Eliane Chouery

Autosomal recessive Limb-Girdle Muscular Dystrophy type R28 (LGMDR28; OMIM #620375) is one of the most recently identified subtypes of recessive LGMD. To date, 17 affected individuals from eight unrelated families have been reported to harbor biallelic variants in the HMGCR gene. Here, we report eleven individuals from six unrelated Middle Eastern families diagnosed with LGMDR28 and carrying homozygous variants in HMGCR . Our cohort recapitulated most of the previously described clinical features of the HMGCR-related phenotype. In addition, we also report a family with congenital onset of the condition as well as two affected individuals with liver failure. Through genome and exome sequencing, we identified three novel homozygous missense variants; c.2519G >A, p.(Arg840Gln), c.1784G >A, p.(Arg595His), and c.1783C>T, p.(Arg595Cys) and a homozygous in-frame deletion (c.1522_1524del, p.(Ser508del)) previously reported in compound heterozygous state with a second relevant variant and very recently as homozygous in an unrelated proband. This study consolidates the pathogenic role of HMGCR in LGMDR28 while expanding the phenotypic and mutations spectrum of LGMDR28.

Consanguinity is associated with an increased risk of autosomal recessive diseases. Its prevalence varies globally, with notably high prevalence in Middle-Eastern countries. Gaining insight into both the prevalence of consanguineous marriages and societal attitudes toward them is essential for designing effective public health interventions. This study examines the current prevalence of consanguinity in Lebanon and explores its contributing risk factors. It further evaluates the knowledge of the Lebanese population regarding this practice and premarital genetic screening, as well as their attitudes toward consanguinity and genetic counseling. A cross-sectional survey was conducted among 984 Lebanese individuals, aged 18 to 65 years, using an online self-administered questionnaire. The prevalence of consanguinity in Lebanon was found to be 24.5%, with first-cousin marriages comprising 46.5% of these unions; place of residence was the only independent factors affecting consanguinity prevalence among our sample. Most participants had a good understanding of consanguinity but misconceptions about specific genetic risks persisted. Attitudes varied, with participants from consanguineous backgrounds showing greater acceptance of the practice. Logistic regression identified gender, education, occupational status, and age as independent predictors of consanguinity while insufficient income, having consanguineous parents, and having a poor knowledge were associated with a positive attitude towards consanguinity. While the prevalence of consanguinity remains high and consistent over time, societal beliefs and cultural practices continue to influence this phenomenon. Public health interventions should focus on raising awareness and disseminating accurate information about the implications of consanguinity and the importance of genetic counseling, particularly among communities with high prevalence of consanguinity.

Newborn screening programs (NSPs) are public health initiatives that aim to detect specific genetic conditions in asymptomatic newborns early enough to allow timely interventions, and decrease disease-associated morbidity. Despite the existing criteria for selecting disorders to be included in NSP, establishing a standardized global program remains challenging due to genetic diversity across regions. To better tailor the Lebanese national NSP, exome sequencing (ES) of 969 Lebanese individuals was analyzed for a panel of 109 genes associated with NSPs worldwide. A total of 168 pathogenic/likely pathogenic variants were detected in 54 genes, including 41 involved in metabolic diseases and 8 in severe primary immunodeficiencies (PID). The CFTR gene was found to be the most mutated gene (4.38% carrier rate), with c.1210-11T > G, associated with congenital bilateral absence of vas deferens, being the most common variant. The subsequent most commonly mutated genes were CYP21A2 (3.5%) , G6PD (2.75%) , MCCC2 (1.86%) and PAH (1.80%). Both CFTR and CYP21A2 are not currently included in the Lebanese NSP. Besides, 1.33% of our cohort carry pathogenic variants in genes involved in severe PID. In conclusion, this is the first ES-based study in the Lebanese population for NSP genes. Our findings underscore the value of integrating local genetic data and ES-based approaches into NSPs, to better reduce the burden of genetic diseases and improve public health outcomes.

The molecular genetic diagnosis of prelingual sensorineural hearing impairment (HI) is essential for genetic counseling and patient management. Effective diagnosis requires a knowledge of the genetic architecture of HI, which is often lacking. We established a cohort of 450 unrelated patients with familial (at least two affected relatives) severe-to-profound bilateral prelingual HI in five countries with high consanguinity rates: Tunisia, Jordan, Algeria, Morocco, and Mauritania (the TJAMM cohort). Recessive and dominant inheritance were observed in 92% and 8% of cases, respectively; 14% were syndromic. Genome analysis detected 211 different mutations (36% not reported before) in 49 deafness genes, and fully resolved 90% of cases of autosomal recessive isolated deafness (DFNB forms), 89% of the mutations being homozygous. The deafness genes involved were similar in different countries, but their mutations, except a few in GJB2 and LRTOMT , differed considerably, suggesting an overrepresentation of private mutations. Biallelic missense mutations in MYO7A , CDH23 , PCDH15 , USH1C cause either DFNB forms or Usher syndrome type 1 (USH1) ( USH1/DFNB genes). Such mutations were overrepresented (13% of patients), highlighting the importance of distinguishing between these two mutation classes. We hypothesized that current difficulties might stem from the misclassification of certain mutations. By studying the 65 USH1/DFNB missense mutations reported to cause DFNB in the homozygous state, we identified some that, when associated with a loss-of-function mutation, resulted in USH1, a characteristic pattern of some recessive hypomorphic mutations. This reappraised classification of USH1/DFNB mutations has the potential to improve molecular diagnosis and patient management significantly.

Introduction: Neurodevelopmental and multiple malformation disorders spanning large phenotypic series can often lead to obscure diagnoses in the clinic. Blended phenotypes from multiple etiologies can compound this issue. We present a rare familial case of two siblings with Nicolaides-Baraitser syndrome (NCBRS) complicated by an initial diagnosis of syndromic craniosynostosis in one of the patients. Case Presentation: Whole exome sequencing (WES) was performed for the affected siblings using the Agilent SureSelect kit and Illumina HiSeq 2500 system, followed by GATK variant calling and in-house annotation. Sanger sequencing was used to validate candidate variants in all immediate family members. A pathogenic de novo variant in TCF12 (p.Gln646Ter), consistent with craniosynostosis type 3 (CRS3), was identified in the proband, along with a novel likely pathogenic variant in SMARCA2 (p.Ile833Phe) involved in NCBRS. The latter was also detected in the sister and is thus suspected to have arisen through germline mosaicism. Various overlapping phenotypic manifestations complicated clinical diagnosis. Conclusion: This case expands the molecular and clinical spectrum of NCBRS and CRS3 and underscores the utility of trio-based WES in detecting blended phenotypes of disorders with growing phenotypic spectrums. Paternal germline mosaicism may underlie high recurrence and inform reproductive counseling.

Background: Duchenne muscular dystrophy (DMD) is a severe X-linked neuromuscular disorder caused by pathogenic variants in the DMD gene, leading to dystrophin deficiency and progressive muscle degeneration. Thousands of variants with diverse types have been reported in DMD , contributing to a broad clinical spectrum. While typically associated with severe phenotypes, pathogenic DMD variants may also cause Becker muscular dystrophy (BMD), a milder form with later-onset muscle weakness, or isolated dilated cardiomyopathy with minimal skeletal muscle involvement. Rarely, asymptomatic individuals carry putative pathogenic variants, challenging established genotype-phenotype correlations. Methods: This study includes five unrelated Lebanese families who presented for genetic counseling or pre-marital screening and subsequently underwent genetic testing. Results: Exome sequencing revealed a predicted protein-truncating variant in exon 71 of DMD p.(Trp3416*) in multiple individuals, including three hemizygous healthy males aged 35, 65 and 67. Despite being classified as pathogenic, the variant's presence in asymptomatic males raises questions about its actual pathogenicity. In silico tools (e.g., Franklin, Varsome, CADD score: 52.0) predicted a strong deleterious effect. The variant is extremely rare in population databases and has conflicting interpretations in ClinVar, previously associated with DMD, BMD, and cardiomyopathy. Although other truncating variants in exon 71 are known to cause DMD, the identification of p.(Trp3416*) in healthy individuals with normal neuromuscular and cardiac function suggests the possibility of alternative splicing, modifier genes, or compensatory mechanisms mitigating the effect of dystrophin loss. Conclusion: This study underscores the importance of functional validation and long-term clinical monitoring to refine variant classification and guide accurate genetic counseling.

Advances in next-generation sequencing enabled its integration into genetic diagnosis and have led to the uncovering of secondary findings. In this paper, we analyzed 500 Lebanese participants for pathogenic and likely-pathogenic variants in 81 recommended genes listed by the American College of Medical Genetics (ACMG). In this retrospective study, 500 individuals seeking genetic diagnosis through Exome Sequencing were included. Variants were analyzed and their pathogenicity assessed based on ACMG/AMP criteria and ClinVar. Secondary findings were identified in 16.8% of cases based on ACMG/AMP criteria, which decreased to 6% when relying on ClinVar. Dominant cardiovascular disease variants were predominant, constituting 6.6% based on ACMG/AMP assessments and 2% according to ClinVar. Additionally, using ACMG/AMP criteria, dominant oncogenic variants were identified in 4.2% of individuals, while recessive pathogenic variants were found in 4.8%. In contrast, ClinVar-based analysis reported these variants in 1% and 2.6% of the cohort, respectively. The high discordance between ACMG/AMP and ClinVar classifications (16.8% vs. 6%) underscores ethical dilemmas in deciding which criteria to prioritize for patient disclosure. Indeed, the absence of ACMG-classified pathogenic or likely pathogenic variants in ClinVar complicates reporting due to a lack of evidence linking them to disease in other individuals. Finally, the significant discrepancy between ACMG/AMP and ClinVar classifications emphasizes the urgent need to harmonize variant databases and update ClinVar entries, particularly for understudied populations such as the Lebanese cohort.

To investigate the potential impact of the additional chromosome 21 on the gut microbiome in patients with Down syndrome (DS), two monozygotic (MZ) and two dizygotic (DZ) twin pairs discordant for DS were studied. Whole-genome shotgun sequencing was conducted to analyze the taxonomic and functional profiles of the gut microbial community in the twins and assess whether the gut microbiome composition influences the development of psychological pathologies. Sequencing generated a total of 2,338,132 reads, combined across the four samples. The number of contigs ranged from 98,521 to 122,000, and the GC content was 46.34-47.15%. The Simpson index at the species level in the DS of our study was distinctly higher in the DZ-DS but not in the MZ-DS. Taxonomic classification revealed a Western diversity profile in the twins, where the dominant bacterial phyla were Firmicutes, Bacteroidetes, and Actinomycetota. Each sample had a diversity of ten families at abundance >0.5%, of which Prevotellaceae, Lachnospiraceae, and Bacteroidaceae were the most prevalent. The Prevotellaceae family was detected at a high level in all samples, except in the DZ-DS, where Lachnospiraceae was the most abundant family. At the genus level, marked differences were observed between the DZ-DS twins compared to the others. Prevotella was not detected in the DZ-DS twin whereas it was the dominant genus in the MZ-DS and both healthy twins. The variation in predicted metagenomes between DS and non-DS showed that the average relative abundances for DS were comparable to those for non-DS. The two MZ twins discordant for DS appear to have relatively similar microbiomes, suggesting that the added chromosome 21 did not have a significant impact on gut microbiome composition. Identifying biomarkers of DS that modulate the gut composition and affect the overall health needs to be further studied, along with the potential role of Prevotella.

Introduction: Blended phenotypes resulting from the contribution of two or more genetic variants to the disease of a patient pose a significant diagnostic challenge. Correlating between the phenotypes and the genotypes of the affected patients is difficult in these cases, especially in the absence of a large family segregating the condition. Case Presentation: We report a child born to consanguineous Syrian parents with a complex phenotype including a skeletal dysplasia, characterized by a small thorax and phalangeal shortening, as well as cardiac anomalies and sensorineural hearing loss. Molecular analysis identified the presence of three potentially disease-causing genetic variants. These include homozygous variants in the IHH and TTC12B genes, known to be associated with acrocapitofemoral dysplasia (OMIM# 607778) and a form of short-rib thoracic dysplasia (OMIM# 613819), respectively, in addition to a heterozygous variant in the COL11A1 gene, associated with dominant forms of skeletal dysplasia, such as Marshall (OMIM# 154780) and Stickler (OMIM# 608481) syndromes, and hearing loss (OMIM# 618533). Conclusion: We propose that the complex phenotype observed in the patient results from the contribution of l three of these variants. This case highlights some of the challenges encountered in the genetic counseling of families with rare genetic conditions.