Genetic Center Research Articles

Updates on the molecular spectrum of MEFV variants in lebanese patients with Familial Mediterranean Fever

Familial Mediterranean Fever (FMF) is a hereditary autoinflammatory disorder, particularly present in the Mediterranean populations, and associated with pathogenic variants in the MEFV gene. This study aims to investigate the distribution of MEFV variants in a large cohort of Lebanese patients, and to explore the genotype-phenotype correlation among affected individuals. A retrospective analysis was conducted on 3,167 patients referred for MEFV sequencing at the Medical Genetics and Genomics Center(CGGM) at Saint-Joseph University of Beirut-Lebanon, from 2006 to 2023. Sanger sequencing was used to detect MEFV variants, focusing initially on hot-spot exons. Among the 3,167 patients, 46.73% (N = 1,480) carried at least one MEFV variant. The most common variants detected were M694V and V726A, both found in 28.98% of cases, followed by E148Q(27.83%) and M694I(13.98%). Moreover, Shiites and Sunni Muslims, and individuals from South and North Lebanon exhibited the highest frequency of variants. Interestingly, family history was found to be significantly higher in patients having two MEFV variants than those with one variant (p = 0.0026). The most commonly reported symptoms were fever(78%), abdominal pain(88%), joint pain(65%), and thoracic pain(46%). The genotype-phenotype correlation analysis revealed a more severe phenotype in patients carrying the M694V or V726A mutations compared to those with the homozygous E148Q genotype. This study, the largest in Lebanon, highlights the high prevalence of MEFV variants, particularly M694V and V726A, in FMF patients. Our data provide valuable insights into the genetic landscape of FMF in Lebanon and emphasize the importance of early genetic screening for a better disease management and genetic counselling.

The application of the facial analysis program Face2Gene in a single genetic counseling center: a retrospective study

BackgroundFace2Gene (F2G) is a software program, widely used in clinical genetics and dysmorphology for recognizing children with genetic disorders. In order to assess its accuracy in real clinical context, we applied F2G to patients from our genetic counseling center.ResultsWe randomly selected 151 children, who were referred to genetic counseling because of dysmorphic features and later diagnosed with a particular genetic condition. A frontal photograph was uploaded to the program, and at least three phenotypic traits were selected for each case. Date of birth, sex, weight, height, and head circumference were also entered in the software. The efficacy of the program to correctly diagnose the syndrome based on the facial analysis and/or phenotypic traits was assessed. In 56% (84 cases) of the patients, the F2G program accurately identified the correct diagnosis in its top three suggestions. Forty-seven percent (71 cases) of the patients had the correct diagnosis after applying only facial analysis. There was a statistically significant difference between the two types of analysis—p = 0.001. In 19 of the cases where F2G was unable to identify the correct diagnosis among the top three options based on phenotypic and facial analysis, the diagnosis was included among the 30 suggested syndromes, yielding a total success rate of 68%. The diagnosis was found in the ultra-rare syndromes’ suggestions area in six more cases.ConclusionsOur results show that F2G has a good overall performance, but adding phenotypic features to the case under study may increase even further its diagnostic capacity.

Comprehensive copy number analysis of spinal muscular atrophy among the Iranian population

Copy number variations in the SMN1 gene on chromosome 5 are the primary cause of Spinal Muscular Atrophy (SMA) disease, characterized by muscle weakness and degeneration due to impaired alpha motor neurons in the spinal cord. To obtain a comprehensive molecular understanding of the SMA, including carriers, silent carriers, and patients in the Iranian population, we analyzed data from 5224 individuals referred to Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran, between 2006 and 2023 using MLPA and quantitative RT-PCR methods. The carrier frequency of SMA was estimated to be 5.55%. Furthermore, 3.06% of SMA parents (n = 24) had two copies of the SMN1 gene. Among 725 patients, those with an earlier onset of SMA were more likely to have two copies of the SMN2 gene (46.45%) and no copies of the NAIP gene (49.36%). Among the 654 fetal samples screened for SMA, 22.33% were found to be affected, while 3.46% of their parents tested normal. These findings are valuable for genetic counseling, carrier screening, and prenatal diagnosis of SMA in Iran. Furthermore, they underscore the importance of CNV analysis of SMN1, SMN2, and NAIP genes for accurate diagnosis and prognosis of SMA.

Coffee Improvement by Interspecific Hybridization in Ethiopia

Ethiopia is fortunate in this aspect because it is the origin and genetic diversity center for Arabica coffee. This study's goal was to provide a succinct overview of Ethiopia's hybrid coffee variety development and successes. The main issue is a lack of improved hybrid types, despite the population of coffee having a high genetic variety, which offers enormous prospects for development programs. It is clear that current genetic and breeding research on coffee is insufficient to address the country's different agro-ecologies. Some of the fundamental breeding strategies to deal with such issues include combining ability analysis and hybridization investigation through heterosis. The presence of heterosis was reported in crosses of selected indigenous C. arabica L. varieties in Ethiopia under different set of studies, primarily due to the presence of diverse parental lines. Some studies had been conducted on assessment of heterosis and combining ability analysis for yield and morphological characteristics of coffee in Ethiopia. These findings unmistakably pointed to the potential for heterosis and combining ability analyses to significantly improve coffee. Generally, in Ethiopia starting from 1998 to 2023 only nine hybrid coffee variety released nationally. In order to create hybrids with improved performance and high yields for coffee with an Ethiopian origin, a continual crossing program should be necessary to obtain many additional cross combinations.

Evaluation of Cardiomyopathy-Related Target Genes by Next-Generation Sequencing Method and Investigation of the Phenotype-Genotype Relationship

Background: Primary heart muscle diseases called cardiomyopathy (CMP) constitute an important group of subsequent heart disorders. CMPs are basically divided into four subgroups associated with the heart muscle but clinically distinguishable: hypertrophic CMP (HCM), dilated CMP (DCM), restrictive CMP (RCM), and left ventricular non-compaction CMP. Material and Methods: The results of the patients who applied to the Genetic Diseases Evaluation Center with the preliminary diagnosis of clinical CMP were evaluated retrospectively in the current study. In the current study, 103 cases were included and evaluated for phenotype-genotype association with the CMP next-generation sequencing (NGS) panel. Results: Fifty-eight different variants were identified in 45 patients. Sixteen out of those 58 variants were novel. Of these variants, 19 (32.75%) were likely pathogenic (LP)/pathogenic (P), and 35 (60.34%) were variants of uncertain significance. Conclusion: The prevalence of pathogenic variants in target genes associated with CMP is important for our current country's population, and multiple gene groups associated with CMP can be screened through NGS. The contribution rate to the clinical diagnosis was 18.44% in terms of the individual population who applied to our medical genetics center and were compatible with the CMP indication.

Genetic Variants Linked to Opioid Addiction: A Genome-Wide Association Study.

Opioid use disorder (OUD) affects millions of people worldwide. While it is known that OUD originates from many factors, including social and environmental factors, the role of genetic variants in developing the disease has also been reported. This study aims to investigate the genetic variants associated with the risk of developing OUD upon exposure. Twenty-three subjects who had previously been given opioid-based painkillers to undergo minor surgical treatment were recruited at Prisma Health Upstate clinic and elsewhere. Eleven were considered nonpersistent opioid users (controls), and 12 were persistent opioid users (cases) at the time of sample collection after an initial surgery. The subjects were asked to provide saliva samples, which were subjected to DNA sequencing at Clemson University Center for Human Genetics, and variant calling was performed. The genome-wide association studies (GWASs) for genes known to be associated with OUD resulted in 13 variants (intronic or SNV) with genome-wide significance (raw p-value < 0.01) and two missense variants, rs6265 (p.Val66Met in BNDF isoform a) and rs1799971 (p.Asn40Asp) in OPRM1, previously reported in the literature. Furthermore, extending the GWASs to find all genomic variants and filtering the variants to include only variants found in cases (persistent opioid users) but not in controls (nonpersistent opioid users) resulted in 11 new variants (p-value < 0.005). Considering that OUD is a complex disease and the effect might come from different variants in the same genes, we performed a co-occurrence analysis of variants on the genes. We identified eight additional genes that harbor multiple variants, including four genes: LRFN3, ZMIZ1, RYR3, and OR1L6, with three or more variants in the case subjects but not in the control individuals. The performed PPI network construction, along with functional enrichment, indicated that the variants occur in calcium signaling, circadian entrainment, morphine addiction, alcoholism, and opioid signaling pathways, which are closely related to OUD or addiction in general.

Metabolic syndrome among patients with type 2 diabetes in Jordan: A cross-sectional study.

Metabolic syndrome is a major public health problem worldwide and an independent predictor of cardiovascular disease in patients with type 2 diabetes (T2DM). This study aimed to determine the prevalence of metabolic syndrome and its individual components among Jordanian patients with T2DM. A cross-sectional design was conducted among T2DM patients at the National Center for Diabetes, Endocrinology and Genetics in Jordan. Data were collected using a structured questionnaire and clinical data extracted from medical records. The National Cholesterol Education Program-Adult Treatment Panel III (ATP III) and International Diabetes Federation (IDF) diagnostic criteria were used to define metabolic syndrome. Among 1017 participants aged between 22 and 90 years, the overall prevalence of IDF defined metabolic syndrome was 84.2% (72.5% and 96.2% among males and females, respectively). Using ATP III criteria, overall prevalence was 79.1% (77.4% and 80.8% among males and females, respectively). Advancing age, female gender, nonadherence to a diet regimen, sedentary lifestyle or insufficient physical activity, and duration of diabetes ≥10 years were significantly associated with increased odds of metabolic syndrome, regardless of the definition used. Current smoking status and family history of cardiovascular diseases were significantly associated with increased likelihood of ATP III defined metabolic syndrome. The prevalence of metabolic syndrome among Jordanian patients with T2DM is extremely high. The main modifiable risk factors of metabolic syndrome among these patients include nonadherence to a diet regimen, insufficient physical activity, being overweight/obese and smoking. It is recommended that healthcare providers counsel patients on the importance of maintaining physical activity, smoking cessation, and adherence to a diet regimen.

Looks Can Be Deceiving: Diagnostic Power of Exome Sequencing in Debunking 15q11.2 Copy Number Variations.

Background/Objectives: The pathogenetic role of 15q11.2 Copy Number Variations (CNVs) remains contentious in the scientific community, as microdeletions and microduplications in this region are linked to neurodevelopmental disorders with variable expressivity. This study aims to explore the diagnostic utility of Exome Sequencing (ES) in a cohort of pediatric patients with 15q11.2 CNVs. Methods: We enrolled 35 probands with 15q11.2 microdeletions or microduplications from two genetic centers between January 2021 and January 2023. Chromosomal Microarray Analysis (CMA) and ES were performed with written consent obtained from all parents. Pathogenic variants were classified according to ACMG guidelines. Results: CMA identified additional pathogenic CNVs in 3 of 35 children (9%). Subsequent ES revealed likely pathogenic or pathogenic variants in 11 of 32 children (34%). Notably, a higher percentage of isolated autism spectrum disorder (ASD) diagnoses was observed in patients without other CNVs or point mutations (p = 0.019). Conclusions: The ES analysis provided a diagnostic yield of 34% in this pediatric cohort with 15q11.2 CNVs. While the study does not dismiss the contribution of the CNV to the clinical phenotype, the findings suggest that ES may uncover the underlying causes of neurodevelopmental disorders. Continuous monitoring and further genetic testing are recommended for all 15q11.2 CNV carriers to optimize clinical management and familial counseling.

KRAS G12C mutation in NSCLC in a small genetic center: insights into sotorasib therapy response potential

Lung cancer remains a significant health challenge, characterized by aberrant tissue growth within the pulmonary system. Early carcinogenic events often involve genomic instability and the emergence of a mutator phenotype. In this study, we aimed to explore the mutator phenotype in 89 patients diagnosed with non-small-cell lung cancer (NSCLC). RNA isolation from formalin-fixed paraffin-embedded (FFPE) tissue samples was performed using the Promega ReliaPrep RNA Miniprep System, facilitating gene amplification relevant to cancer through the Archer® FusionPlexComprehensiveThyroid and Lung (CTL) kit. Next-generation sequencing (NGS) on the Illumina NextSeq platform enabled comprehensive analysis of target areas. Utilizing Archer Analysis software, secondary analyses involving data cleansing, alignment, and variant/fusion identification were executed against the human reference genome hg19 (GRCh37). Expression patterns were visualized using HeatMap graphics. Our findings revealed a notable presence of KRAS gene mutations in approximately 20% of NSCLC patients. Among these mutations, the G12C variant was predominant at 50%, followed by G12V and G12D variants at 11.2% each. Notably, patients harboring the G12C variant responded favorably to sotorasib medication. These results underscore the importance of mutational profiling and targeted therapeutic approaches in managing NSCLC, particularly highlighting the promising efficacy of sotorasib in G12C-mutated cases.

High precision newborn screening for mucopolysaccharidosis type I by enzymatic activity followed by endogenous, non-reducing end glycosaminoglycan analysis

Measurement of enzymatic activity in newborn dried blood spots (DBS) is the preferred first-tier method in newborn screening (NBS) for mucopolysaccharidosis (MPS) disorders. However, false positives are observed due mainly to the presence of pseudodeficiencies. Our previous publications on glycosaminoglycan (GAG) biomarker levels in dried blood spots (DBS) for mucopolysaccharidoses demonstrated that second-tier GAG biomarker analysis can dramatically reduce the false positive rate in NBS. In the present study, we extend this approach to the analysis of a large number of false positives for MPS-I obtained from the Illinois, New York, and Tennessee NBS programs and from Greenwood Genetics Center. Results show that GAG levels measured by the Endogenous-Non-Reducing End method (Endogenous-NRE) are in the normal reference range for all samples. In a second study, we analyzed 166 samples. That showed below-cutoff MPS-I enzymatic activity level after testing 384,144 newborns in the Ontario, Canada NBS program. Both genotype and Endogenous-NRE GAG levels were determined for all 166 samples. Newborns at high risk for MPS-I based on genotype also showed elevated GAG levels and were clinically confirmed to be symptomatic for MPS-I. All newborns with pseudodeficiency or carrier status by genotyping all showed normal levels of the appropriate GAG biomarker. Samples found to be inconclusive based on one or more variants of unknown significance (VUS) all showed normal GAG biomarker levels and were found to be clinically normal during follow-up. These studies show that the Endogenous-NRE GAG second-tier NBS method is preferred over second-tier DNA analysis for the NBS of MPS-I with minimal false positives.

Second Primary Cancer Risks After Breast Cancer in BRCA1 and BRCA2 Pathogenic Variant Carriers.

Second primary cancer (SPC) risks after breast cancer (BC) in BRCA1/BRCA2 pathogenic variant (PV) carriers are uncertain. We estimated relative and absolute risks using a novel linkage of genetic testing data to population-scale National Disease Registration Service and Hospital Episode Statistics electronic health records. We followed 25,811 females and 480 males diagnosed with BC and tested for germline BRCA1/BRCA2 PVs in NHS Clinical Genetics centers in England between 1995 and 2019 until SPC diagnosis, death, migration, contralateral breast/ovarian surgery plus 1 year, or the 31st of December 2020. We estimated standardized incidence ratios (SIRs) using English population incidences, hazard ratios (HRs) comparing carriers to noncarriers using Cox regression, and Kaplan-Meier 10-year cumulative risks. There were 1,840 BRCA1 and 1,750 BRCA2 female PV carriers. Compared with population incidences, BRCA1 carriers had elevated contralateral BC (CBC; SIR, 15.6 [95% CI, 11.8 to 20.2]), ovarian (SIR, 44.0 [95% CI, 31.4 to 59.9]), combined nonbreast/ovarian (SIR, 2.18 [95% CI, 1.59 to 2.92]), colorectal (SIR, 4.80 [95% CI, 2.62 to 8.05]), and endometrial (SIR, 2.92 [95% CI, 1.07 to 6.35]) SPC risks. BRCA2 carriers had elevated CBC (SIR, 7.70 [95% CI, 5.45 to 10.6]), ovarian (SIR, 16.8 [95% CI, 10.3 to 26.0]), pancreatic (SIR, 5.42 [95% CI, 2.09 to 12.5]), and combined nonbreast/ovarian (SIR, 1.68 [95% CI, 1.24 to 2.23]) SPC risks. Compared with females without BRCA1/BRCA2 PVs on testing, BRCA1 carriers had elevated CBC (HR, 3.60 [95% CI, 2.65 to 4.90]), ovarian (HR, 33.0 [95% CI, 19.1 to 57.1]), combined nonbreast/ovarian (HR, 1.45 [95% CI, 1.05 to 2.01]), and colorectal (HR, 2.93 [95% CI, 1.53 to 5.62]) SPC risks. BRCA2 carriers had elevated CBC (HR, 2.40 [95% CI, 1.70 to 3.40]), ovarian (HR, 12.0 [95% CI, 6.70 to 21.5]), and pancreatic (HR, 3.56 [95% CI, 1.34 to 9.48]) SPC risks. Ten-year cumulative CBC, ovarian, and combined nonbreast/ovarian cancer risks were 16%/6.3%/7.8% (BRCA1 carriers), 12%/3.0%/6.2% (BRCA2 carriers), and 3.6%/0.4%/4.9% (noncarriers). Male BRCA2 carriers had higher CBC (HR, 13.1 [95% CI, 1.19 to 146]) and prostate (HR, 5.61 [95% CI, 1.96 to 16.0]) SPC risks than noncarriers. Survivors of BC carrying BRCA1 and BRCA2 PVs are at high SPC risk. They may benefit from enhanced surveillance and risk-reduction measures.

Performance of a Protein Language Model for Variant Annotation in Cardiac Disease.

Genetic testing is a cornerstone in the assessment of many cardiac diseases. However, variants are frequently classified as variants of unknown significance, limiting the utility of testing. Recently, the DeepMind group (Google) developed AlphaMissense, a unique artificial intelligence-based model, based on language model principles, for the prediction of missense variant pathogenicity. We aimed to report on the performance of AlphaMissense, accessed by VarCardio, an open web-based variant annotation engine, in a real-world cardiovascular genetics center. All genetic variants from an inherited arrhythmia program were examined using AlphaMissense via VarCard.io and compared with the ClinVar variant classification system, as well as another variant classification platform (Franklin by Genoox). The mutation reclassification rate and genotype-phenotype concordance were examined for all variants in the study. We included 266 patients with heritable cardiac diseases, harboring 339 missense variants. Of those, 230 (67.8%) were classified by ClinVar as either variants of unknown significance or nonclassified. Using VarCard.io, 198 variants of unknown significance (86.1%, 95% CI, 80.9-90.3) were reclassified to either likely pathogenic or likely benign. The reclassification rate was significantly higher for VarCard.io than for Franklin (86.1% versus 34.8%, P<0.001). Genotype-phenotype concordance was highly aligned using VarCard.io predictions, at 95.9% (95% CI, 92.8-97.9) concordance rate. For 109 variants classified as pathogenic, likely pathogenic, benign, or likely benign by ClinVar, concordance with VarCard.io was high (90.5%). AlphaMissense, accessed via VarCard.io, may be a highly efficient tool for cardiac genetic variant interpretation. The engine's notable performance in assessing variants that are classified as variants of unknown significance in ClinVar demonstrates its potential to enhance cardiac genetic testing.

Application of triplet-primer PCR technology for the genetic testing and prenatal diagnosis of patients with Myotonic dystrophy type 1

To explore the application of triplet-primer PCR (TP-PCR) for the genetic testing and prenatal diagnosis in patients with Myotonic dystrophy type 1 (DM1). A total of 60 individuals from 48 pedigrees undergoing genetic testing at the Genetic and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University from May 2018 to October 2022 were selected as the study subjects. TP-PCR combined with capillary electrophoresis was applied to determine the number of CTG repeats of the DMPK gene, and prenatal testing was provided to four DM1 pedigrees. This study was approved by the First Affiliated Hospital of Zhengzhou University (Ethics No. KS-2018-KY-36). A total of 52 DM1 patients were detected, mostly with muscle weakness, muscular atrophy and myotonia as the initial symptoms, along with typical myotonic potentials. Some patients also had abnormalities of other systems. The number of abnormal CTG repeats of the DMPK gene was > 50, whilst the number of CTG repeats on the normal allele had ranged from 5 to 18. The number of the most common normal CAG repeats was 6 (30.77%, 16/52). Among the four DM1 pedigrees undergoing prenatal diagnosis, one fetus was healthy, whilst three fetuses were found to have abnormal CTG repeats (> 50 times) and diagnosed with DM1. TP-PCR can diagnose DM1 patients with speed and accuracy. However, this method cannot accurately determine the number of CTG repeats when it exceeds 50.

A comparison of 2D and 3D with the use of HDlive mode imaging in the diagnosis of endometrial polyps in infertility

Objective: to compare 2D ultrasound and 3D with HDlive mode ultrasound in the diagnosis of endometrial polyps in infertility.Material and methods. The retrospective cohort study included 116 women aged 29 to 43 years (mean age 36.9 ± 3.78) with infertility who were observed at the Nova Clinic Center for Reproduction and Genetics from January 2021 to June 2024. 2D and 3D ultrasounds were performed in all patients. The final conclusion on the presence or absence of pathology was based on the results of the 3D study with HDlive mode. The histological verification of polyps was carried out after hysteroscopy.Results. Hysteroscopy revealed no signs of pathology in 5 (4.3%) patients; moreover, the results of 2D imaging were also negative, and the results of 3D imaging were positive. In other 111 cases (95.7%), the diagnosis of a polyp was confirmed on hysteroscopy. Among them, no signs of pathology were found on 2D ultrasound in 19 (16.4%) patients. According to the obtained results, the use of 3D imaging with HDlive mode leads to overdiagnosis and false positive results with a chance of 4.5%. On the contrary, 2D imaging leads to underdiagnosis and false negative results with a chance of 19.6%, which is statistically significantly higher than the chance of a false positive result using the 3D method (p = 0.008). Thus, the chance of a false result using the 2D mode is 4.4 [1.57; 12.09] times higher than using the 3D mode.Conclusions. The study demonstrated a higher accuracy of the 3D ultrasound compared to 2D ultrasound in diagnosing endometrial polyps.

Therapeutic Effect of Nano-Extract of Nigella Sativa Seeds on The Histological Structure of The Testis In Male Albino Rats Induced With Anemia

Background: The study explores the effect of nanoparticles derived from the aqueous extract of Nigella sativa seeds on the histological structure of the testis in male albino rats with tartrazine-induced anemia. Nanoparticles, ranging in size from 1 to 100 nanometers, possess unique physical and chemical properties that enhance their ability to interact and deliver drugs. Objective: This study focuses on the therapeutic potential of Nigella sativa seed extract nanoparticles in treating testicular histological changes in anemic rats. The testicle is an oval organ involved in sperm formation and hormone production. It contains seminiferous tubules, Sertoli cells, and Leydig cells, which are responsible for sperm production and testosterone synthesis. Methods: The study included 36 male albino mice, aged between 8-12 weeks, and weighing 240-260 grams, from the Iraqi Center for Cancer Research and Medical Genetics. The animals were divided into six groups, each group having six animals. Results: The study showed that tartrazine at a concentration of 20 mg/kg: with Nigella sativa nanoparticles 50 mg/kg: an increase in weight. the body. While tartrazine at a concentration of 20 mg/kg with N.sativa nanoparticles at 75 mg/kg did not show significant differences compared with the control group. The results showed the Nigella sativa seed nanoparticles at a concentration of (50 mg/kg, 75 mg/kg): showed an increase in body weight, while tartrazine at a concentration of 20 mg/kg: a decrease in body weight, and no significant changes were observed in testicle weight in all treatments compared with the control group. Non-significant changes in testicle weight compare with Control group. The study showed that treatment with tartrazine 20 mg/kg showed noticeable histological changes in the histological structure of the testicle. Tartrazine with N.sativa nanoparticles (50 mg/kg, 75 mg/kg): No histological changes, indicating attenuation of tartrazine-induced damage. N.sativa nanoparticles (50 mg/kg, 75 mg/kg): demonstrated normal composition of testicular tissue, indicating no harmful effects on testicular tissue. has protective effects. Conclusion:The study aimed to investigate the potential of using nanoparticles extracted from Nigella sativa seeds to protect against damage caused by tartrazine in male albino rats.with significant therapeutic implications for the use of natural antioxidants in biomedical applications.

Evaluation of the protective dose-dependent effect of metformin for induced osteoarthritis in rats.

To evaluate the potential protective effect of metformin against osteoarthritis development in rats. The experimental study was conducted at the Iraqi Centre for Cancer Research and Medical Genetics, Mustansiriyah University, Baghdad, Iraq, from December 2021 to February 2022, and comprised male Sprague- Dawley mice who were divided into 5 equal groups: negative control group, osteoarthritis group subjected to monoiodoacetate induction, positive control group treated with celecoxib 30mg/kg, metformin 100mg/kg group, and metformin 200mg/kg group. Body mass index, inflammatory biomarkers, and serum C-terminal cross-linked telopeptide of type II collagen levels were noted for all the animals. Data was analysed using SPSS 24. Of the 35 mice, 7(20%) were in each of the 5 groups. Compared to the osteoarthritis group, metformintreated mice showed significantly reduced body mass index, inflammatory biomarker levels, and blood levels of Cterminal cross-linked telopeptide of type II collagen (p=0.05). Metformin 200mg/kg treatment had more beneficial effects than 100mg/kg dose on inflammatory biomarkers and serum C-terminal cross-linked telopeptide of type II collagen (p=0.05). A beneficial protective effect against the onset of osteoarthritis was produced by metformin in a dosedependent way. Additionally, metformin could lessen cartilage damage as demonstrated by a decrease in the serum levels of C-terminal cross-linked telopeptide of type II collagen in the osteoarthritis group.

Genetic analysis of a Chinese pedigree affected with Branchio-oculo-facial syndrome and a literature review

To explore the genetic etiology of a Chinese pedigree affected with Branchio-oculo-facial syndrome (BOFS) and summarize the prenatal phenotype of BOFS patients. A pedigree with BOFS which had presented at the Genetics and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University in December 2021 was selected as the study subject. Clinical data of the pedigree was collected. The fetus was subjected to routine prenatal ultrasound scan. Trio-whole exome sequencing (trio-WES) was carried out for the fetus and its parents, and candidate variant was verified by Sanger sequencing. Relevant literature was searched from the database to summarize the prenatal phenotype of BOFS patients. Ultrasound exam suggested the fetus had cleft lip and palate. Its father had presented with high palatal arch, prematurely grayed hair, occult cleft lip, congenital preauricular fistula, red-green color blindness and unilateral renal agenesis. Its grandfather also had high palatal arch, prematurely gray hair, protruding ears, congenital preauricular fistula and hearing disorders. Trio-WES revealed that the fetus and its father had both harbored a heterozygous c.890-1G>A variant of the TFAP2A gene. The same variant was not found in its mother. Sanger sequencing confirmed that its grandfather had also harbored the same variant. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG), the variant was rated as likely pathogenic (PVS1+PM2_Supporting). Combined with 36 similar cases retrieved from the literature, the prenatal phenotypes of BOFS patients had included growth restriction (25/37), renal abnormalities (10/37), cleft lip and palate (5/37) and oligohydramnios (5/37). The c.890-1G>A variant of the TFAP2A gene probably underlay the pathogenesis of BOFS in this pedigree. Discovery of the novel variant has enriched the mutational spectrum of the TFAP2A gene. The common prenatal phenotypes of BOFS have included growth restriction, renal abnormalities, cleft lip and palate and oligohydramnios. Delineation of the intrauterine phenotype of BOFS may facilitate its prenatal diagnosis, clinical diagnosis, treatment and genetic counseling.

Phenotypic Heterogeneity of Patients With Marfan Syndrome in Puerto Rico: A Case Series.

Previous studies have reported on the cardiovascular, ocular, and musculoskeletal findings in patients with Marfan syndrome (MFS). This study aims to report the ocular and genotypic findings in patients with the syndrome in Puerto Rico. A chart review of a cohort of patients with the syndrome from Puerto Rico was done. Patients were examined by at least one of the authors (NJI). Fibrillin-1 (FBN1) full gene sequencing was done to all patients (Laboratory for Molecular Medicine, Center for Genetics and Genomics, Cambridge, MA). This study was approved by the Institutional Review Board of the Universidad Central del Caribe (approval number: 2024-07). Results: Six patients aged 28-79 years were examined. There were seven female and three male patients. The average visual acuity was 0.49 and 0.52 in the right eye (OD) and left eye (OS), respectively. The average refraction (spherical equivalent) was -1.28 sph OD and -1.07 sph OS. The average intraocular pressure was 14 mmHg in both eyes (OU). A patient had a dislocated lens OD; a patient had lens dislocation OU; and a patient had prosthesis OD and aphakia OS. Upon optical coherence tomography (OCT), the retinal nerve fiber layer (RNFL) average was 75.86 µm OD and 81.85 ​​µm OS; the average cup-to-disc (C/D) ratio was 0.41 and 0.35 in the right and left eye, respectively. Upon visual field testing, the average mean deviation (MD) was -6.27 dB OD and -8.55 dB OS. Our findings underscore the significant phenotypic and genotypic heterogeneity of patients with MFS in Puerto Rico. The identification of several mutations in the FBN1 gene in the Puerto Rican population demonstrates the need for an up-to-date approach to diagnose and co-manage patients with the syndrome. This study contributes to a deeper understanding of the genetic heritage of patients with the syndrome and highlights the potential for personalized therapeutic interventions.

Major Causes of Conflicting Interpretations of Variant Pathogenicity in Rare Disease: A Systematic Analysis.

The identification of the genetic causes of inherited disorders from next-generation sequencing (NGS) data remains a complicated process, in particular due to challenges in interpretation of the vast amount of generated data and hundreds of candidate variants identified. Inconsistencies in variant classification, where genetic centers classify the same variant differently, can hinder accurate diagnoses for rare diseases. Publicly available databases that collect data on human genetic variations and their association with diseases provide ample opportunities to discover conflicts in variant interpretation worldwide. In this study, we explored patterns of variant classification discrepancies using data from ClinVar, a public archive of variant interpretations. We found that 5.7% of variants have conflicting interpretations (COIs) reported, and the vast majority of interpretation conflicts arise for variants of uncertain significance (VUS). As many as 78% of clinically relevant genes harbor variants with COIs, and genes with high COI rates tended to have more exons and longer transcripts, with a greater proportion of genes linked to several distinct conditions. The enrichment analysis of COI-enriched genes revealed that the products of these genes are involved in cardiac disorders, muscle development, and function. To improve diagnoses, we believe that specific variant interpretation rules could be developed for such genes. Additionally, our findings underscore the need for the publication of variant pathogenicity evidence and the importance of considering every variant as VUS unless proven otherwise.

Burden of rare genetic disorders in India: twenty-two years’ experience of a tertiary centre

BackgroundRare disorders comprise of ~ 7500 different conditions affecting multiple systems. Diagnosis of rare diseases is complex due to dearth of specialized medical professionals, testing labs and limited therapeutic options. There is scarcity of data on the prevalence of rare diseases in different populations. India being home to a large population comprising of 4600 population groups, of which several thousand are endogamous, is likely to have a high burden of rare diseases. The present study provides a retrospective overview of a cohort of patients with rare genetic diseases identified at a tertiary genetic test centre in India.ResultsOverall, 3294 patients with 305 rare diseases were identified in the present study cohort. These were categorized into 14 disease groups based on the major organ/ organ system affected. Highest number of rare diseases (D = 149/305, 48.9%) were identified in the neuromuscular and neurodevelopmental (NMND) group followed by inborn errors of metabolism (IEM) (D = 47/305; 15.4%). Majority patients in the present cohort (N = 1992, 61%) were diagnosed under IEM group, of which Gaucher disease constituted maximum cases (N = 224, 11.2%). Under the NMND group, Duchenne muscular dystrophy (N = 291/885, 32.9%), trinucleotide repeat expansion disorders (N = 242/885; 27.3%) and spinal muscular atrophy (N = 141/885, 15.9%) were the most common. Majority cases of β-thalassemia (N = 120/149, 80.5%) and cystic fibrosis (N = 74/75, 98.7%) under the haematological and pulmonary groups were observed, respectively. Founder variants were identified for Tay-Sachs disease and mucopolysaccharidosis IVA diseases. Recurrent variants for Gaucher disease (GBA:c.1448T > C), β-thalassemia (HBB:c.92.+5G > C), non-syndromic hearing loss (GJB2:c.71G > A), albinism (TYR:c.832 C > T), congenital adrenal hyperplasia (CYP21A2:c.29–13 C > G) and progressive pseudo rheumatoid dysplasia (CCN6:c.298T > A) were observed in the present study.ConclusionThe present retrospective study of rare disease patients diagnosed at a tertiary genetic test centre provides first insight into the distribution of rare genetic diseases across the country. This information will likely aid in drafting future health policies, including newborn screening programs, development of target specific panel for affordable diagnosis of rare diseases and eventually build a platform for devising novel treatment strategies for rare diseases.