Molecular Genetic Testing Research Articles

Isolation, identification and antifungal susceptibility of Candida species in postmenopausal women

Abstract— The term "vulvovaginal candidiasis" refers to an inflammatory, non-erosive Vulvovaginitis characterized by symptoms such as itching, pain, dyspareunia, and discharge. The condition is treated with antifungal medication if a positive culture from a low vaginal swab reveals Candida. It should be mentioned that these people had ongoing medical conditions. VVC had previously been classified as acute or recurring. It appears that estrogen is a key permissive factor in VVC. Clinical findings have demonstrated that VVC is uncommon in premenopausal and postmenopausal women and that the post-menopausal vagina rarely contains isolated Candida. The study aimed to know the relationship between Vulvovaginitis and candida in postmenopausal women and effectiveness of some antifungals. A total of 100 postmenopausal women With Vulvovaginitis, aged 45 to 69, had vaginal swabs taken from them. Upon arrival at the laboratory, all samples were cultured on Sabouraud dextrose agar . The species of the isolated yeasts were identified by a variety of methods, including molecular analysis with primers ITS1–ITS4, growth on Chrom agar medium, and biochemical analyses. Result: candida in postmenopausal women is less than in per menopausal due to effectiveness of estrogen hormone in reproductive age . The outcomes On Chrom agar showed, six species of candida—C. albicans, C. glabrata, C. tropicalis, C. parapsilosis, C. krusei, and c. rugosa—were isolated. Among the other species, C. glabrata was discovered to be the most prevalent. The findings demonstrated that four species of yeast-like fungi were identified using molecular diagnosis and genetic testing as follows:

Prospects for the application of radiomics to brain tumors

Radiomics is a new branch in diagnostics based on a quantitative approach to medical imaging able to ensure more efficient use of medical equipment, optimize imaging time per patient, and increase the accuracy of differential diagnostics in various areas of medicine. Radiogenomics is a branch of radionics intended to establish a connection between the patient’s genotype and phenotypic presentation obtained from medical imaging. The review dwells on general issues for radiomics and radiogenomics in oncology with the recent study findings, focusing on the role of these methods in neurooncology and solving problems in diagnosing brain tumors. One of the current topics in neurooncology is disease prognosis in patients with unverified midline gliomas because morphological confirmation of the diagnosis and molecular genetic testing of tissues is impossible. Besides, the high spatial and temporal heterogeneity of malignant neoplasms prevents a complete assessment of the biological properties of the tumor and even using stereotactic biopsy methods. Radiomics methods can help doctors differentiate the tumor grade, acting as a “virtual biopsy” while avoiding invasive procedures. The study findings on radiomics and radiogenomics in neurooncology indicate the undeniable promise of these methods; however, as in other areas of medicine and biology, errors cannot be completely excluded, so the expert team must aim to minimize them.

A therapeutic approach to pantothenate kinase associated neurodegeneration: a pilot study

BackgroundNeurodegeneration with brain iron accumulation (NBIA) is a group of genetic neurological disorders frequently associated with iron accumulation in the basal nuclei of the brain characterized by progressive spasticity, dystonia, muscle rigidity, neuropsychiatric symptoms, and retinal degeneration or optic nerve atrophy. Pantothenate kinase-associated neurodegeneration (PKAN) is one of the most widespread NBIA disorders. The diagnosis of PKAN is established with clinical features and the “eye of the tiger” sign identified on brain MRI and the identification of biallelic pantothenate kinase 2 (PANK2) pathogenic variants on molecular genetic testing. PANK2 catalyzes the first reaction of coenzyme A (CoA) biosynthesis, thus, altered PANK2 activity is expected to induce CoA deficiency as well as low levels of essential metabolic intermediates such as 4′-phosphopantetheine which is a necessary cofactor for critical proteins involved in cytosolic and mitochondrial pathways such as fatty acid biosynthesis, mitochondrial respiratory complex I assembly and lysine and tetrahydrofolate metabolism, among other metabolic processes.MethodsIn this manuscript, we examined the effect of a multitarget complex supplements (pantothenate, pantethine, omega-3 and vitamin E) on in vitro patient-derived cellular models and the clinical outcome of the adjuvant supplements in combination with the baseline neurological medication in three PKAN patients.ResultsMultitarget complex supplements significantly reduced iron accumulation and increased PANK2 and ACP expression levels in the cellular models derived from all three PKAN patients. In addition, the adjunct treatment to the standard neurological medication improved or stabilized the clinical symptoms of patients.ConclusionsOur results suggest that multitarget complex supplements can be clinically useful as augmentation therapy for PKAN patients harboring pathogenic variants with residual enzyme levels.Trial registration: CAAE: 58219522.6.0000.5330. Registered 25 May 2022—Retrospectively registered, https://plataformabrasil.saude.gov.br/visao/pesquisador/gerirPesquisa/gerirPesquisaAgrupador.jsf.

Two coacting shadow enhancers regulate twin of eyeless expression during early Drosophila development.

The Drosophila PAX6 homolog twin of eyeless (toy) sits at the pinnacle of the genetic pathway controlling eye development, the retinal determination network. Expression of toy in the embryo is first detectable at cellular blastoderm stage 5 in an anterior-dorsal band in the presumptive procephalic neuroectoderm, which gives rise to the primordia of the visual system and brain. Although several maternal and gap transcription factors that generate positional information in the embryo have been implicated in controlling toy, the regulation of toy expression in the early embryo is currently not well characterized. In this study, we adopt an integrated experimental approach utilizing bioinformatics, molecular genetic testing of putative enhancers in transgenic reporter gene assays and quantitative analysis of expression patterns in the early embryo, to identify 2 novel coacting enhancers at the toy gene. In addition, we apply mathematical modeling to dissect the regulatory landscape for toy. We demonstrate that relatively simple thermodynamic-based models, incorporating only 5 TF binding sites, can accurately predict gene expression from the 2 coacting enhancers and that the HUNCHBACK TF plays a critical regulatory role through a dual-modality function as an activator and repressor. Our analysis also reveals that the molecular architecture of the 2 enhancers is very different, indicating that the underlying regulatory logic they employ is distinct.

Phenotype driven molecular genetic test recommendation for diagnosing pediatric rare disorders

Patients with rare diseases often experience prolonged diagnostic delays. Ordering appropriate genetic tests is crucial yet challenging, especially for general pediatricians without genetic expertise. Recent American College of Medical Genetics (ACMG) guidelines embrace early use of exome sequencing (ES) or genome sequencing (GS) for conditions like congenital anomalies or developmental delays while still recommend gene panels for patients exhibiting strong manifestations of a specific disease. Recognizing the difficulty in navigating these options, we developed a machine learning model trained on 1005 patient records from Columbia University Irving Medical Center to recommend appropriate genetic tests based on the phenotype information. The model achieved a remarkable performance with an AUROC of 0.823 and AUPRC of 0.918, aligning closely with decisions made by genetic specialists, and demonstrated strong generalizability (AUROC:0.77, AUPRC: 0.816) in an external cohort, indicating its potential value for general pediatricians to expedite rare disease diagnosis by enhancing genetic test ordering.

Possibilities of Predicting Methotrexate-associated Toxicity in Oncohematology Based on Molecular Genetic Testing Methods

The development of highly effective protocols for the treatment of acute lymphoblastic leukemia (ALL) and non-Hodgkin lymphomas (NHL) followed the path of escalation of doses of cytostatic agents and improvement of supportive care. Methotrexate (MTX), used in high doses (1000–5000 mg/m2), radically changed the results of treatment of ALL and NHL in children, increasing patient survival rates. The downside of the anti-tumor effect of MTX is its organ toxicity, and therefore the development of methods for predicting the development of toxic effects of MTX is an important scientific and practical task. In recent years, the genetic factors of the patient’s organism have been considered as one of the reasons for the individual variability of pharmacokinetic and pharmacodynamic parameters of MTX. Abnormal function of folate cycle enzymes, methotrexate transporter proteins, due to gene polymorphism, may affect the effectiveness and toxicity of the drug. This review summarizes and analyzes the known genetic polymorphisms involved in MTX metabolism. The possibilities of predicting toxicity, as well as the prospects for individualizing therapy, taking into account the results of pharmacogenetic testing, are presented.

The polygenic risk score in the breast cancer treatment

Breast cancer (BC) remains the most common cause of death in women worldwide, but advances in science have allowed earlier diagnosis and more comprehensive treatment. This review highlights the impact of extensive molecular genetic testing in assessing the risk of BC susceptibility, as well as possible responses to chemotherapy and radiotherapy. Studies in the literature show that several Single Nucleotide Polymorphisms (SNPs) of genes involved in molecular pathways may become predictors of the risk of developing BC. For example, SNPs in genes such as RAD51 and XRCC3 , already known to be linked with high BC susceptibility, were also correlated with a different response to radiotherapy and related adverse effects. In addition, the SNP ESR1 PvuII (rs2234693), on the ESR1 gene, has been associated with a poor prognosis in advanced BC, but can be a good predictor of the therapeutic effect of hormonal treatment. Therefore, SNPs can be considered as possible new biomarkers for BC risk and prognosis. In this view, it is important to evaluate Polygenic Risk Score, an essential component for accurate BC risk prediction, which may potentially improve screening and prevention strategies. Bioinformatics tools are available to calculate polygenic risk by assessing the presence of SNPs and patients’ family and personal history. This represents an important step forward in the era of personalized medicine for BC.

Genetic, Clinical, and Biochemical Characterization ofa Large Cohort of Palestinian Patients With Fanconi-Bickel Syndrome.

This study aims to investigate the clinical, biochemical, and genetic characteristics of Fanconi-Bickel syndrome (FBS) in a cohort of 20 individuals from Palestine and to identify novel pathogenic variants. A retrospective analysis was conducted on medical records from Al-Makassed Hospital's pediatric department spanning 2015 to 2023. Individuals diagnosed with FBS via molecular genetic testing were included in the study. Among the 20 genetically confirmed FBS patients, hepatomegaly was prevalent in 95%, whereas 70% exhibited both developmental delay and hypophosphatemic rickets, and 68.4% experienced growth retardation. Hypertriglyceridemia (HTG) was universal. Elevated liver enzymes and alkaline phosphatase were common, along with hypophosphatemia (95%) and urinary abnormalities. Genetic analysis revealed five distinct SLC2A2 pathogenic variants, including three previously unreported variants: p.Gln23Arg (c.68A > G), p.Thr353Arg (c.1058_1059delinsGG), and an exon 7 deletion. This study presents the largest single-center cohort of FBS patients, expanding our understanding of the disorder's phenotypic and genotypic spectrum. Despite FBS generally carrying a favorable prognosis, timely diagnosis remains crucial to prevent severe complications.

Phenotypic Resistance to Rifampicin of Mycobacterium tuberculosis with the rpoB Leu430Pro Mutation

The objective: to determine the role of the rpoB Leu430Pro mutation in the degree of phenotypic resistance of Mycobacterium tuberculosis to rifampicin.Subjects and Methods. The WHO classifies the rpoB Leu430Pro mutation of Mycobacterium tuberculosis as a borderline resistance mutation but of clinical significance. From an array of cultures, we selected and analyzed 14 isolates of M. tuberculosis with discrepancies in the results of molecular genetic and phenotypic testing, carrying only this mutation in rpoB. For all samples, the phenotypic resistance level (MIC) of these isolates to rifampicin was determined using BACTEC MGIT 960 and Middlebrook 7H11 medium.Results. It was found out that 12 of 14 isolates had the rifampicin MIC below the current critical concentration when tested by both methods, thus they were phenotypically sensitive. One isolate was resistant when tested with Middlebrook 7H11 but susceptible when tested with BACTEC MGIT 960. Only one isolate which had the additional rpoB F425L mutation demonstrated high-level phenotypic resistance when tested by the same tests. Our data indicate that the clinical significance of this mutation requires clarification since even a decrease in the critical concentration of rifampicin does not lead to unambiguous results of molecular genetic and phenotypic tests. It is necessary to standardize the use of various molecular genetic tests and principles of their clinical interpretation to optimize strategies for managing patients with tuberculosis caused by M. tuberculosis with the rpoB Leu430Pro mutation.

Hyperkalaemic acidosis: blood pressure is the diagnostic clue.

Pseudohypoaldosteronism type 2 (PHA2) is a rare inherited condition of altered tubular salt handling. It is characterized by the specific constellation of hyperkalaemic hyporeninemic hypertension, hyperchloremic metabolic acidosis and hypercalciuria. Molecular genetic testing confirms the diagnosis in the majority of cases. Thiazides constitute effective treatment. Due to its rarity, the diagnosis is often delayed. We here present two children with PHA2, who were initially treated with fludrocortisone and bicarbonate complicated mainly by exacerbation of their hypertension. Discontinuation of their previous therapy and commencement of thiazide diuretics led to normalisation of their blood pressure and electrolyte and acid-base status.

Prenatal diagnosis of fetal skeletal anomalies via whole-exome sequencing in a tertiary referral center

The accurate prenatal diagnosis of skeletal anomaly (SKA) using prenatal imaging alone remains challenging. We aimed to investigate the efficacy of whole-exome sequencing (WES) in the prenatal molecular genetic diagnosis of skeletal system abnormalities, with or without additional ultrasound anomalies. All fetuses with SKA were subjected to sequential genetic tests, and after excluding fetal chromosomal abnormalities and clinically significant copy number variations (CNVs) consistent with the observed phenotype, the affected fetuses were further subjected to WES. The clinical features of fetal SKA were collected, and the results of molecular genetic testing and perinatal outcomes were analyzed. Following negative routine genetic test results of the 78 fetuses, trio-WES was conducted for 73 fetuses, and fetus-only WES (single WES) was performed for five fetuses due to parental refusal. Fetal skeletal system abnormalities in our cohort were subdivided into seven groups: 39 (50%) had short long bones, 14 (17.9%) had abnormal limb morphology, 4 (5.1%) had polydactyly, 4 (5.1%) had the absence of the radius tibia or tibiofibula, 5 (6.4%) had spine anomalies, 6 (7.7%) had strephenopodia, and 6 (7.7%) had multiple deformities. In total, we identified the molecular diagnoses for 32/78 fetuses with SKAs, and confirmed 41 pathogenic/likely pathogenic variants in 28 genes, including nine novel variants in our cohort. The overall diagnostic rate was 41% (32/78). Our findings demonstrate that WES can greatly improve the genetic diagnostic rate of fetal SKAs following routine genetic testing, which can comprehensively guide perinatal management and help assess the risk of recurrence in future pregnancies. Our data also provide a basis for the association between the SKA phenotype and related genotypes and expand the spectrum of fetal SKA phenotypes and related genes.

Modification of the hi-c technology for molecular genetic analysis of formalin-fixed paraffin-embedded sections of tumor tissues

Molecular genetic analysis of tumor tissues is the most important step towards understanding the mechanisms of cancer development, and it is also necessary for the choice of targeted therapy. Hi-C (high-throughput chromatin conformation capture) technology can be used to detect various types of genomic variants, including balanced chromosomal rearrangements: inversions and translocations. In this work, we propose a modification of the Hi-C method for the analysis of chromatin contacts in formalin-fixed paraffin-embedded (FFPE) sections of tumor tissues. Our results demonstrate that this protocol allow to generate high-quality Hi-C data and detect all types of chromosomal rearrangements. We have analyzed various databases to compile a comprehensive list of translocations that hold clinical importance for targeted therapy selection. The practical value of molecular genetic testing is its ability to influence patient treatment strategies and provide prognostic insights. Detecting specific chromosomal rearrangements can guide the choice of targeted therapies, which is a critical aspect of personalized medicine in oncology.

Genetic diagnosis in XY disorders of sex development

XY disorders of sex development (XY DSD) comprise a class of heterogeneous genetic entities that result in discrepancies between chromosomal, gonadal, and phenotypic sex due to a reduction in androgen synthesis or action. The chief categories of disorders include gonadal dysgenesis, disorders with reduced androgen production (biosynthetic defect – either alone or in conjunction with impaired glucocorticoid and/or mineralocorticoid synthesis), and insensitivity to androgen action. While conventional diagnostic modalities, encompassing karyotyping, biochemistry, radiology, and, in a few cases, diagnostic laparoscopy, help in formulating a provisional diagnosis, molecular genetic testing is key to arriving at a precise etiology. Besides ending the diagnostic uncertainty, a molecular diagnosis helps to predict the natural course in terms of pubertal development and potential for fertility, thus contributing to decisions on the gender of rearing; and guides on surveillance for extragenital features and the risk of recurrence in subsequent pregnancies. This paper broadly discusses the genetic basis of XY DSD, different modalities of genetic testing, and their utility and limitations.

Fanconi Anemia: Challenges in Diagnosis and Management-A Case Series Report.

Fanconi anemia (FA) is a rare inherited disorder characterized by congenital abnormalities, progressive bone marrow failure, and a predisposition to malignancies. Detecting FA can be challenging, as it involves identifying increased chromosomal sensitivity to DNA cross-linking agents and detecting causative genetic variants via genome sequencing. We report two cases of siblings with FA, both confirmed to have the FANCD2 variant through whole-exome sequencing (WES). The first patient presented with epistaxis, petechiae, ecchymosis, and lower limb edema. The second patient exhibited epistaxis, diabetes, developmental delay, and physical abnormalities. Interestingly, both patients had negative results on the initial chromosomal breakage test with mitomycin C, a commonly used diagnostic tool for FA. However, further investigation with WES revealed the presence of the FANCD2 variant, confirming the FA diagnosis. This case report highlights the challenges in diagnosing FA, particularly when initial screening tests yield negative results. Molecular genetic testing, such as WES, can provide a definitive diagnosis and guide appropriate management strategies. Early and accurate diagnosis is crucial for improving outcomes in individuals with this potentially fatal illness, as promising advancements in treatments such as hematopoietic stem cell transplantation and gene therapy offer hope for addressing FA.

High-sensitivity label-free electrochemical genosensors for carbon nanotube plasmon-assisted detection of somatic mutations in nucleic acids from formalin-fixed paraffin-embedded tissues

Currently, molecular genetic testing of somatic point mutations in the genome of cancer tumors for targeted therapy requires high-performance tools for studies of spatial gene expression and spatial genome profiling in formalin-fixed paraffin-embedded (FFPE) tissue samples. We offer new high-performance label-free electrochemical impedimetric deoxyribonucleic-acid (DNA) nanosensors. The sensors based on a platform of crystalline carbon nanotube plasmonic assemblies are fabricated by the Langmuir–Blodgett deposition technique. The carbon-nanotube assemblies are suspended on nanoporous supports. Incorporation of fast Fourier transforms in the impedance spectroscopy led to the introduction of a new information parameter, the integral value of capacitance changes. The allele-sensitive assay based on plasmon-assisted effects in the assemblies of electrically active conjugates between DNA and few-walled carbon nanotubes has been used for discrimination of allele single-nucleotide polymorphisms (SNPs) of Kirsten Rat Sarcoma viral oncogene homologue (KRAS gene). Using 19- and 20-mer single-stranded (ss) probe oligonucleotides and 35- and 47-mer toehold probes, we explored the probe length and the target location. The genotyping technology allows discrimination of single-nucleotide variations in the target 35-base oligonucleotide at the attomolar concentration level. Human genomic DNAs were isolated from FFPE colorectal cancer tumor tissue samples. The KRAS-gene exon 2, codon 12, c.35G>A mutation has been successfully discriminated in the genomic DNAs with a significance level, P, of 0.001–0.02. The assay has a sensitivity with 0.33-ng/ml limit of detection (LOD) for native genomic DNA.

Atypical Milroy's disease with predominant unilateral involvement: a case report

Milroy's disease (MD), known as hereditary lymphedema type I, is a rare autosomal dominant primary lymphedema. It accounts for about twenty percent of all primary lymphedema. MD typically presents clinically with bilateral lower extremity lymphedema. Our case report describes a rare case of MD presenting with unilateral upper and lower extremity lymphedema in a patient admitted to our clinic. A 24-year-old woman who had been followed for lymphedema since the age of 8 was diagnosed with MD at our hospital by physical examination, venous Doppler ultrasound, whole-body lymphoscintigraphy, and molecular genetic testing. Partial improvement was observed with complete decongestive therapy, considered the gold standard treatment for lymphedema. Genetic counseling may be beneficial for the patient and family. Although MD is uncommon in the literature, many more studies are needed to identify carrier variants in the community.

Circumscribed choroidal hemangioma in Sturge-Weber syndrome

We report on a19-year-old patient with Sturge-Weber syndrome (SWS), accompanied by aNaevus flammeus, secondary glaucoma, and glaucomatous optic atrophy of the right eye. The painful and blind eye was enucleated. Histopathological analysis revealed acircumscribed choroidal hemangioma around the optic nerve and asmaller extrascleral hemangioma. Molecular genetic testing excluded GNA11, GNAQ, or GNAS mutations. Our work illuminates the clinical, histological, and molecular genetic aspects of this rare case, contributing to the differential diagnosis of ocular conditions in patients with SWS.

Clinical genome sequencing in patients with suspected rare genetic disease in Peru

There is limited access to molecular genetic testing in most low- and middle-income countries. The iHope program provides clinical genome sequencing (cGS) to underserved individuals with signs or symptoms of rare genetic diseases and limited or no access to molecular genetic testing. Here we describe the performance and impact of cGS in 247 patients from three clinics in Peru. Although most patients had at least one genetic test prior to cGS (70.9%), the most frequent was karyotyping (53.4%). The diagnostic yield of cGS was 54.3%, with candidate variants reported in an additional 22.3% of patients. Clinical GS results impacted clinician diagnostic evaluation in 85.0% and genetic counseling in 72.1% of cases. Changes in management were reported in 71.3%, inclusive of referrals (64.7%), therapeutics (26.3%), laboratory or physiological testing (25.5%), imaging (19%), and palliative care (17.4%), suggesting that increased availability of genomic testing in Peru would enable improved patient management.

Congenital enteropathies in children: An algorithm for differential diagnosis and therapeutic management. Case report

Infant diarrhea may be caused by infectious, allergic, or surgical diseases. A distinct group comprises congenital enteropathies, a heterogeneous group of genetically determined diseases, including defects in the absorption and transport of nutrients and electrolytes, impaired differentiation of enterocytes and enteroendocrine cells, and defects in the modulation of the intestinal immune response. The final diagnosis of enteropathies is based on the results of molecular genetic tests; however, a detailed assessment of clinical and medical history data and the results of laboratory and instrumental studies enables quick diagnostic search direction and choice of the correct therapeutic tactics. The article considers the algorithm for the differential diagnosis of congenital diarrhea, presents a clinical case of congenital osmotic diarrhea due to disaccharidase insufficiency, and considers the difficulties of the diagnostic search and approaches to diet therapy. The prospective of using a fructose-based formula, Galactomin-19, in the diet therapy of glucose-galactose malabsorption, is presented.

Expanding the Role of Molecular Genetic Expertise in Crime Detection and Investigation

Molecular genetic testing using DNA plays a crucial role in the field of justice. Beyond the analysis of genomic DNA sequences, advanced methods such as mitochondrial DNA analysis, epigenetic marker identification, and RNA profiling are being developed. A particularly promising approach is forensic phenotyping, which involves predicting human characteristics from DNA samples, including appearance, biogeographic origin, and age.