Genetic Center Research Articles

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.

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.

Estrogen Receptor-α rs9340799 Polymorphism Influences Bone Mineral Density in Women Over 60 Years of Age and Women Who are Postmenopausal for More than 10 Years

Background: Osteoporosis is a multifactorial disorder where genetic and environmental factors contribute to changes in bone mineral density. Several genetic polymorphisms are associated with low bone mineral density and osteoporosis risk, including estrogen receptor-α rs2234693 and rs9340799 single nucleotide polymorphisms. Objective: To determine the allele frequencies of these polymorphisms among postmenopausal Jordanian women and to assess their association with low bone mineral density and osteoporosis among studied subjects. Methods: This cross-sectional study enrolled 450 postmenopausal Jordanian women having dual-energy X-ray absorptiometry scans at the National Center for Diabetes, Endocrinology, and Genetics. The study protocol was approved by this center "Institutional Review Board." The estrogen receptor-α gene sequence containing rs2234693 and rs9340799 polymorphisms was identified by polymerase chain reaction, followed by restriction fragment length polymorphism. Results: The wild-type allele frequencies of rs2234693 (T) and rs9340799 (A) were 54% and 59%, respectively. The rs9340799 GG genotype was significantly associated with lower femoral neck T-scores in women who were postmenopausal for more than 10 years (p = 0.023) and was significantly associated with lower lumbar spine (p = 0.033) and femoral neck (p = 0.002) T-scores in women older than 60 years of age. However, there was no association between rs2234693, rs9340799, or their haplotypes with osteoporosis or bone mineral density T-score values. The two polymorphisms were in Heidy-Weinberg equilibrium and exhibited strong but incomplete linkage disequilibrium. Conclusion: The data suggest that rs9340799 polymorphism may render some women more susceptible to osteoporosis than others.

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.

In-Vitro Growth of Transgenic Sengon Resulting From Co-Cultivation Using Agrobacterium Tumefaciens Bacteria

Sengon (Paraserianthes falcataria (L) Nielsen) is a forestry plant often developed for industrial purposes in Indonesia. Sengon is a fast-growing species and has a relatively short-cutting period. Sengon wood is widely used in the production of carpentry wood, plywood raw materials, and pulp. The purpose of this study was to optimize the transformation of the entC and pmsB genes into sengon plants using the embryo injury method through Agrobacterium tumefaciens as an intermediary and to determine the efficiency of the transformation using the injury to sengon embryos. This research was conducted from September 2022 to March 2023. The research was conducted at the Genetically Modified Organism (GMO) Tissue Culture Laboratory, Recombinant Protein (Microbe) Laboratory, and Greenhouse of the Genetic Engineering Center, National Research and Innovation Agency (BRIN) Cibinong, Bogor, Java West. The research procedure consisted of several steps, namely Preparation of MS Media, Preparation of LB Media, Preparation of Sengon Seed Infection Using Agrobacterium tumefaciens, Sterilization and Planting of Sengon Seeds, Acclimatization, and Molecular Analysis (including Sengon DNA isolation, PCR Amplification, and Electrophoresis). Transformation efficiency was calculated by the positive strain of hpt PCR bands compared to the number of transformed embryos and multiplied by 100%. In the results of the PCR analysis, it was found that one plant sample carried the hpt marker, which indicates the integration of the entC and pmsB genes. which when analyzed using transformation efficiency calculations, the data obtained for the entire transformation stage was 0.8%, where the success of the transformation obtained was still classified as low. Factors that cause the low success of transformation include the method of transformation, the growth phase of bacteria, genetic material, and culture aseptic conditions.

Genetic associations and parent-of-origin effects of PVRL1 in non-syndromic cleft lip with or without cleft palate across multiple ethnic populations.

This study investigated the associations of PVRL1 gene variants with non-syndromic cleft lip with or without cleft palate (NSCL/P) by evaluating transmission distortion and parent-of-origin (POO) effects in multiple ethnic populations. We conducted allelic and genotypic transmission disequilibrium tests (TDT) on 10 single-nucleotide variants (SNVs) in PVRL1 using data from 142 Korean families with an affected child. POO effects were analyzed using the POO likelihood ratio test, comparing transmission rates of maternally and paternally inherited alleles. To assess generalizability and ethnic heterogeneity, we compared results from Korean families with data from the Center for Craniofacial and Dental Genetics, which included 2,226 individuals from 497 European and 245 Asian trios. TDT analysis identified significant over-transmission of the rs7940667 (G361V) C allele in Korean families (p=0.007), a finding replicated in both Asian (p=6.5×10-7) and European families (p=1.6×10-10). Eight SNVs showed strong TDT evidence in larger Asian and European datasets after multiple comparison corrections (p<0.0073). Of these, 4 SNVs (rs7940667, rs7103685, rs7129848, and rs4409845) showed particularly robust association (p<5×10-8). POO analysis revealed significant maternal over-transmission of the rs10790330-A allele in Korean families (p=0.044). This finding was replicated in European families (p=9.0×10-4). Additionally, 3 other SNVs, rs7129848 (p=0.001) and the linked SNVs rs3935406 and rs10892434 (p=0.025), exhibited maternal over-transmission in the validation datasets. Our findings provide robust evidence supporting the associations of PVRL1 variants with NSCL/P susceptibility. Further research is necessary to explore the potential clinical applications of these findings.

Inconsistencies between prenatal diagnostic and genetic testing laboratories on variant validation of rare monogenic diseases.

The advent of next-generation sequencing (NGS) has enhanced the diagnostic efficacy for monogenic diseases, while presenting challenges in achieving consistent diagnoses. We retrospectively analyzed the concordance rate and reasons for the inconsistency between the original diagnostic result from the genetic testing laboratory and the variant validation result from the prenatal diagnostic center. The validation procedure comprised three stages: validation of variant detection, reevaluation of variant classification, and assessment of recurrence risk, which involved verifying the mode of inheritance and parental carriage. In total, 17 (6%) of the 286 families affected by rare monogenic diseases showed different results during the variant validation procedure. These cases comprised four (23.5%) with variant detection errors, 12 (70.5%) with inconsistent interpretation, and one (6%) with non-Mendelian inheritance patterns. False-positive NGS results confirmed by Sanger sequencing were related to pseudogenes and GC-rich regions. The classification of the 17 variants was altered in the 12 cases owing to various factors. The case with an atypical inheritance pattern was originally considered autosomal recessiveinheritance, but was diagnosed as maternal uniparental disomy after additional genetic analysis. We underscored the significance of variant validation by prenatal diagnostic centers. Families affected by monogenic diseases with reproductive plans should be referred to prenatal genetic centers as early as possible to avoid different results that may postpone subsequent prenatal diagnosis.

Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks

In this paper, we aim to build a platform that will help bridge the gap between high-dimensional computation and wet-lab experimentation by allowing users to interrogate genomic signatures at multiple molecular levels and identify best next actionable steps for downstream decision making. We introduce Multioviz: a publicly accessible R package and web application platform to easily perform in silico hypothesis testing of generated gene regulatory networks. We demonstrate the utility of Multioviz by conducting an end-to-end analysis in a statistical genetics application focused on measuring the effect of in silico perturbations of complex trait architecture. By using a real dataset from the Wellcome Trust Centre for Human Genetics, we both recapitulate previous findings and propose hypotheses about the genes involved in the percentage of immune CD8+ cells found in heterogeneous stocks of mice. Source code for the MultiovizR package is available at https://github.com/lcrawlab/multio-viz and an interactive version of the platform is available at https://multioviz.ccv.brown.edu/.

Investigation of Targeted Genes and Identification of Novel Variants with Next Generation Sequencing Method in Hearing Loss.

Hearing loss is a widespread condition throughout the world. It may affect patients from newborns to the elderly. There are too many reasons for hearing loss, including congenital hearing loss, virus infections, age-related situations, and traumatic situations, which may be related to the immune-mediated system. Fifty percent of hearing loss is related to genetic mutations and defects; genetic causes are highly heterogeneous, so the analysis of new variants are important for diagnosis. We aimed to describe the importance of detected gene variations by using targeted gene panels in the Next-Generation-Sequencing (NGS) platform. Eighty-one hearing loss targeted genes were investigated using Illumina NextSeq550 technology in 100 participants with hearing loss between 2017 and 2022 in our Genetic Diseases Evaluation Center. Targeted genes were performed on 100 patients with hearing loss diagnosis. The total number of detected variants was 77. Forty-seven cases have likely pathogenic/pathogenic variants. Thirty of them have uncertain clinical significance variants, and from the detected variants, 8 are novel. In this research, we highlighted that earlier detection of hearing loss using molecular genetic methods may help us understand the etiology and orient for a better prognosis. Results detected by using the NGS platform can assist and improve the diagnosis. In this study, the diagnostic rate with targeted genes was detected as 35.29%. It has an important role in clinical practice as the recommendation of cochlear implants. Clarifying the genotype and phenotype correlation helps us figure out the etiology of hearing loss and also the worth of genetic counseling in hereditary hearing loss.

Genetic analysis of a fetus with Rhizomelic skeletal dysplasia

To explore the clinical features and genetic basis for a fetus featuring Rhizomelic skeletal dysplasia. A fetus diagnosed at the Reproductive and Genetic Center of Suzhou Municipal Hospital in November 2020 was selected as the study subject. Whole exome sequencing (WES) was carried out for the fetus and its parents. Candidate variants were verified by Sanger sequencing. Peripheral blood smears of both parents were also examined. The fetus was found to have a small chest and short limbs, which had suggested skeletal dysplasia. Genetic testing revealed that the fetus has harbored compound heterozygous variants of the LBR gene, including a paternally derived c.1687+1G>A and a maternally derived c.1757G>A (p.Arg586His). The blood smear of the father showed Pelger-Huet anomaly with hyposegmentation of neutrophil nuclei, while the neutrophils of the mother appeared to be normal. Based on the guidelines from the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP), the c.1757G>A (p.Arg586His) variant was classified as likely pathogenic (PM3_Strong+PM2_Supporting+PP3), and so was the c.1687+1G>A variant (PVS1-Moderate+PM3+PM2-Supporting+PP4). The compound heterozygous variants of the LBR gene probably underlay the pathogenesis of skeletal dysplasia in this fetus.

Research to classrooms: a co-designed curriculum brings All of Us data to secondary schools.

We describe new curriculum materials for engaging secondary school students in exploring the "big data" in the NIH All of Us Research Program's Public Data Browser and the co-design processes used to collaboratively develop the materials. We also describe the methods used to develop and validate assessment items for studying the efficacy of the materials for student learning as well as preliminary findings from these studies. Secondary-level biology teachers from across the United States participated in a 2.5-day Co-design Summer Institute. After learning about the All of Us Research Program and its Data Browser, they collaboratively developed learning objectives and initial ideas for learning experiences related to exploring the Data Browser and big data. The Genetic Science Learning Center team at the University of Utah further developed the educators' ideas. Additional teachers and their students participated in classroom pilot studies to validate a 22-item instrument that assesses students' knowledge. Educators completed surveys about the materials and their experiences. The "Exploring Big Data with the All of Us Data Browser" curriculum module includes 3 data exploration guides that engage students in using the Data Browser, 3 related multimedia pieces, and teacher support materials. Pilot testing showed substantial growth in students' understanding of key big data concepts and research applications. Our co-design process provides a model for educator engagement. The new curriculum module serves as a model for introducing secondary students to big data and precision medicine research by exploring diverse real-world datasets.