 59 genes, linked to conditions mostly responsive to medical interventions, as per the ACMG guidelines. Our analysis allowed us to detect 19 pathogenic/likely pathogenic variants in 24 individuals from our cohort. Dominant actionable variants were found in 17 individuals representing 6% of the studied population. Genes associated with dominant cardiac diseases were the most frequently mutated: variants were found in 2.1% of our cohort. Genetic predisposition to cancer syndromes was observed in 1.07% of the cases. In parallel to dominant disease alleles, our analysis identified a recessive pathogenic disease allele in 2.5% of the individuals included in this study. Of interest, some variants were detected in different patients from our cohort thus urging the study of their prevalence in our population and the implementation, when needed, of specific genetic testing in the neonatal screening panel. In conclusion, here we report the first study estimating the actionable pathogenic variant load in the Lebanese population. Communicating current findings to the patients will enable them to benefit from a multi-disciplinary approach. Furthermore, tailoring the ACMG guidelines to the population is suggested, especially in highly consanguineous populations where the information related to recessive alleles might be highly beneficial to patients and their families.

This study investigated the mitochondrial DNA (mtDNA) control region variation in Middle Eastern populations (610 individuals from Lebanon, Jordan and the Kingdom of Bahrain) for which population data are scarce. FST comparison among populations revealed that there are significant differences in mtDNA distributions between Bahrain and the two other populations, while Lebanon and Jordan showed no significant differences. This was also reflected by the distribution of the observed lineages that differed prominently between Bahrain and the other two investigated populations. Jordan and Lebanon fit the hitherto known genetic results of the Levant population. Data are available via EMPOP (https://empop.online) and GenBank.

Familial Mediterranean fever (FMF) is a recessively inherited autoinflammatory disorder. The caspase-1-dependent cytokine, IL-1β, plays an important role in FMF pathogenesis, and RAC1 protein has been recently involved in IL-1β secretion. This study aims to investigate RAC1 expression and role in IL-1β and caspase-1 production and oxidative stress generation in FMF. The study included 25 FMF patients (nine during attack and remission, and 16 during remission only), and 25 controls. RAC1 expression levels were analyzed by real-time PCR. Ex vivo production of caspase-1, IL-1β, IL-6 and markers of oxidative stress (malondialdehyde, catalase, and glutathione system) were evaluated respectively in supernatants of patients’ and controls’ PBMC and PMN cultures, in the presence and absence of RAC1 inhibitor. RAC1 gene expression and IL-1β levels were increased in patients in crises compared to those in remission or controls. RAC1 expression levels were correlated with MEFV genotypes, patients carrying the M694V/M694V genotype having a two-fold increase in the expression levels compared to those carrying other genotypes. Caspase-1 levels were higher in LPS-induced PBMC of patients in remission than controls. Spontaneous and LPS-induced IL-1β production were comparable in patients in remission and controls, whereas LPS-induced IL-6 production was enhanced in patients, compared to controls. RAC1 inhibition resulted in a decrease in caspase-1 and IL-1β, but not IL-6, levels. Malondialdehyde levels produced by LPS-stimulated PMNs were increased in patients in remission compared to those in controls, but decreased following RAC1 inhibition. Catalase and GSH activities were reduced in unstimulated PMN culture supernatants of patients in remission compared to controls and were increased in the presence of RAC1 inhibitor. These results show the involvement of RAC1 in the inflammatory process of FMF by enhancing IL-1β production, through caspase-1 activation, and generating oxidative stress, even during asymptomatic periods.

Phenotypic heterogeneity is often observed in patients with telomeropathies caused by pathogenic variants in telomere biology genes. However, the roles of recessive variants in these different phenotypes are not fully characterized. Our goal is to describe the biological roles of a novel homozygous RTEL1 variant identified in a consanguineous Lebanese family with unusual presentation of telomeropathies. A proband was screened for germline variants in telomere biology genes by whole exome sequencing. Leukocytes' telomere length was measured in the proband and eight relatives. We identified a novel homozygous p.E665K RTEL1 variant in the proband, his mother, and seven siblings that associated with telomere shortening and a broad spectrum of clinical manifestations, ranging from mild unspecific findings to severe phenotypes. Consanguinity in at least three family generations led to increased frequency of the homozygous p.E665K variant in the youngest generation and progressive telomere shortening. The increased frequency of the homozygous RTEL1 variant due to consanguinity in this Lebanese family allowed us to infer novel behaviors of recessive RTEL1 variants, as the expressivity and penetrance of this gene are very heterogenous between inter- and intra-generations. Progressive telomere shortening was associated with disease anticipation, first reported in recessive autosomal telomeropathies. Both genetic testing and telomere length measurement were critical for the clinical diagnosis of this family with telomere diseases marked by phenotypic heterogeneity.

e13045 Background: Hereditary breast (BC) and ovarian cancer (OC) genetic alterations are considered the most prevalent among familial cancer. To date, four studies have exposed the mutations related to hereditary BC predisposition in the Lebanese population , with percentage of BRCA-related pathogenic mutations ranging between 5 % and 15 %. Methods: Between 2017 and 2019, 117 patients with high risk hereditary breast and ovarian cancer were referred to undergo the testing at the Unité de Génétique médicale (UGM) of Saint-Joseph University of Beirut, Lebanon. The sequencing was accomplished by using the 21-panel Next-Generation Sequencing (NGS) method for all of our patients, to which we also added the MLPA technique followed by the Sanger sequencing for validation whenever a genetic alteration was found. Results: From 117 Lebanese women with high-risk hereditary breast and ovarian cancer predisposition, 19 pathogenic mutations were identified in this study: 11 BRCA1, 1 BRCA2, 2 PALB2, 1 ATM, 1 CDH1, 1 MSH6, 1 RAD51C, and 1 BRIP1. Among those, 13 patients had BC, one had OC and five were healthy individuals. Five similar mutations were found within the BRCA1 gene, the p.C44F mutation, accounting for 45.4 %, thus suggesting a founder effect. Average age at diagnosis in the BC patients carrying a mutation was 41 years and 38.5% had a triple negative BC. Conclusions: The overall pathogenic mutation rate was equal to 16.2% while the BRCA deleterious mutation rate was 10.3% lower to those reported in the literature. The p.C44F mutation appeared five times suggesting a founder effect. [Table: see text]

Background Hyaline fibromatosis syndrome (HFS) is a recently introduced alternative term for two disorders that were previously known as juvenile hyaline fibromatosis (JHF) and infantile systemic hyalinosis (ISH). These two variants are secondary to mutations in the anthrax toxin receptor 2 gene (ANTXR2) located on chromosome 4q21. The main clinical features of both entities include papular and/or nodular skin lesions, gingival hyperplasia, joint contractures and osteolytic bone lesions that appear in the first few years of life, and the syndrome typically progresses with the appearance of new lesions. Methods We describe five Lebanese patients from one family, aged between 28 and 58 years, and presenting with nodular and papular skin lesions, gingival hyperplasia, joint contractures and bone lesions. Because of the particular clinical features and the absence of a clinical diagnosis, Whole Genome Sequencing (WGS) was carried out on DNA samples from the proband and his parents. Results A mutation in ANTXR2 (p. Gly116Val) that yielded a diagnosis of HFS was noted. Conclusions The main goal of this paper is to add to the knowledge related to the clinical and radiographic aspects of HFS in adulthood and to show the importance of Next-Generation Sequencing (NGS) techniques in resolving such puzzling cases.

Pyridoxine dependent epilepsy (PDE) is a rare autosomal recessive neurometabolic disorder. In the classical form, seizures are observed within the first month of life, while in the atypical form seizures appear later in life, sometimes as late as at the age of 3 years of life. Both types are unresponsive to conventional anticonvulsant therapy, but can be controlled with pyridoxine monotherapy. Mutations in the ALDH7A1 gene, encoding α-aminoadipic semialdehyde dehydrogenase have been reported to cause this disease in most patients. Here, we report on a boy with developmental delay, dysmorphic facial features, and uncontrolled episodes of seizures that appeared at the age of 18 months. By whole exome sequencing (WES) a homozygous missense mutation in ALDH7A1 (NM_001182: c.239T > G, p.V80G) was found. We discuss the importance of WES in such atypical cases.

WOS: 000286501500003, PubMed ID: 21194678, Microphthalmia with limb anomalies (MLA) is a rare autosomal-recessive disorder, presenting with anophthalmia or microphthalmia and hand and/or foot malformation. We mapped the MLA locus to 14q24 and successfully identified three homozygous (one nonsense and two splice site) mutations in the SPARC (secreted protein acidic and rich in cysteine)-related modular calcium binding 1 (SMOC1) in three families. Smoc1 is expressed in the developing optic stalk, ventral optic cup, and limbs of mouse embryos. Smoc1 null mice recapitulated MLA phenotypes, including aplasia or hypoplasia of optic nerves, hypoplastic fibula and bowed tibia, and syndactyly in limbs. A thinned and irregular ganglion cell layer and atrophy of the anteroventral part of the retina were also observed. Soft tissue syndactyly, resulting from inhibited apoptosis, was related to disturbed expression of genes involved in BMP signaling in the interdigital mesenchyme. Our findings indicate that SMOC1/Smoc1 is essential for ocular and limb development in both humans and mice., Ministry of Health, Labour and WelfareMinistry of Health, Labour and Welfare, Japan; Japan Science and Technology AgencyJapan Science & Technology Agency (JST); Japan Society for the Promotion of ScienceMinistry of Education, Culture, Sports, Science and Technology, Japan (MEXT)Japan Society for the Promotion of Science, We would like to thank the patients and their families for their participation in this study. We thank Yoshiko Takahashi (Nara Institute of Science and Technology) and Atsushi Yamada (Showa University) for providing the Bmp2 and Sox9 probes; Elizabeth J. Robertson (University of Oxford) and Makoto Ishibashi (Kyoto University) for the Bmp7 probe; Robert E. Maxson, Jr. (University of Southern California Keck School of Medicine) for the Msx2 probe; Tomonori Hirose, Kazunori Akimoto, and Kazunori Sasaki (Yokohama City University) for providing useful information about mouse breeding, taking photos on a stereo microscope, and mRNA quantification; and Kohei Shiota and Sumiko Kimura (Kyoto University) for helpful comments about NB staining and limb anomalies. This work was supported by research grants from the Ministry of Health, Labour and Welfare (T. Furuichi, N. Miyake, N. Matsumoto, and H.S.) and the Japan Science and Technology Agency (N. Matsumoto), a Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (T. Furuichi and N. Matsumoto), and a Grant-in-Aid for Young Scientist from the Japan Society for the Promotion of Science (K.N., H.D., N. Miyake, and H.S.). This work has been carried out at the Advanced Medical Research Center of Yokohama City University.

We report on a 10.5-year-old girl with a mild form of campomelic dysplasia. She presented with short stature of prenatal onset, dysmorphic facial features, limitation of supination and pronation of the forearms, dysplastic nails, and bone abnormalities consisting especially of cone-shaped epiphyses of the middle phalanx of the 2nd fingers, brachydactyly and clinodactyly of the middle phalanx of both 5th fingers, short 4th metacarpals, radial and femoral head subluxation, hypoplastic scapulae, humeral and ulnar epiphyseal abnormalities, unossified symphysis pubis, and a significant delay in bone age. Molecular analysis of the SOX9 gene revealed the presence of a de novo missense mutation: p.P170L (c.509C>T). Mild and surviving cases of campomelic dysplasia are reviewed.

We report on a consanguineous Lebanese family where two sibs had an axial hypotonia, developmental delay, hirsutism, large fontanels with delayed closure, and dysmorphic facial features that consist of frontal bossing, prominent eyes, slightly down-slanting palpebral fissures, hypertelorism, telecanthus, long eyelashes, gum hypertrophy, and pointed chin. In addition, they had short neck, abnormal thoracic configuration, wrinkled skin on the hands and abdomen, hepato-splenomegaly and neonatal spontaneous fractures. Their overall health and hepatic function deteriorated every time they had fever. The eldest boy died at the age of 18 months secondary to a hepatic failure. Laboratory exams did not reveal any anomaly except for the hepatic function. Differential diagnoses are discussed and the possibility that we might be reporting on a new metabolic syndrome is raised.

Background Chromosomal microarray analysis (CMA) is currently the most widely adopted clinical test for patients with unexplained intellectual disability (ID), developmental delay (DD), and congenital anomalies. Its use has revealed the capacity to detect copy number variants (CNVs), as well as regions of homozygosity, that, based on their distribution on chromosomes, indicate uniparental disomy or parental consanguinity that is suggestive of an increased probability of recessive disease. Results We screened 149 Lebanese probands with ID/DD and 99 healthy controls using the Affymetrix Cyto 2.7 M and SNP6.0 arrays. We report all identified CNVs, which we divided into groups. Pathogenic CNVs were identified in 12.1% of the patients. We review the genotype/phenotype correlation in a patient with a 1q44 microdeletion and refine the minimal critical regions responsible for the 10q26 and 16q monosomy syndromes. Several likely causative CNVs were also detected, including new homozygous microdeletions (9p23p24.1, 10q25.2, and 8p23.1) in 3 patients born to consanguineous parents, involving potential candidate genes. However, the clinical interpretation of several other CNVs remains uncertain, including a microdeletion affecting ATRNL1. This CNV of unknown significance was inherited from the patient’s unaffected-mother; therefore, additional ethnically matched controls must be screened to obtain enough evidence for classification of this CNV. Conclusion This study has provided supporting evidence that whole-genome analysis is a powerful method for uncovering chromosomal imbalances, regardless of consanguinity in the parents of patients and despite the challenge presented by analyzing some CNVs. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0130-y) contains supplementary material, which is available to authorized users.

Familial Mediterranean fever (FMF) is an autosomal recessive disease mostly frequent in Mediterranean populations. Over 50 mutations have been identified in the gene responsible for the disease, MEFV. The present study reports the frequencies of MEFV mutations in 558 Lebanese and 55 Jordanian FMF patients and points out the severity of the M694V frequently observed mutation among these patients. Three novel mutations, T177I, S108R and E474K were also identified in the Lebanese group. An excess of homozygotes and a deficit of heterozygotes were observed in both samples when compared to the expected number of observed genotypes under the Hardy-Weinberg hypothesis. Homozygotes for M694V and M694I were still in excess in the Lebanese group of patients, even after consanguinous homozygotes were removed, or population structure was considered. This excess is therefore neither due to consanguinity nor to subgroups in the Lebanese population, but rather to more remote consanguinity or to a selection bias favoring the census of these genotypes. The fact that FMF female patients were less censed than male patients may be due to the greater resistance of females to pain and to the possibility of confusing abdominal and gynecological pain. The phenotypic heterogeneity of the FMF could then originate both from genetic causes like allelic heterogeneity or modulating genes, and cultural background facing the physiological consequences of genotypes at risk.

Baller‐Gerold syndrome (BGS) is a rare autosomal recessive condition with radial aplasia/hypoplasia and craniosynostosis (OMIM 218600). Of >20 cases reported so far, a few appear atypical and have been reassigned to other nosologic entities, including Fanconi anaemia, Roberts SC phocomelia, and Pfeiffer syndromes after demonstration of corresponding cytogenetic or molecular abnormalities. Clinical overlap between BGS, Rothmund‐Thomson syndrome (RTS), and RAPADILINO syndrome is noticeable. Because patients with RAPADILINO syndrome and a subset of patients with RTS have RECQL4 mutations, we reassessed two previously reported BGS families and found causal mutations in RECQL4 in both. In the first family, four affected offspring had craniosynostosis and radial defect and one of them developed poikiloderma. In this family, compound heterozygosity for a R1021W missense mutation and a g.2886delT frameshift mutation of exon 9 was found. In the second family, the affected male had craniosynostosis, radial ray defect, poikiloderma, and short stature. He had a homozygous splice site mutation (IVS17‐2A>C). In both families, the affected offspring had craniosynostosis, radial defects, and growth retardation, and two developed poikiloderma. Our results confirm that BGS in a subgroup of patients is due to RECQL4 mutations and could be integrated into a clinical spectrum that encompasses RTS and RAPADILINO syndrome.

The facio-oculo-acoustico-renal syndrome (FOAR) is a rare autosomal recessive syndrome characterized by the presence of dysmorphic facial features, ocular anomalies, sensorineural hearing loss, and proteinuria. Diaphragmatic hernia, exomphalos, absent or abnormal corpus callosum, and myopia, can also be part of the syndrome. The disorder is caused by mutations of the LRP2 gene located on chromosome 2q23.3-q31.1. We hereby report the case of a 56-year-old female patient with typical FOAR features. Molecular study of the LRP2 gene revealed the presence of a novel splice-site mutation. In addition to what was reported in FOAR syndrome, this patient had a megadolichocolon complicated by a volvulus and a late-onset renal failure which necessitated hemodyalisis and renal transplantation. Reporting aging patients with genetic syndromes will provide information about their special needs and lead to improvements in their follow-up.

Consanguineous marriages have been widely practiced in several global communities with varying rates depending on religion, culture, and geography. In consanguineous marriages, parents pass to their children autozygous segments known as homozygous by descent segments. In this study, single-nucleotide polymorphisms were analyzed in 165 unrelated Lebanese people from Greek Orthodox, Maronite, Shiite and Sunni communities. Runs of homozygosity, total inbreeding levels, remote consanguinity, and population admixture and structure were estimated. The inbreeding coefficient value was estimated to be 1.61% in offspring of unrelated parents over three generations and 8.33% in offspring of first cousins. From these values, remote consanguinity values, resulting from genetic drift or recurrent consanguineous unions, were estimated in offspring of unrelated and first-cousin parents to be 0.61 and 1.2%, respectively. This remote consanguinity value suggests that for any unrelated marriages in Lebanon, the mates could be related as third cousins or as second cousins once removed. Under the assumption that 25% of marriages occur between first cousins, the mean inbreeding value of 2.3% may explain the increased incidence of recessive disease in offspring. Our analysis reveals a common ancestral population in the four Lebanese communities we studied.

Rare, atypical, and undiagnosed autosomal-recessive disorders frequently occur in the offspring of consanguineous couples. Current routine diagnostic genetic tests fail to establish a diagnosis in many cases. We employed exome sequencing to identify the underlying molecular defects in patients with unresolved but putatively autosomal-recessive disorders in consanguineous families and postulated that the pathogenic variants would reside within homozygous regions. Fifty consanguineous families participated in the study, with a wide spectrum of clinical phenotypes suggestive of autosomal-recessive inheritance, but with no definitive molecular diagnosis. DNA samples from the patient(s), unaffected sibling(s), and the parents were genotyped with a 720K SNP array. Exome sequencing and array CGH (comparative genomic hybridization) were then performed on one affected individual per family. High-confidence pathogenic variants were found in homozygosity in known disease-causing genes in 18 families (36%) (one by array CGH and 17 by exome sequencing), accounting for the clinical phenotype in whole or in part. In the remainder of the families, no causative variant in a known pathogenic gene was identified. Our study shows that exome sequencing, in addition to being a powerful diagnostic tool, promises to rapidly expand our knowledge of rare genetic Mendelian disorders and can be used to establish more detailed causative links between mutant genotypes and clinical phenotypes.

To identify the genetic basis of a recessive inheritance form of retinal dystrophy (RD) in a Lebanese family.Clinical data were recorded for five patients of the 14 family members. Genetic linkage was carried out using Affymetrix 250 K Nspl SNP array followed by sequencing.The patients showed variable phenotypes ranging from Leber Congenital Amaurosis (LCA) to progressive forms of Retinitis Pigmentosa (RP). A 46.1 Mb chromosomal region at chromosome 1q23.3-32.2 was identified by homozygosity mapping. This region contained the Crumbs homologue-1, CRB1, a gene responsible for recessive retinal dystrophies. CRB1 is required for photoreceptor morphogenesis, and it has been associated with RP and LCA. Sequencing of CRB1 revealed two mutations: a novel deletion in exon 6 (c.1772_1775delGCAT; p.C591Sfs*28) and a missense mutation in exon 7 (c.2234CT; p.T745M).We report a novel CRB1 mutation in inherited RD in a Lebanese family, and confirm the considerable phenotype heterogeneity that may exist between individuals sharing the same mutations.

Breast cancer is the most prevalent malignancy in women in Western countries, currently accounting for one third of all female cancers. Familial aggregation is thought to account for 5–10 % of all BC cases, and germline mutations in BRCA1 and BRCA2 account for less of the half of these inherited cases. In Lebanon, breast cancer represents the principal death-causing malignancy among women, with 50 % of the cases diagnosed before the age of 50 years. In order to study BRCA1/2 mutation spectra in the Lebanese population, 72 unrelated patients with a reported family history of breast and/or ovarian cancers or with an early onset breast cancer were tested. Fluorescent direct sequencing of the entire coding region and intronic sequences flanking each exon was performed. A total of 38 BRCA1 and 40 BRCA2 sequence variants were found. Seventeen of them were novel. Seven confirmed deleterious mutations were identified in 9 subjects providing a frequency of mutations of 12.5 %. Fifteen variants were considered of unknown clinical significance according to BIC and UMD-BRCA1/BRCA2 databases. In conclusion, this study represents the first evaluation of the deleterious and unclassified genetic variants in the BRCA1/2 genes found in a Lebanese population with a relatively high risk of breast cancer.

Leukodystrophies are a heterogeneous group of inherited neurodegenerative disorders characterized by abnormal white matter visible by brain imaging. It is estimated that at least 30% to 40% of individuals remain without a precise diagnosis despite extensive investigations. We mapped tremor-ataxia with central hypomyelination (TACH) to 10q22.3-23.1 in French-Canadian families and sequenced candidate genes within this interval. Two missense and one insertion mutations in five individuals with TACH were uncovered in POLR3A, which codes for the largest subunit of RNA polymerase III (Pol III). Because these families were mapped to the same locus as leukodystrophy with oligodontia (LO) and presented clinical and radiological overlap with individuals with hypomyelination, hypodontia and hypogonadotropic hypogonadism (4H) syndrome, we sequenced this gene in nine individuals with 4H and eight with LO. In total, 14 recessive mutations were found in 19 individuals with TACH, 4H, or LO, establishing that these leukodystrophies are allelic. No individual was found to carry two nonsense mutations. Immunoblots on 4H fibroblasts and on the autopsied brain of an individual diagnosed with 4H documented a significant decrease in POLR3A levels, and there was a more significant decrease in the cerebral white matter compared to that in the cortex. Pol III has a wide set of target RNA transcripts, including all nuclear-coded tRNA. We hypothesize that the decrease in POLR3A leads to dysregulation of the expression of certain Pol III targets and thereby perturbs cytoplasmic protein synthesis. This type of broad alteration in protein synthesis is predicted to occur in other leukoencephalopathies such as hypomyelinating leukodystrophy-3, caused by mutations in aminoacyl-tRNA synthetase complex-interacting multifunctional protein 1 (AIMP1).

International audience; We report on two siblings with hypotonia, ambiguous genitalia, microcephaly, ptosis, microretrognathia, thin lips, seizures, absent ossification of pubic rami, and brain abnormalities at the MRI. The two siblings died at 5 and 8 months, respectively. Molecular analysis indicated that SOX9, ARX, and DHCR7 genes were normal. Comparative genomic hybridization (CGH)-array analysis performed on the younger boy indicated two notable deletions, one on paternally inherited chromosome 4, and one on maternally inherited chromosome 5. The same deletions were found in a normal sister. Differential diagnoses and the possibility of a hitherto unreported syndrome are discussed. © 2011 Wiley-Liss, Inc.

We report on two sibs, a girl, and a boy, with tall stature, long, and triangular faces, prominent foreheads with high frontal hairlines, telecanthus, downward slanting of the palpebral fissures, ptosis of the eyelids, everted lower eyelids, large ears, long noses, full, and everted vermilions, highly arched and narrow palates, tooth crowding, thin and long uvulae, coloboma of the alae, hyperextensible joints, long digits, positive thumb signs, flat feet, slightly diminished muscle strength, myopia, astigmatia, inguinal hernia, and vesical diverticula. Total body X-rays showed the presence of advanced bone age in both sibs and bilateral hallux valgus in the girl. Array-CGH did not reveal any pathological CNV. Molecular analysis of FBN1, FBN2, TGFBR1, TGFBR2, and CHST14 gene was normal, and SNP linkage analysis excluded more candidate genes. Differential diagnoses and the possibility that we might be reporting on a hitherto unreported syndrome are discussed.

Dentoleukoencephalopathies with autosomal recessive inheritance are very rare. Recently, a large inbred Syrian pedigree was reported with oligodontia in association with a degenerative neurologic condition characterized by progressive ataxia and pyramidal syndrome and abnormalities in the white matter and cortical atrophy. A whole-genome screening of this family using 382 microsatellite markers was completed, but no evidence was found of linkage to any chromosomal region. A genome-wide linkage analysis using the 260K single nucleotide polymorphism Affymetrix array was then undertaken and a maximum multipoint logarithm of the odds score of 5.66 (NPL score = 7.65) was detected on chromosome 10q22 region. This genomic interval contains 95 known genes including the Prosaposin gene (PSAP) responsible for metachromatic leukodystrophy, which was excluded. Seventeen additional candidate genes were tested and excluded. Sequencing of the whole candidate locus is in progress and should allow the identification of the causative gene in this rare disease, thereby improving the understanding of the physiopathology of this disease.

Seventeen autosomal STRs were analyzed (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, CSF1PO, FGA, TH01, TPOX, vWA, Penta D, and Penta E) in the Lebanese population. A total of 192 unrelated individuals were genotyped for the 15 autosomal STRs in the Promega PowerPlex 16 STR kit. An additional 275 unrelated individuals were genotyped for the Applied Biosystems AmpFlSTR Identifiler and SGM+STR kits. Allele frequencies for the shared CODIS 13 loci among the three STR kits tested were not significantly different among individuals within the Lebanese population. Forensic and population genetic parameters for the 17 loci were calculated. We also compared the allele frequencies from this population with other populations in the same geographic vicinity.

Primary torsion dystonia is a clinically and genetically heterogeneous group of movement disorders. Fifteen different types of dystonia have been described to date, of whom 14 loci have been mapped, but only seven genes identified. Several different modes of inheritance have been described, including autosomal dominant transmission with reduced penetrance (12 loci), recessive X-linked (one locus), and autosomal recessive transmission (three loci). In this study, we describe the localization of a novel form of autosomal recessive, primary focal torsion dystonia using a genomewide search in a large consanguineous Lebanese family with three affected individuals. Homozygosity mapping with 382 microsatellite markers was conducted. Linkage analysis and haplotype construction allowed us to identify a novel locus designated as DYT17, within a 20.5-Mb interval on chromosome 20. Of the 270 known genes spread on this interval, 27 candidate genes were tested and excluded as responsible for the disease. Fine mapping by identification of other dystonia families linked to chromosome 20 and sequencing of candidate genes in the refined interval is required in order to identify the causative gene in DYT17.

Haplotype analysis of 376 Familial Mediterranean Fever (FMF) patients and 100 controls from Lebanon was performed using 4 microsatellite loci to study founder effects for the five most frequent mutations within the MEFV gene (M694V, M694I, V726A, M680I and E148Q). Each of these mutations was associated with a particular haplotype that was less frequent among controls, confirming that they have probably arisen from unique mutation events and that the carrier chromosomes derived from a common ancestor. The estimated ages of the most recent common ancestor for each of the 5 mutations, using the ESTIAGE program, were 7000, 8500, 15000, 23000 and 30000 years for M694V, M694I, V726A, M680I and E148Q, respectively. Varying the mutation rate at one of the markers led to younger age estimates, but the mutation E148Q remained the oldest one. Comparison of haplotype distributions among the different Lebanese religious groups confirmed that Muslim sub-populations (Shiites and Sunnites) as well as Christian ones, including Armenians who were formerly settled in the South-Eastern part of Asia Minor (Cilicia), are all derived from an ancient common ancestral population in which most of the MEFV mutations were already present with their respective associated haplotypes.

International audience; The extensive genetic heterogeneity of Bardet-Biedl syndrome (BBS) is documented by the identification, by classical linkage analysis complemented recently by comparative genomic approaches, of nine genes (BBS1-9) that account cumulatively for about 50% of patients. The BBS genes appear implicated in cilia and basal body assembly or function. In order to find new BBS genes, we performed SNP homozygosity mapping analysis in an extended consanguineous family living in a small Lebanese village. This uncovered an unexpectedly complex pattern of mutations, and led us to identify a novel BBS gene (BBS10). In one sibship of the pedigree, a BBS2 homozygous mutation was identified, while in three other sibships, a homozygous missense mutation was identified in a gene encoding a vertebrate-specific chaperonine-like protein (BBS10). The single patient in the last sibship was a compound heterozygote for the above BBS10 mutation and another one in the same gene. Although triallelism (three deleterious alleles in the same patient) has been described in some BBS families, we have to date no evidence that this is the case in the present family. The analysis of this family challenged linkage analysis based on the expectation of a single locus and mutation. The very high informativeness of SNP arrays was instrumental in elucidating this case, which illustrates possible pitfalls of homozygosity mapping in extended families, and that can be explained by the rather high prevalence of heterozygous carriers of BBS mutations (estimated at one in 50 in Europeans).

Kallmann syndrome (KS) is a developmental disease that combines hypogonadotropic hypogonadism and anosmia/hyposmia. Other congenital abnormalities may also coexist. This present report describes two sisters, aged 13 and 12 years, born from Lebanese consanguineous parents. The two sisters have complete androgen insensitivity (normal female appearance and an XY karyotype) due to a novel mutation, a C-to-G transversion in intron 2 of the androgen receptor gene, resulting in an aberrant splicing leading to an insertion of 66 nucleotides in the mRNA. In addition, the older sister has KS, together with synkinesia and multiple skeletal abnormalities, mainly kyphosis, vertebral abnormalities, and short right hand and feet. Her testosterone, FSH and LH levels were very low compared with her younger sister. No mutation in the KAL1 and FGFR1/KAL2 genes were found. This unique report raises the possibility of an autosomal recessive or X-linked form of KS with new phenotypic expression.

Consanguinity and inbreeding increase the sharing of alleles among individuals; thus a considerable number of autosomal recessive phenotypes occur in offspring(s) of consanguineous couples. We have collected samples from consanguineous families with different phenotypes of unknown etiology that are compatible with autosomal recessive transmission, in order to identify the responsible functional genomic variation. 42 families of different ethnic background have been collected so far. From each family, DNA from the patient(s), unaffected siblings and the parents is extracted. Samples are i/analyzed by array-CGH for the detection of homozygous deletions; ii/genotyped with a 720K SNP-array in order to identify Runs of Homozygosity and the areas of the genome that could include the causative variant; iii/exome sequenced (one affected individual/family). Mean coverage is 130x and 98.2% of the coding region of RefSeq is covered at least 8x. By comparing the genotyping and sequencing data, we found that Single Nucleotide Variants (that passed the quality threshold) were detected with a specificity of 99.95%, sensitivity of 97.7%, Positive Predictive Value 99.2% and Negative Predictive Value 98.6%. On average we identified 21901 variants/exome. So far we analysed 26 families and identified the causative variation in known genes in 3 of them:VLDLR, FKTN and DMP1. In 12 families 23 candidate genes/variants have been identified(more than 1 candidate genes/family). In 11 families the likely molecular defect has not been identified. Consanguineous families provide an opportunity to identify pathogenic variants responsible for recessive phenotypes and rapidly fill in the gap between genotype and phenotype.

Background Familial Mediterranean fever is a recessive autoinflammatory disease frequently encountered in Armenians, Jews, Arabs and Turks. The MEFV gene is responsible for the disease. It encodes a protein called pyrin/marenostrin involved in the innate immune system. A large number of clinically diagnosed FMF patients carry only one MEFV mutation. This study aims at studying the MEFV gene splicing pattern in heterozygous FMF patients and healthy individuals, in an attempt to understand the mechanism underlying the disease in these patients. Methods RNA was extracted from peripheral blood leucocytes of 41 FMF patients and 34 healthy individuals. RT-PCR was then performed, and the amplified products were migrated on a polyacrylamide electrophoresis gel, characterized by gel extraction of the corresponding bands followed by sequencing. Results Five novel splicing events were observed in both patients and controls deleting either exons 3, 4 (del34), or exons 2, 3, 4 (del234), or exons 2, 3, 4, 5 (del2345) or exon7 (del7) or exons 7 and 8 (del78). Conclusions The observation of such qualitative variability in the expression of the MEFV gene suggests a complex transcriptional regulation. However, the expression of these novel transcripts in both patients and controls is not in favour of a severe pathogenic effect.

Background Familial breast cancer (BC) represents 5 to 10% of all BC cases. Mutations in two high susceptibility BRCA1 and BRCA2 genes explain 16–40% of familial BC, while other high, moderate and low susceptibility genes explain up to 20% more of BC families. The Lebanese reported prevalence of BRCA1 and BRCA2 deleterious mutations (5.6% and 12.5%) were lower than those reported in the literature. Methods In the presented study, 45 Lebanese patients with a reported family history of BC were tested using Whole Exome Sequencing (WES) technique followed by Sanger sequencing validation. Results Nineteen pathogenic mutations were identified in this study. These 19 mutations were found in 13 different genes such as: ABCC12, APC, ATM, BRCA1, BRCA2, CDH1, ERCC6, MSH2, POLH, PRF1, SLX4, STK11 and TP53. Conclusions In this first application of WES on BC in Lebanon, we detected six BRCA1 and BRCA2 deleterious mutations in seven patients, with a total prevalence of 15.5%, a figure that is lower than those reported in the Western literature. The p.C44F mutation in the BRCA1 gene appeared twice in this study, suggesting a founder effect. Importantly, the overall mutation prevalence was equal to 40%, justifying the urgent need to deploy WES for the identification of genetic variants responsible for familial BC in the Lebanese population. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0244-7) contains supplementary material, which is available to authorized users.