Advances In Molecular Diagnosis Research Articles

Overcoming genetic neuromuscular diagnostic pitfalls in a middle-income country.

Neuromuscular disorders affect almost 20 million people worldwide. Advances in molecular diagnosis have provided valuable insights into neuromuscular disorders, allowing for improved standards of care and targeted therapeutic approaches. Despite this progress, access to genomic diagnosis remains scarce and inconsistent in middle-income countries such as Brazil. The lack of public health policies to enable feasible genetic diagnosis and the shortage of neuromuscular disorders specialists are the main reasons in this process. We report our experience in a transcontinental genomic consortium for neuromuscular disorders highlighting how collaborative efforts have helped overcome various obstacles in diagnosing our patients. We describe several challenging cases categorized into three major themes, underlining significant gaps in genetic diagnosis: (i) reverse phenotyping and variant validation, (ii) deep phenotyping and identifying a bespoke molecular approach, and (iii) exploring the use of genomic tests beyond whole exome sequencing. We applied a qualitative case-based approach to exemplify common pitfalls in genomic diagnosis in a middle-income country. Our experience has shown that establishing a virtual transcontinental partnership is viable, offering effective exchange of scientific experiences, providing both guidance for rational decision-making and specialized training on a local level and access to diverse molecular diagnosis strategies and functional analyses. Collaborative efforts such as these have the potential to overcome local obstacles, strengthen scientific capabilities, foster diverse multi-ethnic cohorts, and ultimately provide improved care for patients.

Feline respiratory disease complex: insights into the role of viral and bacterial co-infections.

Feline respiratory disease complex (FRDC) is a highly prevalent syndrome in cats that often result in fatal outcomes. FRDC etiology is complex, and often, multiple viral and bacterial pathogens are simultaneously associated with disease causation. There is limited information about the role of co-infections in pathogenesis and the current prevalence of pathogens in North America. We aimed to conduct a study using technical advances in molecular diagnosis and statistical modeling analysis to elucidate the occurrence of pathogens and how co-infections affect disease severity. We attained information from three diagnostic laboratories in North America regarding the occurrence of Bordetella bronchiseptica, Chlamydia felis, Mycoplasma, Felid alphaherpesvirus 1 (FeHV-1), feline calicivirus (FCV), and influenza A, along with age, seasonality, sex, and clinical signs. We also evaluated the role of co-infections in disease severity. These pathogens were also investigated in clinically normal cats (control). The most detected pathogens were Mycoplasma, FCV, and FeHV-1. Most pathogens were detected in the control group, highlighting the challenge of interpreting positive testing results. Co-infections of Mycoplasma and FCV, as well as Mycoplasma and FeHV-1, were important predictors of disease severity. Age, sex, and season had a minor impact on pathogen occurrence. This study provides new insights into FRDC and underlines the relevance of diagnostic panels to screen for a range of pathogens, providing knowledge for timely diagnosis and therapeutic interventions.

The Recent Advances in Molecular Diagnosis of Soft Tissue Tumors

Soft tissue tumors are rare mesenchymal tumors with divergent differentiation. The diagnosis of soft tissue tumors is challenging for pathologists owing to the diversity of tumor types and histological overlap among the tumor entities. Present-day understanding of the molecular pathogenesis of soft tissue tumors has rapidly increased with the development of molecular genetic techniques (e.g., next-generation sequencing). Additionally, immunohistochemical markers that serve as surrogate markers for recurrent translocations in soft tissue tumors have been developed. This review aims to provide an update on recently described molecular findings and relevant novel immunohistochemical markers in selected soft tissue tumors.

Changing trends in the diagnosis of genitourinary tuberculosis in post Covid-19 pandemic era

efforts to achieve a TB-free world by 2030. The health professionals and the health care support team suffered a major setback in reaching out to the patients due to various restrictions imposed on them during this pandemic period. Patients found it difficult to reach out to the health care team, owing largely to the fear factor and also due to inaccessibility to health care services. The delay in TB notifications, emergence of drug resistant strains and restrictions in the supply- chain added further to the difficulties faced. India is a nation with one of the largest numbers of TB victims. The strategic measures taken by the Government of India (GOI) took a sudden jolt with the onset of the COVID-19 pandemic. The TB elimination measures reverted back to TB containment measures. Various African countries including Ethiopia recorded a massive fall out of more than 75% during the various lockdown measures imposed. However, India took collateral measures to combat this setback. Its National Tuberculosis Elimination Programme (NTEP) involved private players to combat TB epidemic, recruited Patient provider support agencies and actively engaged Private Sectors through innovative patient provider incentives to bring down numbers of the TB victims. The diagnostic methods that took about 4 to 6 weeks to confirm the diagnosis of TB had earlier put the diagnosis and management of TB to the back seat. However, recent innovations in the molecular biology, immunology and genomic sequencing techniques have greatly aided an earlier and accurate diagnosis of tuberculosis. One individual, one health agency or one Government cannot achieve the goal TB elimination by 2030. A global effort is the basic pre-requisite, incorporating advanced molecular diagnosis and appropriate treatment would ensure achieving a TB free world by 2030.

Viral metagenomics analysis of stool specimens from children with unresolved gastroenteritis in Qatar.

Acute gastroenteritis (AGE) is associated with significant global morbidity and mortality, especially among children under five years of age. Viruses are well established as etiologic agents of gastroenteritis since they are the most common pathogens that contribute to the disease burden in developing countries. Despite the advances in molecular diagnosis, a substantial proportion of AGE etiology remain unresolved. We implemented a viral metagenomics pipeline to determine the potential viral etiology associated with AGE among children under the age of five years in Qatar with undiagnosed etiology. Following enriching for the viral genome, ∼1.3 billion sequences were generated from 89 stool specimens using the Illumina HiSeq platform, of which 7% were mapped to viral genomes. Human viruses were detected in 34 specimens (38.2%); 14 were adenovirus, nine coxsackievirus A16, five rotavirus (G9P[8] and G4P[8]), four norovirus (GII), one influenza A virus (H3), and one respiratory syncytial virus A (RSVA). In conclusion, the viral metagenomics approach is useful for determining AGE's etiology when routine molecular diagnostic assays fail.

Recent Advances in Molecular Diagnosis of Pulmonary Fibrosis for Precision Medicine.

Pulmonary fibrosis is a serious, progressive lung disease characterized by scarring and stiffening lung tissues, affecting the respiratory system and leading to organ failure. It is a complex disease consisting of alveolar damage, chronic inflammation, and a varying degree of lung fibrosis. Significant challenges with pulmonary fibrosis include the lack of effective means to diagnose the disease at early stages, identify patients at higher risks of progress, and assess disease progression and treatment response. Precision medicine powered by accurate molecular profiling and phenotyping could significantly improve our understanding of the disease's heterogeneity, potential biomarkers for diagnosis and prognosis, and molecular targets for treatment development. This Review discusses various translational model systems, including organoids and lung-on-a-chip systems, biomarkers in single cells and extracellular vesicles, and functional pharmacodynamic markers. We also highlight emerging sensing technologies for molecular characterization of pulmonary fibrosis and biomarker detection.

HGG-50. Specific sensitivity of pediatric high-grade glioma with ATRX inactivation to PARP inhibitor combinations

Pediatric high-grade gliomas (pHGG) account for approximately 12% of pediatric brain tumors. Despite advances in molecular diagnosis and identification of discrete molecular subtypes, pHGG are the leading cause of cancer-related death in children. Thus, current research focuses on identifying novel therapeutic targets. Sequencing analyses across pediatric cancer types identified DNA repair perturbations as potentially targetable events in certain types of pediatric brain tumors. Herein, we investigated the potential of PARP inhibitors (PARPi), impeding the central role of PARP in DNA damage repair, in pHGG. We screened a patient-derived primary pHGG cell line panel (n=7) for their sensitivity towards 6 different PARPi (niraparib, olaparib, pamiparib, rucaparib, talazoparib, veliparib) using cell viability assays. Basal expression of DNA repair related proteins was assessed by immunoblot, and propidium iodide-based flow cytometry was used for cell cycle analysis. All pHGG were resistant towards single compound PARP inhibition. Interestingly, two H3F3A-G34R mutant pHGG models harboring inactivating ATRX mutations were characterized by elevated basal levels of pH2AX, suggesting increased stress resulting from DNA damage. Consequently, simultaneous targeting of PARP and other components of DNA repair in the respective models showed strong synergistic effects on cell viability, which was not observed to a comparable extent in other models such as BRAFV600E/TERT promotor mutant pHGG. Combination of talazoparib and irinotecan resulted in S-phase arrest. Within a precision oncology approach, we treated a 11-year-old child suffering from H3F3A-G34R mutant pHGG with ATRX mutation, that progressed during radiation, with niraparib and topotecan. The patient achieved partial remission and disease stabilization for 1 year. Taken together, PARPi combinations show potential for the treatment of pHGG with ATRX mutations. Currently, all cell models are characterized for DNA repair signatures by DNA sequencing. Further, in depth characterization of DNA damage responses upon concomitant PARP and topoisomerase inhibition in ATRX-mutated pHGG are ongoing.

Therapeutic significance of nano- and biosensor technology in combating SARS-CoV-2: a review.

The diagnosis of novel coronavirus (COVID-19) has gained the spotlight of the world’s scientific community since December 2019 and it remains an important issue due to the emergence of novel variants around the globe. Early diagnosis of coronavirus is captious to prevent and hard to control. This pandemic can be eradicated by implementing suppressing strategies which can lead to better outcomes and more lives being saved. Therefore, the analysis showed that COVID-19 can only be managed by adopting public health measures, such as testing, isolation and social distancing. Much work has been done to diagnose coronavirus. Various testing technologies have been developed, opted and modified for rapid and accurate detection. The advanced molecular diagnosis relies on the detection of SARS-CoV-2 as it has been considered the main causative agent of this pandemic. Studies have shown that several molecular tests are considered essential for the confirmation of coronavirus infection. Various serology-based tests are also used in the detection and diagnosis of coronavirus including point-of-care assays and high-throughput enzyme immunoassays that aid in the diagnosis of COVID-19. Both these assays are time-consuming and have less diagnostic accuracy. Nanotechnology has the potential to develop new strategies to combat COVID-19 by developing diagnostics and therapeutics. In this review, we have focused on the nanotechnology-based detection techniques including nanoparticles and biosensors to obstruct the spread of SARS-CoV-2.

Parasitosis con manifestaciones digestivas

Infections due to gastrointestinal parasites in human beings have a worldwide distribution and an important impact on healthcare and high overall morbidity and mortality. Although they are more common in endemic areas of developing countries with few resources, immigration, travel, dietary changes, and food importation has increased the global incidence of these parasitic diseases. In the developed world, the incidence of infections due to protozoa is greater than those due to helminths. The clinical symptoms depend on the causative parasite, the location of the involvement, its local or disseminated invasion, and the host's immune status. The spectrum of involvements is also broad, from carriers who may remain asymptomatic for years to severe, fulminant cases to chronic, severe cases. To make a diagnosis, it is necessary to know the epidemiology, the parasite's life cycle, the etiopathogenesis, and the clinical manifestations and, in addition, other gastrointestinal diseases must be ruled out. At present, routine diagnostic techniques should be used together with advances in molecular diagnosis. This way, early treatment can be started to avoid complications, which can be severe; avoid chronicity of some infections; and prevent their transmission.

Muscle Biopsy: A Requirement for Precision Medicine in Adult-Onset Myopathy.

Muscle biopsy is a fundamental procedure to assist the final diagnosis of myopathy. With the recent advances in molecular diagnosis, serology tests, and mechanism-based classification in myopathy, the précised diagnosis for myopathy required the applications of multiple tools. This study intends to reappraise the benefit of muscle biopsy in adult-onset myopathy under the setting of an optimized muscle biopsy protocol and comprehensive serology tests. A one-group pretest-posttest study design was used. The pre- and post-biopsy diagnoses and treatments in 69 adult patients were compared. Muscle biopsy yielded 85.5% of definitive diagnoses, including changes in pre-biopsy diagnoses (40.6%) and narrowing down the suspicious myopathies (49.3%). The demographic data and clinical parameters between the group “with change” and “without change” after biopsy were not different. Among those with changes in diagnosis, 39.3% also had a corresponding shift in treatment, which benefits the patients significantly. Regarding the most common adult-onset myopathy, idiopathic inflammatory myopathy (IIM), 41% of patients with pre-biopsy diagnosis as IIM had changes in their IIM subtype diagnosis, and 53% was finally not IIM after muscle biopsy. Although there have been advances in molecular diagnosis recently, muscle biopsy still undoubtedly critically guided the diagnosis and treatment of adult-onset myopathy in the era of precision medicine.

Molecular Diagnosis of Dengue.

Several protocols for genomic amplification using reverse transcription followed by polymerase chain reaction (RT-PCR), important in the identification of the infecting serotype, have been used in the rapid diagnosis of Dengue Virus (DENV) infections. The qualitative protocol described by Lanciotti et al. (J Clin Microbiol 30: 545-551, 1992) suggested by WHO detects the four DENV serotypes simultaneously in one procedure "semi-nested," generating amplified products with specific sizes in base pairs for each serotype and it has been the most used in the past two decades. However, advances in molecular diagnosis have enabled the development of RT-PCR in real time (qRT-PCR) based on the use of dyes and probes (SYBR green and TaqMan), which is performed in a single step and is capable of providing quantitative data. In addition to quantification, the advantages of qRT-PCR over conventional RT-PCR include speed, greater sensitivity and specificity, and low rate of false positives. Several protocols for the diagnosis and/or quantification of DENV have already been described. Non-PCR-based methods such as reverse transcription loop-mediated isothermal amplification have shown high sensitivities and specificities. RT-PCR and qRT-PCR techniques can be performed using serum, plasma, infected cells, mosquitoes, fresh, and paraffin-embedded tissues. However, despite fast and accurate, they are limited to samples collected during the acute phase of infection (up to 7days after the onset of symptoms) and require specialized equipment and trained staff.

Global scenario and recent advances in molecular diagnosis and management of drug-resistant tuberculosis

Tuberculosis (TB) is one of the oldest communicable bacterial diseases, spreads predominantly by inhalation of infected respiratory droplets. It is a curable and preventable disease yet remains the leading infectious cause of human death worldwide. The TB burden is high among developing nations of Asia and Africa. Major obstacles in controlling TB are patient’s non-compliance to the anti-tubercular therapy, co-infection with Human immunodeficiency virus (HIV), low socioeconomic status, crowded living condition, inadequate rapid diagnostic testing facilities especially in resource-poor developing countries, delay in diagnosis and initiation of therapy, and the emergence of drug-resistant strains of Mycobacterium tuberculosis (MTB). Multidrug-resistant (MDR-TB), extensively drug-resistant (XDR-TB), and total drug-resistant (TDR-TB) MTB strains are difficult to treat and are associated with frequent treatment failures and high mortality. The recent advent of molecular techniques including nucleic acid amplification tests (NAATs) and whole-genome sequencing (WGS) have significantly ameliorated the rapid detection of TB cases and drug-resistant MTB. This, in turn, enabled the early initiation of therapy and development of novel treatment plans which is crucial for the global TB elimination target. The World Health Organization (WHO) 2020 guideline prioritizes the use of newer drugs as part of all-oral regimens for the treatment of MDR-TB. Apart from the use of newer drug delivery methods, host factors including immune functions and cytokine responses as well as mycobacterial enzymatic pathways are targeted in TB drug development. Adjuvant therapy employing host-directed approaches is increasingly studied through the time-tested pathogen-targeted approach remains the mainstay in the current treatment of MDR-TB.

Application of Next Generation Sequencing Genetic Studies of Urea Cycle Disorders

Urea cycle disorder is a group of rare, inherited metabolic disorders in the pathway transforming ammonia to urea. The mutations in genes coding for 6 enzymes that are participated including carbamoyl phosphate synthase I (CPSI), ornithine transcarbamylase (OTC), argininosuccinate synthase (ASS1), argininosuccinate lyase (ASL), arginase (ARG1), and N-acetyl glutamate synthase (NAGS), and 2 transport systems ((ornithine translocase (ONT1), citrin)) in the urea cycle are responsible for ammonia accumulation in the blood. Hyperammonemia is the cause of severe neurological symptoms and even death. In almost all cases, clinical examinations and biochemical experiments are necessary, but insufficient information for an accurate diagnosis. Mutation analysis is an effective method to confirm the diagnosis and could be the basis for genetic counseling. The rapid development and widely using of next generation sequencing (NGS) have brought incredible advances in molecular diagnosis of genetic diseases in general. In this article, we systematize the UCD genetic studies applying NGS method, thereby providing a basis for not only disease diagnosis but also future research

Current Guidelines for Management of Medullary Thyroid Carcinoma.

Medullary thyroid carcinoma (MTC) is a rare neuroendocrine tumor originating from the parafollicular cells. The diagnostic and therapeutic strategies for the condition are different from those used for well-differentiated thyroid cancer. Since the 2015 American Thyroid Association guidelines for the diagnosis and treatment of MTC, the latest, including the National Comprehensive Cancer Network and European Association for Medical Oncology guidelines have been updated to reflect several recent advances in the management of MTC. Advances in molecular diagnosis and postoperative risk stratification systems have led to individualized treatment and follow-up strategies. Multi-kinase inhibitors, such as vandetanib and cabozantinib, can prolong disease progression-free survival with favorable adverse effects. In addition, potent selective rearranged during transfection (RET) inhibitors (selpercatinib and pralsetinib) have shown a promising efficacy in recent clinical trials. This review summarizes the management of MTC in recent guidelines focused on sporadic MTC.

Stargardt disease: Multimodal imaging: A review.

Stargardt disease (STGD1) is an autosomal recessive retinal dystrophy, characterised by bilateral progressive central vision loss and subretinal deposition of lipofuscin‐like substances. Recent advances in molecular diagnosis and therapeutic options are complemented by the increasing recognition of new multimodal imaging biomarkers that may predict genotype and disease progression. Unique non‐invasive imaging features of STDG1 are useful for gene variant interpretation and may even provide insight into the underlying molecular pathophysiology. In addition, pathognomonic imaging features of STGD1 have been used to train neural networks to improve time efficiency in lesion segmentation and disease progression measurements. This review will discuss the role of key imaging modalities, correlate imaging signs across varied STGD1 presentations and illustrate the use of multimodal imaging as an outcome measure in determining the efficacy of emerging STGD1 specific therapies.

Clinical and Laboratory Characteristics of a Large Iranian Kindred Afflicted with Von Hippel Lindau Disease.

BackgroundVon Hippel Lindau (VHL) disease is a hereditary disorder characterized by the development of benign or malignant tumors in the brain, spinal cord, eyes, adrenal medulla, kidney, pancreas, and many other organs. Advances in molecular diagnosis have led to the identification of the affected members of families at earlier stages. We present the clinical, laboratory, and genetic characteristics of five generations of a large Iranian kindred with VHL.MethodsThe proband, a 52-year-old Iranian man, was recognized with VHL. All family members underwent clinical, laboratory, imaging, and genetic evaluation. Medical files and histopathology reports of patients who had been operated on before were also reviewed. Diagnosis of the disease was based on clinical findings, positive family history of VHL, and development of a central nervous system or retinal hemangioblastoma or pheochromocytoma.ResultsBased on diagnostic criteria, our initial evaluations revealed that 10 members of the family had already been affected by the disease. Among them, nine had pheochromocytoma, and one had retinal hemangioblastoma. There was no case of kidney tumors among the kindred.ConclusionsStudy results show the high penetrance of the disease and focus on the large burden imposed by the disease on the health and quality of life of patients afflicted with the disease, emphasizing the importance of surveillance from early childhood for detection and management of the disease as early as possible.

BK Polyomavirus Nephropathy in Kidney Transplantation: Balancing Rejection and Infection.

BK polyomavirus nephropathy (BKVN) and allograft rejection are two closely-associated diseases on opposite ends of the immune scale in kidney transplant recipients. The principle of balancing the immune system remains the mainstay of therapeutic strategy. While patient outcomes can be improved through screening, risk factors identification, and rapid reduction of immunosuppressants, a lack of standard curative therapy is the primary concern during clinical practice. Additionally, difficulty in pathological differential diagnosis and clinicopathology’s dissociation pose problems for a definite diagnosis. This article discusses the delicate evaluation needed to optimize immunosuppression and reviews recent advances in molecular diagnosis and immunological therapy for BKVN patients. New biomarkers for BKVN diagnosis are under development. For example, measurement of virus-specific T cell level may play a role in steering immunosuppressants. The development of cellular therapy may provide prevention, even a cure, for BKVN, a complex post-transplant complication.

IDH-Mutant Low-grade Glioma: Advances in Molecular Diagnosis, Management, and Future Directions.

IDH-mutant low-grade gliomas (LGG) have emerged as a distinct clinical and molecular entity with unique treatment considerations. Here, we review updates in IDH-mutant LGG diagnosis and classification, imaging biomarkers, therapies, and neurocognitive and patient-reported outcomes. CDKN2A/B homozygous deletion in IDH-mutant astrocytoma is associated with shorter survival, similar to WHO grade 4. The T2-FLAIR mismatch, a highly specific but insensitive sign, is diagnostic of IDH-mutant astrocytoma. Maximal safe resection is currently indicated in all LGG cases. Radiotherapy with subsequent PCV (procarbazine, lomustine, vincristine) provides longer overall survival compared to radiotherapy alone. Temozolomide in place of PCV is reasonable, but high-level evidence is still lacking. LGG adjuvant treatment has important quality of life and neurocognitive side effects that should be considered. Although incurable, IDH-mutant LGG have a favorable survival compared to IDH-WT glioma. Recent advances in molecular-based classification, imaging, and targeted therapies will hopefully improve survival and quality of life.

Challenges and Advances in Molecular Diagnosis of Myopathies and Dystrophies in Perspective of Their Use in Developing Countries: Past, Present, and Future.

Proper diagnosis is the first and most critical step for effective identification and treatment of myopathy and dystrophy disorders. Although various histochemical and biochemical studies have paved the way for efficient testing of these disorders, they are insufficient for accurate diagnosis. To overcome this, the diagnostic procedure has now shifted more toward the "genetic first approach," with the remarkable role played by various genetic and molecular techniques. In developing countries, successful diagnosis of such disorders is affected by the shortage of hospitals, poor lab setup, limited diagnostic methods, and unavailability of technical expertise. As a major population living in developing countries faces such inadequate healthcare facilities, there has always been a need for identifying effective diagnostic techniques that could identify genetic alterations more prone in such regions. This article reviews studies done in the last few years that primarily use nonsequencing-based molecular diagnosis methods to identify myopathy- and dystrophy-specific gene alterations and thus could equally hold potential for screening key genetic alterations reported in certain regions in developing countries. Further, this review deals with new emerging sequencing and next-generation sequencing (NGS)-based approach and their potential in providing an adequate diagnosis. This study promotes nonsequencing-based molecular methods to be an effective method for early-stage diagnosis and management of myopathies and dystrophies in developing countries and suggests the high importance of emerging NGS methods in proper diagnosis and identifying new players in neuromuscular disorders.

Diagnostic and therapeutic advances in neuroendocrine tumours

Neuroendocrine neoplasms are derived from the diffuse endocrine system and represent a spectrum of tumours with a diverse range of molecular abnormalities, functionality and anatomical locations. Here, some key advances in molecular diagnosis, functional imaging and therapeutic strategies that have been published in 2020 are discussed.