The genetic basis of disease

Novel SLC16A2 Frameshift Mutation as a Cause of Allan-Herndon-Dudley Syndrome and its Implications for Carrier Screening

Background

Allan-Herndon-Dudley syndrome (AHDS) is a rare X-linked neurodevelopmental disorder caused by mutations in the solute carrier family 16-member 2 (SLC16A2) gene. This syndrome leads to significant psychomotor disabilities, thyroid dysfunction, and abnormal brain development. This case report describes the genetic cause of AHDS in a male proband and to expanding the mutation spectrum of the SLC16A2 gene.

Methods

A blood specimen was collected from a one-year-old child with delayed development and abnormal thyroid function and this was followed by whole-exome sequencing (WES) was performed on the proband to identify potential genetic mutations. Sanger sequencing was subsequently used to confirm the findings and determine the inheritance pattern of the mutation within the family.

Results

The proband, who presented with developmental delay, thyroid dysfunction, and abnormal brain development, was found to have a novel hemizygous frameshift mutation, c.513_538del (p.Ile172Cysfs*60), in the SLC16A2 gene (NM_006517.5). This mutation was inherited from his asymptomatic mother, confirming the X-linked inheritance pattern. The mutation is classified as likely pathogenic, contributing to the clinical presentation observed in the proband.

Conclusion

This study identified a novel frameshift mutation in the SLC16A2 gene associated with AHDS, thereby expanding the known mutation spectrum of this gene. Given the significant impact of AHDS on neural development and hormone secretion, it is recommended that this gene be included in carrier screening panels in China, particularly for families with a history of related neurodevelopmental disorders.

Adeno-associated viral vector targeted evolution for neurofibromatosis gene delivery

Neurofibromatosis type 1 (NF1) is an inherited genetic disease resulting from pathogenic mutations in NF1 that drive tumor formation along peripheral nerves, leading to many functional consequences. Tumor removal or treatment often results in regrowth and/or nerve damage. Addressing NF1 pathogenic variations at the cellular level through gene therapy holds great potential for long-term treatment of patients with NF1. Adeno-associated viruses (AAVs) are broadly used gene delivery vehicles for gene therapies because of their low pathogenicity, ability to transduce nondividing cells, and potential for long-term gene expression. This article explores the landscape of AAV-mediated gene delivery strategies for NF1, discusses the challenges of efficient delivery to relevant cell types, and highlights the progress in vector design strategies.

Mitochondrial respiratory complex IV deficiency recapitulates amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is categorized into ~10% familial and ~90% sporadic cases. While familial ALS is caused by mutations in many genes of diverse functions, the underlying pathogenic mechanisms of ALS, especially in sporadic ALS (sALS), are largely unknown. Notably, about half of the cases with sALS showed defects in mitochondrial respiratory complex IV (CIV). To determine the causal role of this defect in ALS, we used transcription activator-like effector-based mitochondrial genome editing to introduce mutations in CIV subunits in rat neurons. Our results demonstrate that neuronal CIV deficiency is sufficient to cause a number of ALS-like phenotypes, including cytosolic TAR DNA-binding protein 43 redistribution, selective motor neuron loss and paralysis. These results highlight CIV deficiency as a potential cause of sALS and shed light on the specific vulnerability of motor neurons, marking an important advance in understanding and therapeutic development of sALS.

In silico development of HASDI-G2 as a novel agent for selective recognition of the DNA sequence

Genetic information, which is mostly encoded in the form of DNA sequence, is the basis of life. Its deviations are often the cause of the most deadly diseases such as cancer. Accordingly, the development of methods to control the transcription of certain DNA parts is an important direction of modern pharmacological and biological research. Within the scope of this work, we are investigating the second generation of a polyintercalating agent that we developed earlier, potentially capable of recognizing 16-bp DNA sequences. In order to confirm its ability for advanced selective DNA recognition a series of simulation experiments was conducted. We differentially investigated the stability of HASDI-G2 complexes with mutated targeting sequences and their native variants. Firstly, we confirmed the ability of HASDI-G2 to clearly discriminate the target sequence (EBNA1) from a random site in the human genome (KCNH2). That repeated the experiment of the polyintercalator's previous version and additionally showed better results of the next-generation structure. Next, we examined HASDI-G2 under conditions where the target sequence differed from the random one increasingly slightly. And we found that even a one-nucleotide mismatch leads to a similar complex destabilization as a mismatch of 3 or 4 nucleotides. Such complexes showed significant conformational rearrangements, accompanied by a sharp decrease in the hydrogen bonds quantity, a drop in the binding free energy, and local melting of the DNA duplex. Moreover, the latter applied not only to sites of direct incompatibility, but also to parts where HASDI-G2 fully corresponded to the sequence of intercalation.

Genetic Variants Associated with Suspected Neonatal Hypoxic Ischaemic Encephalopathy: A Study in a South African Context

Neonatal encephalopathy suspected to be due to hypoxic ischaemic encephalopathy (NESHIE) carries the risk of death or severe disability (cognitive defects and cerebral palsy). Previous genetic studies on NESHIE have predominantly focused on exomes or targeted genes. The objective of this study was to identify genetic variants associated with moderate-severe NESHIE through whole-genome, unbiased analysis. Variant filtering and prioritization were performed, followed by association testing both on a case-control basis and to compare the grades of severity and/or progression. Association testing on neonates with NESHIE (N = 172) and ancestry-matched controls (N = 288) produced 71 significant genetic variants (false discovery rate corrected p-value < 6.2 × 10-4), all located in non-coding regions and not previously implicated in NESHIE. Disease-associated variants in non-coding regions are considered to affect regulatory functions, possibly by modifying gene expression, promoters, enhancers, or DNA structure. The most significant variant was at position 6:162010973 in the Parkin RBR E3 ubiquitin protein ligase (PRKN) intron. Intronic variants were also identified in genes involved in inflammatory processes (SLCO3A1), DNA repair (ZGRF1), synaptogenesis (CNTN5), haematopoiesis (ASXL2), and the transcriptional response to hypoxia (PADI4). Ten variants were associated with a higher severity or lack of improvement in NESHIE, including one in ADAMTS3, which encodes a procollagen amino protease with a role in angiogenesis and lymphangiogenesis. This analysis represents one of the first efforts to analyze whole-genome data to investigate the genetic complexity of NESHIE in diverse ethnolinguistic groups of African origin and provides direction for further study.

Mitochondrial Dysfunction in Neurodegenerative Diseases

Mitochondrial dysfunction represents a pivotal characteristic of numerous neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. These conditions, distinguished by unique clinical and pathological features, exhibit shared pathways leading to neuronal damage, all of which are closely associated with mitochondrial dysfunction. The high metabolic requirements of neurons make even minor mitochondrial deficiencies highly impactful, driving oxidative stress, energy deficits, and aberrant protein processing. Growing evidence from genetic, biochemical, and cellular investigations associates impaired electron transport chain activity and disrupted quality-control mechanisms, such as mitophagy, with the initial phases of disease progression. Furthermore, the overproduction of reactive oxygen species and persistent neuroinflammation can establish feedforward cycles that exacerbate neuronal deterioration. Recent clinical research has increasingly focused on interventions aimed at enhancing mitochondrial resilience-through antioxidants, small molecules that modulate the balance of mitochondrial fusion and fission, or gene-based therapeutic strategies. Concurrently, initiatives to identify dependable mitochondrial biomarkers seek to detect pathological changes prior to the manifestation of overt symptoms. By integrating the current body of knowledge, this review emphasizes the critical role of preserving mitochondrial homeostasis as a viable therapeutic approach. It also addresses the complexities of translating these findings into clinical practice and underscores the potential of innovative strategies designed to delay or potentially halt neurodegenerative processes.

Awareness and Attitude of the General Population Towards Inherited Hemoglobinopathies in the Premarital Screening Program in the Northern Region of Saudi Arabia

Background: Premarital screening (PMS) is a nationwide program that helps high-risk individuals make decisions to avoid genetic and sexually transmitted diseases from spreading to their spouse or future offspring. This study examined the knowledge and attitudes towards inherited hemoglobinopathies in PMS among the people of Northern Border Region in Saudi Arabia and their relationship to various sociodemographic factors. Methods: A cross-sectional study was undertaken in the Northern region of Saudi Arabia from January to March 2024. Data were gathered via questionnaire from 478 Saudi participants aged 18 years and older. The chi-square test was employed to determine the association between categorical variables. Results: All participants in the study were familiar with the PMS program. A significant portion of participants, 79.3%, acknowledged that consanguinity can increase the risk of hereditary blood disorders, while 69.9% believed that if both parents are carriers of the same genetic blood disease, their child may inherit it. Higher education, female gender, and age group (30-40) were found to be the main predictors of knowledge regarding PMS. Most of the participants (98.5%) had a positive attitude regarding the necessity of PMS as a prerequisite for marriage completion. About 82.8% indicated they would not continue with the marriage if the PMS results were incompatible. Conclusions: The study indicates a growing awareness and positive attitude towards premarital screening among the general population, with an increasing number of individuals opting for it. The findings suggest that PMS programs contribute to informed decision making, as evidenced by the rise in participants choosing to forgo marriage due to partner incompatibility. The study recommends the enhancement of health education campaigns by considering demographic factors such as age, education, and marital status. Additionally, it advocates for expanding the scope of PMS to include a wider range of health and genetic disorders to improve its overall efficacy.

Gene therapy for genetic diseases: challenges and future directions

Genetic diseases constitute the majority of rare human diseases, resulting from abnormalities in an individual's genetic composition. Traditional treatments offer limited relief for these challenging conditions. In contrast, the rapid advancement of gene therapy presents significant advantages by directly addressing the underlying causes of genetic diseases, thereby providing the potential for precision treatment and the possibility of curing these disorders. This review aims to delineate the mechanisms and outcomes of current gene therapy approaches in clinical applications across various genetic diseases affecting different body systems. Additionally, genetic muscular disorders will be examined as a case study to investigate innovative strategies of novel therapeutic approaches, including gene replacement, gene suppression, gene supplementation, and gene editing, along with their associated advantages and limitations at both clinical and preclinical levels. Finally, this review emphasizes the existing challenges of gene therapy, such as vector packaging limitations, immunotoxicity, therapy specificity, and the subcellular localization and immunogenicity of therapeutic cargos, while discussing potential optimization directions for future research. Achieving delivery specificity, as well as long-term effectiveness and safety, will be crucial for the future development of gene therapies targeting genetic diseases.

Genomic exploration of pediatric neurological disorders: a case series

BACKGROUND

Pediatric neurological disorders include neurodegenerative diseases causing cognitive impairment and vision loss. They are one of the important causes of morbidity and mortality in children with diverse etiologies. Diagnosis is difficult despite genetic work, and a final diagnosis can be achieved in only 60% of cases.

CASE PRESENTATION

We explore three Indian cases of pediatric neurological diseases (with age presented at the clinic), viz. arthrogryposis (8 years), autism (18 months), and congenital bilateral cataract (3 years), by analyzing clinical exomes. In this work, we attempt to understand rare neurological disorders in an Indian pediatric cohort using exome studies.

CONCLUSION

We used our benchmarked CONVEX pipeline for screening consensus variants, wherein EIF2B2 was found to be inherently pathogenic. We map the association of variants and genes and disease correlation to neuroleptic malignant syndrome, which matches the phenotype to the cases.

High-throughput sequencing: a breakthrough in molecular diagnosis for precision medicine

High-resolution insights into the nucleotide arrangement within an organism's genome are pivotal for deciphering its genetic composition, function, and evolutionary trajectory. Over the years, nucleic acid sequencing has been instrumental in driving significant advancements in genomics and molecular biology. The advent of high-throughput or next-generation sequencing (NGS) technologies has revolutionized whole genome sequencing, revealing novel and intriguing features of genomes, such as single nucleotide polymorphisms and lethal mutations in both coding and non-coding regions. These platforms provide a practical approach to comprehensively identifying and analyzing whole genomes with remarkable throughput, accuracy, and scalability within a short time frame. The resulting data holds immense potential for enhancing healthcare systems, developing novel and personalized therapies, and preparing for future pandemics and outbreaks. Given the wide array of available high-throughput sequencing platforms, selecting the appropriate technology based on specific needs is crucial. However, there is limited information regarding sample preparation, sequencing principles, and output data to facilitate a comparative evaluation of these platforms. This review details various NGS technologies and approaches, examining their advantages, limitations, and future potential. Despite being in their early stages and facing challenges, ongoing advancements in NGS are expected to yield significant future benefits.

A genomic strategy for precision medicine in rare diseases: integrating customized algorithms into clinical practice

BACKGROUND

Despite the use of Next-Generation Sequencing (NGS) as the gold standard for the diagnosis of rare diseases, its clinical implementation has been challenging, limiting the cost-effectiveness of NGS and the understanding, control and safety essential for decision-making in clinical applications. Here, we describe a personalized NGS-based strategy integrating precision medicine into a public healthcare system and its implementation in the routine diagnosis process during a five-year pilot program.

METHODS

Our approach involved customized probe designs, the generation of virtual panels and the development of a personalized medicine module (PMM) for variant prioritization. This strategy was applied to 6500 individuals including 6267 index patients and 233 NGS-based carrier screenings.

RESULTS

Causative variants were identified in 2061 index patients (average 32.9%, ranging from 12 to 62% by condition). Also, 131 autosomal-recessive cases could be partially genetically diagnosed. These results led to over 5000 additional studies including carrier, prenatal and preimplantational tests or pharmacological and gene therapy treatments.

CONCLUSION

This strategy has shown promising improvements in the diagnostic rate, facilitating timely diagnosis and gradually expanding our services portfolio for rare diseases. The steps taken towards the integration of clinical and genomic data are opening new possibilities for conducting both retrospective and prospective healthcare studies. Overall, this study represents a major milestone in the ongoing efforts to improve our understanding and clinical management of rare diseases, a crucial area of medical research and care.

Decoding complexity: The role of long-read sequencing in unraveling genetic disease etiologies

In recent years, next-generation high-throughput sequencing technology has been widely used in clinical practice for the identification and diagnosis of Mendelian diseases as an auxiliary detection method. Nevertheless, due to the limitations in read length and poor coverage of complex genomic regions, the etiology of many genetic diseases is unclear. Long-read sequencing (LRS) addresses these limitations of next-generation sequencing. LRS is an effective tool for the clinical study of the etiology of complex genetic diseases. In this review, we summarized the current research on the application of LRS in diseases across various systems. We also reported the improvements in the diagnostic rate and common variant types of LRS in different studies, providing a foundation for the discovery of new disease mechanisms, which is anticipated to play a crucial role in future research on genetic diseases.

Prenatal Silicon Dioxide Nanoparticles Exposure Reduces Female Offspring Fertility Without Affecting Males

Silicon dioxide nanoparticles (SiO2 NPs) are widely utilized in biomedicine due to their controllable size and biocompatibility. While previous studies have demonstrated that prenatal exposure to SiO2 NPs can traverse the placental barrier and induce neurotoxicity in offspring. However, their reproductive toxicity remains unclear. Here, it is found that prenatal SiO2 NPs exposure led to subfertility in female offspring, evidenced by decreased ovulation potential, ovarian reserve, and litter size. In contrast, male offspring maintained normal sperm production and fertility. Mechanistic analyses revealed that prenatal SiO2 NPs exposure disrupted meiotic recombination and increased oocyte apoptosis, resulting in reduced postnatal primordial follicle formation in females. Conversely, meiotic recombination occurring postnatally in male offspring remained unaffected. Notably, treatment with carboxylate (COOH)-functionalized SiO2 nanoparticles (SiO2-COOH NPs) has a minimal impact on fertility in female offspring. Further research, including clinical studies, is needed to confirm these findings in humans. These findings demonstrated gender-specific reproductive toxicity induced by prenatal SiO2 NPs exposure and highlighted the importance of considering nanoparticle safety in prenatal contexts.

The three-parent baby: Medicolegal, forensic and ethical concerns

In the recent past, human genetics and in vitro fertilization (IVF) have undergone various advances to combat with several congenital and developmental disorders. These advances are a boon for the families and patients who were restricted from having a child due to one or the other reasons. One such reason is the mitochondrial DNA (mtDNA) mutations, which are definitely transmitted from the mother to the child due to uniparental/maternal inheritance of mitochondria. Depending upon the range of the mutation (mutation loads) present, the mtDNA mutation leads to various devitalizing to fatal disorders, all of which are incurable. Scientists and researchers developed a technique known as mitochondrial donation technique or mitochondrial replacement therapy (MRT) to combat with the mtDNA mutations. The technique relies on the replacement of faulty mitochondria in the mother's egg with the normal wild-type from a donor female resulting in a "three-parent baby." On the other side, forensic scientists and anthropologists continuously explore the mtDNA in various medicolegal cases and in uncoupling the mystery of human origin and migration respectively. In this regard, we explored the genetic, forensic and ethical aspects of a "three-parent baby." The present communication also attempts to highlight the importance and limitations of the MRT technique/three-parent baby in a medicolegal context.

Advances in CRISPR-Cas technology and its applications: revolutionising precision medicine

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated proteins) has undergone marked advancements since its discovery as an adaptive immune system in bacteria and archaea, emerged as a potent gene-editing tool after the successful engineering of its synthetic guide RNA (sgRNA) toward the targeting of specific DNA sequences with high accuracy. Besides its DNA editing ability, further-developed Cas variants can also edit the epigenome, rendering the CRISPR-Cas system a versatile tool for genome and epigenome manipulation and a pioneering force in precision medicine. This review explores the latest advancements in CRISPR-Cas technology and its therapeutic and biomedical applications, highlighting its transformative impact on precision medicine. Moreover, the current status of CRISPR therapeutics in clinical trials is discussed. Finally, we address the persisting challenges and prospects of CRISPR-Cas technology.

Dose-Related Mutagenic and Clastogenic Effects of Benzo[b]fluoranthene in Mouse Somatic Tissues Detected by Duplex Sequencing and the Micronucleus Assay

Polycyclic aromatic hydrocarbons (PAHs) are common environmental pollutants that originate from the incomplete combustion of organic materials. We investigated the clastogenicity and mutagenicity of benzo[b]fluoranthene (BbF), one of 16 priority PAHs, in MutaMouse males after a 28 day oral exposure. BbF causes robust dose-dependent increases in micronucleus frequency in peripheral blood, indicative of chromosome damage. Duplex sequencing (DS), an error-corrected sequencing technology, reveals that BbF induces dose-dependent increases in mutation frequencies in bone marrow (BM) and liver. Mutagenicity is increased in intergenic relative to genic regions, suggesting a role for transcription-coupled repair of BbF-induced DNA damage. At higher doses, the maximum mutagenic response to BbF is higher in liver, which has a lower mitotic index but higher metabolic capacity than BM; however, mutagenic potency is comparable between the two tissues. BbF induces primarily C:G > A:T mutations, followed by C:G > T:A and C:G > G:C, indicating that BbF metabolites mainly target guanines and cytosines. The mutation spectrum of BbF correlates with cancer mutational signatures associated with tobacco exposure, supporting its contribution to the carcinogenicity of combustion-derived PAHs in humans. Overall, BbF's mutagenic effects are similar to benzo[a]pyrene, a well-studied mutagenic PAH. Our work showcases the utility of DS for effective mutagenicity assessment of environmental pollutants.

Recent Applications of In Silico Approaches for Studying Receptor Mutations Associated with Human Pathologies

In recent years, the advent of computational techniques to predict the potential activity of a drug interacting with a receptor or to predict the structure of unidentified proteins with aberrant characteristics has significantly impacted the field of drug design. We provide a comprehensive review of the current state of in silico approaches and software for investigating the effects of receptor mutations associated with human diseases, focusing on both frequent and rare mutations. The reported techniques include virtual screening, homology modeling, threading, docking, and molecular dynamics. This review clearly shows that it is common for successful studies to integrate different techniques in drug design, with docking and molecular dynamics being the most frequently used techniques. This trend reflects the current emphasis on developing novel therapies for diseases resulting from receptor mutations with the recently discovered AlphaFold algorithm as the driving force.

Xeno Nucleic Acids as Functional Materials: From Biophysical Properties to Application

Xeno nucleic acid (XNA) are artificial nucleic acids, in which the chemical composition of the sugar moiety is changed. These modifications impart distinct physical and chemical properties to XNAs, leading to changes in their biological, chemical, and physical stability. Additionally, these alterations influence the binding dynamics of XNAs to their target molecules. Consequently, XNAs find expanded applications as functional materials in diverse fields. This review provides a comprehensive summary of the distinctive biophysical properties exhibited by various modified XNAs and explores their applications as innovative functional materials in expanded fields.

Genomics and Bioinformatics in One Health: Transdisciplinary Approaches for Health Promotion and Disease Prevention

The One Health concept underscores the interconnectedness of human, animal, and environmental health, necessitating an integrated, transdisciplinary approach to tackle contemporary health challenges. This perspective paper explores the pivotal role of genomics and bioinformatics in advancing One Health initiatives. By leveraging genomic technologies and bioinformatics tools, researchers can decode complex biological data, enabling comprehensive insights into pathogen evolution, transmission dynamics, and host-pathogen interactions across species and environments (or ecosystems). These insights are crucial for predicting and mitigating zoonotic disease outbreaks, understanding antimicrobial resistance patterns, and developing targeted interventions for health promotion and disease prevention. Furthermore, integrating genomic data with environmental and epidemiological information enhances the precision of public health responses. Here we discuss case studies demonstrating successful applications of genomics and bioinformatics in One Health contexts, such as including data integration, standardization, and ethical considerations in genomic research. By fostering collaboration among geneticists, bioinformaticians, epidemiologists, zoologists, and data scientists, the One Health approach can harness the full potential of genomics and bioinformatics to safeguard global health. This perspective underscores the necessity of continued investment in interdisciplinary education, research infrastructure, and policy frameworks to effectively employ these technologies in the service of a healthier planet.

The pathological anatomical collection of the Natural History Museum Vienna

The pathological anatomical collection Vienna (Pathologisch-Anatomische Sammlung Wien; PASW) is a living and still growing research collection. It was established as early as 1796 as part of the Medical University of Vienna, acquired the status of an independent federal museum in 1971, and was assigned to the Natural History Museum Vienna in 2012. It houses a wide range of human wet and dry specimens and further objects, such as moulages, medical devices, microbiological and histological specimens, and a photo archive (approximately 50,000 objects), which, as a meaningful source, may contribute to disclosing not only aspects of the medical history and the development of corresponding museums in Vienna, but is also considered a collection of cultural and current scientific relevance, quite comparable to today's biobanks. Most of the tissue amassment represents wet organic specimens and human skeletons or skeletal elements representing, e.g., congenital and metabolic disorders, infectious diseases, injuries, neoplasms, or musculoskeletal diseases, basically collected as descriptive anatomical teaching aids. This article reviews the current medical issues on which research has been and is being conducted by including PASW specimens (hereby using the ICD-10 code), and the extent to and ethical conditions under which this important heritage could be used as a reference collection for clinical and bioanthropological (paleopathological and palaeoepidemiological) studies; finally, this article reflects on the value and future research prospects, taking into account different positions and the ongoing discussions in pathological anatomical human tissue collections.

Schizophrenia and Rheumatoid Arthritis Genetic Scenery: Potential Non-HLA Genes Involved in Both Diseases Relationship

Background: The link between rheumatoid arthritis (RA) and schizophrenia (SZ) has long been a hot topic of deliberation among scientists from various fields. Especially when it comes to genetics, the connection between RA and SZ is still up for discussion, as can be observed in this study. The HLA genes are the most disputed in identifying a connection between the two diseases, but a more thorough investigation of other genes that may be ignored could yield something even more interesting. Thus, finding the genes responsible for this long-sought relationship will necessitate looking for them. Materials and Methods: Shared and overlapped associated genes involved between SZ and RA were extracted from four databases. The overlapping genes were examined using Database for Annotation, Visualization and Integrated Discovery (DAVID) and InnateDB to search the pertinent genes that concatenate between these two disorders. Results: A total of 91 overlapped genes were discovered, and that 13 genes, divided into two clusters, showed a similarity in function, suggesting that they may serve as an important meeting point. FCGR2A, IL18R, BTNL2, AGER, and CTLA4 are five non-HLA genes related to the immune system, which could lead to new discoveries about the connection between these two disorders. Conclusion: An in-depth investigation of these functionally comparable non-HLA genes that overlap could reveal new interesting information in both diseases. Understanding the molecular and immune-related aspects of RA and SZ may shed light on their etiology and inform future research on targeted treatment strategies.

Current approaches in CRISPR-Cas systems for hereditary diseases

CRISPR-Cas technologies have drastically revolutionized genetic engineering and also dramatically changed the potential for treating inherited disorders. The potential to correct genetic mutations responsible for numerous hereditary disorders from single-gene disorders to complex polygenic diseases through precise DNA editing is feasible. The tactic now employed in CRISPR-Cas systems for treating inherited disorders is the usage of particular guide RNAs to target and edit disease-causing mutations in the patient's genome. Several methods such as CRISPR-Cas9, CRISPR-Cas12, and CRISPR-Cas13 are being thoroughly researched and optimized to increase effectiveness, accuracy, and safety in gene editing. Additionally, it is predicted that CRISPR-based therapies will be able to treat complex genetic illnesses such as cancer predisposition syndromes, neurological disorders, and cardiovascular conditions in addition to single-gene disorders. The available editing tools and creation of base editing technology facilitate the simultaneous correction of many mutations or accurate nucleotide changes leading to further advances in the development of multiplex editing tools and base editing technology fiction. When combined with other paradigms such as gene therapy using stem cell treatment, CRISPR-Cas promises improved efficacy. Patient treatment and lowering side effects significantly in individual genetic profiles will guide CRISPR-based treatments. These procedures will undoubtedly lead to therapies that are both efficient and curative of a wide range of genetic diseases, ushering in a new era of precision medicine. This chapter discusses about CRISPR Cas9 mechanism and its significance in the treatment of Hereditary disorders.

The known and unknown about attention deficit hyperactivity disorder (ADHD) genetics: a special emphasis on Arab population

Attention deficit hyperactivity disorder (ADHD) is a clinically and genetically heterogeneous neurodevelopmental syndrome characterized by behavioral appearances such as impulsivity, inattention, and hyperactivity. The prevalence of ADHD is high in childhood when compared to adults. ADHD has been significantly advanced by genetic research over the past 25 years. However, it is logically conceivable that both genetic and/or non-genetic factors, such as postnatal environmental and social influences, are associated with ADHD phenotype in Arab populations. While genetic influences are strongly linked with the etiology of ADHD, it remains obscure how consanguinity which is an underlying factor for many genetic diseases, contributes to ADHD subtypes. Arabian Gulf Nations have one the highest rates of consanguineous marriages, and consanguinity plays an important contributing factor in many genetic diseases that exist in higher percentages in Arabian Gulf Nations. Therefore, the current review aims to shed light on the genetic variants associated with ADHD subtypes in Arabian Gulf nations and Saudi Arabia in particular. It also focuses on the symptoms and the diagnosis of ADHD before turning to the neuropsychological pathways and subgroups of ADHD. The impact of a consanguinity-based understanding of the ADHD subtype will help to understand the genetic variability of the Arabian Gulf population in comparison with the other parts of the world and will provide novel information to develop new avenues for future research in ADHD.

Unlocking new avenues for neuropsychiatric disease therapy: the emerging potential of Peroxisome proliferator-activated receptors as promising therapeutic targets

RATIONALE

Peroxisome proliferator-activated receptors (PPARs) are transcription factors that regulate various physiological processes such as inflammation, lipid metabolism, and glucose homeostasis. Recent studies suggest that targeting PPARs could be beneficial in treating neuropsychiatric disorders by modulating neuronal function and signaling pathways in the brain. PPAR-α, PPAR-δ, and PPAR-γ have been found to play important roles in cognitive function, neuroinflammation, and neuroprotection. Dysregulation of PPARs has been associated with neuropsychiatric disorders like bipolar disorder, schizophrenia, major depression disorder, and autism spectrum disorder. The limitations and side effects of current treatments have prompted research to target PPARs as a promising novel therapeutic strategy. Preclinical and clinical studies have shown the potential of PPAR agonists and antagonists to improve symptoms associated with these disorders.

OBJECTIVE

This review aims to provide an overview of the current understanding of PPARs in neuropsychiatric disorders, their potential as therapeutic targets, and the challenges and future directions for developing PPAR-based therapies.

METHODS

An extensive literature review of various search engines like PubMed, Medline, Bentham, Scopus, and EMBASE (Elsevier) databases was carried out with the keywords "PPAR, Neuropsychiatric disorders, Oxidative stress, Inflammation, Bipolar Disorder, Schizophrenia, Major depression disorder, Autism spectrum disorder, molecular pathway".

RESULT & CONCLUSION

Although PPARs present a hopeful direction for innovative therapeutic approaches in neuropsychiatric conditions, additional research is required to address obstacles and convert this potential into clinically viable and individualized treatments.

Dose-related Mutagenic and Clastogenic Effects of Benzo[b]fluoranthene in Mouse Somatic Tissues Detected by Duplex Sequencing and the Micronucleus Assay

Polycyclic aromatic hydrocarbons (PAHs) are common environmental pollutants that originate from the incomplete combustion of organic materials. We investigated the clastogenicity and mutagenicity of benzo[ b ]fluoranthene (BbF), one of 16 priority PAHs, in MutaMouse males after a 28-day oral exposure. BbF causes robust dose-dependent increases in micronucleus frequency in peripheral blood, indicative of chromosome damage. Duplex Sequencing (DS), an error-corrected sequencing technology, reveals that BbF induces dose-dependent increases in mutation frequencies in bone marrow (BM) and liver. Mutagenicity is increased in intergenic relative to genic regions, suggesting a role for transcription-coupled repair of BbF-induced DNA damage. At higher doses, the maximum mutagenic response to BbF is higher in liver, which has a lower mitotic index but higher metabolic capacity than BM; however, mutagenic potency is comparable between the two tissues. BbF induces primarily C:G>A:T mutations, followed by C:G>T:A and C:G>G:C, indicating that BbF metabolites mainly target guanines and cytosines. The mutation spectrum of BbF correlates with cancer mutational signatures associated with tobacco exposure, supporting its contribution to the carcinogenicity of combustion-derived PAHs in humans. Overall, BbF's mutagenic effects are similar to benzo[ a ]pyrene, a well-studied mutagenic PAH. Our work showcases the utility of DS for effective mutagenicity assessment of environmental pollutants.

Synopsis

We used Duplex Sequencing to study the mutagenicity of benzo[ b ]fluoranthene across the mouse genome. Dose-dependent changes in mutation frequency and spectrum quantify its role in PAH-induced carcinogenicity.

Comparative Study of 1444 nm Laser Monotherapy versus Integrated Liposuction in the Treatment of Axillary Osmidrosis

Background and Objectives: The 1444 nm wavelength Neodymium:Yttrium-Aluminum-Garnet (Nd:YAG) laser treatment is an efficient method for treating axillary osmidrosis (AO); however, it has a relatively low treatment persistence. To address this issue, we performed integrated liposuction surgery with a laser to treat AO and compared the results with those of a group treated only with a laser. Materials and Methods: This study compared the outcomes of AO treatment between the two groups up to six months postoperatively. The first group of 18 patients underwent laser treatment alone, and the second group of 12 patients underwent integrated liposuction surgery in addition to laser treatment. Outcomes were assessed using the following variables: degree of malodor (DOM), sweating area, patient satisfaction, pain levels, and complications, such as burns, swelling, and contractures. Results: Compared to the laser-only group, the integrated liposuction group demonstrated significantly superior outcomes in terms of DOM (p = 0.002) and patient satisfaction (p = 0.006), as well as a reduction in the sweating area (p = 0.012). The pain rating was higher in the liposuction group, but the difference was not statistically significant (p = 0.054). Compared with the patients in the integrated liposuction treatment group, those in the laser treatment group exhibited a significantly higher number of burns under the axillae (p = 0.025). However, no significant differences were observed in the swelling or contracture between the groups. Conclusions: Integrated liposuction with laser therapy significantly improved treatment outcomes, including malodor, patient satisfaction, sweat test results, and decreased complication rates.

Molecular findings in patients for whole exome sequencing and mitochondrial genome assessment

OBJECTIVE

Whole exome sequencing (WES) is becoming more widely used as a diagnostic tool in the field of medicine. In this article, we reported the diagnostic yield of WES and mitochondrial genome assessment in 2226 consecutive cases in a single clinical laboratory.

MATERIALS AND METHODS

We retrospectively analyzed consecutive WES reports from 2226 patients with various genetic disorders. WES-process was focused exclusively on the probands and aimed at a higher diagnostic capacity. We determined the diagnostic rate of WES overall and by phenotypic category, mode of inheritance, mitochondrial genome variant, and copy number variants (CNVs).

RESULTS

Among the 2226 patients who had diagnostic WES proband-only, the overall diagnostic yield of WES was 34.59% (770/2226). The highest diagnostic yield was observed in autosomal dominant disorders, at 45.58% (351/770), followed by autosomal recessive at 31.95%(246/770), X-linked disorder at 9.61%(74/770), and mitochondrial diseases at a notably lower 0.65%(5/770). The 12.21% (94/770) diagnoses were based on a total of 94 copy number variants reported from WES data. CNVs in children accounted for 67.02% of the total CNVs. While majority of the molecular diagnoses were related to nuclear genes, the inclusion of mitochondrial genome sequencing in the WES test contributed to five diagnoses. all mitochondrial diseases were identified in adults.

CONCLUSIONS

The proband-only WES provided a definitive molecular diagnosis for 34.59% of a large cohort of patients while analysis of WES simultaneously analyzed the SNVs, exons, mitochondrial genome, and CNVs, thereby improving the diagnostic yield significantly compared to the single-detection WES method; and facilitating the identification of novel candidate genes.

Effects of Chemotherapy on Aneuploidy Rates in Sperm from Male Patients with Testicular Cancer or Hodgkin's Lymphoma-A Systematic Review

BACKGROUND

Testicular cancer and Hodgkin's lymphoma are prevalent malignancies among young males aged 20 to 39. The incidence of testicular cancer and lymphoma has risen in recent years, with orchiectomy often followed by adjuvant chemotherapy as the primary treatment for testicular cancer and chemotherapy for lymphoma. Chemotherapy has been associated with an increased risk of aneuploidy and reduced fertility.

METHOD

This systematic review included seven studies, both case-control and longitudinal prospective designs, from the PubMed, Embase, and Cochrane Library databases. The screening process was conducted using the online tool covidence.org.

RESULTS

The study outcomes indicate varied impacts of chemotherapy on aneuploidy rates. An increase in the aneuploidy rates, notably for the sex chromosomes, immediately post-treatment was a common trend, followed by a decline in pretreatment values.

CONCLUSION

This systematic review presents the effects of chemotherapy on the aneuploidy rates of testicular cancer and Hodgkin's lymphoma patients, with a decrease post-treatment. The findings underscore the need for larger, well-designed studies with a longer study period.

Severity of effect considerations regarding the use of mutation as a toxicological endpoint for risk assessment: A report from the 8th International Workshop on Genotoxicity Testing (IWGT)

Exposure levels without appreciable human health risk may be determined by dividing a point of departure on a dose-response curve (e.g., benchmark dose) by a composite adjustment factor (AF). An "effect severity" AF (ESAF) is employed in some regulatory contexts. An ESAF of 10 may be incorporated in the derivation of a health-based guidance value (HBGV) when a "severe" toxicological endpoint, such as teratogenicity, irreversible reproductive effects, neurotoxicity, or cancer was observed in the reference study. Although mutation data have been used historically for hazard identification, this endpoint is suitable for quantitative dose-response modeling and risk assessment. As part of the 8th International Workshops on Genotoxicity Testing, a sub-group of the Quantitative Analysis Work Group (WG) explored how the concept of effect severity could be applied to mutation. To approach this question, the WG reviewed the prevailing regulatory guidance on how an ESAF is incorporated into risk assessments, evaluated current knowledge of associations between germline or somatic mutation and severe disease risk, and mined available data on the fraction of human germline mutations expected to cause severe disease. Based on this review and given that mutations are irreversible and some cause severe human disease, in regulatory settings where an ESAF is used, a majority of the WG recommends applying an ESAF value between 2 and 10 when deriving a HBGV from mutation data. This recommendation may need to be revisited in the future if direct measurement of disease-causing mutations by error-corrected next generation sequencing clarifies selection of ESAF values.

Single nucleotide variants in lung cancer

Germline genetic variants, including single-nucleotide variants (SNVs) and copy number variants (CNVs), account for interpatient heterogeneity. In the past several decades, genome-wide association studies (GWAS) have identified multiple lung cancer-associated SNVs in Caucasian and Chinese populations. These variants either reside within coding regions and change the structure and function of cancer-related proteins or reside within non-coding regions and alter the expression level of cancer-related proteins. The variants can be used not only for cancer risk assessment and prevention but also for the development of new therapies. In this review, we discuss the lung cancer-associated SNVs identified to date, their contributions to lung tumorigenesis and prognosis, and their potential use in predicting prognosis and implementing therapeutic strategies.

Comprehensive Analysis of Novel Synergistic Antioxidant Formulations: Insights into Pharmacotechnical, Physical, Chemical, and Antioxidant Properties

(1) Background: Oxidative stress plays a pivotal role in the pathogenesis of various diseases, including neurodegenerative disorders, cardiovascular diseases, cancer, and diabetes, highlighting the pressing need for effective antioxidant interventions. (2) Methods: In this study, we aimed to develop and characterise two novel antioxidant formulations, F3 and F4, as therapeutic interventions for oxidative stress-related conditions. (3) Results: The physicochemical characterisation, preformulation analysis, formulation, preparation of filling powders for capsules, capsule content evaluation, and antioxidant activity assessment of the two novel antioxidant formulations were assessed. These formulations comprise a combination of well-established antioxidants like quercetin, biotin, coenzyme Q10, and resveratrol. Through comprehensive testing, the formulations' antioxidant efficacy, stability, and potential synergistic interactions were evaluated. (4) Conclusions: The findings underscore the promising potential of these formulations as therapeutic interventions for oxidative stress-related disorders and highlight the significance of antioxidant interventions in mitigating their progression.

DNA Released by Adeno-Associated Virus Strongly Alters Capsid Aggregation Kinetics in a Physiological Solution

While adeno-associated virus is a leading vector for gene therapy, significant gaps remain in understanding AAV degradation and stability. In this work, we study the degradation of an engineered AAV serotype at physiological pH and ionic strength. Viral particles of varying fractions of encapsulated DNA were incubated between 30 and 60 °C, with changes in molecular weight measured by changes in total light scattering intensity at 90° over time. Mostly full vectors demonstrated a rapid decrease in molecular weight corresponding to the release of capsid DNA, followed by slow aggregation. In contrast, empty vectors demonstrated immediate, rapid colloid-type aggregation. Mixtures of full and empty capsids showed a pronounced decrease in initial aggregation that cannot be explained by a linear superposition of empty and full degradation scattering signatures, indicating interactions between capsids and ejected DNA that influenced aggregation mechanisms. This demonstrates key interactions between AAV capsids and their cargo that influence capsid degradation, aggregation, and DNA release mechanisms in a physiological solution.

Integrative machine learning approaches for predicting disease risk using multi-omics data from the UK Biobank

We train prediction and survival models using multi-omics data for disease risk identification and stratification. Existing work on disease prediction focuses on risk analysis using datasets of individual data types (metabolomic, genomics, demographic), while our study creates an integrated model for disease risk assessment. We compare machine learning models such as Lasso Regression, Multi-Layer Perceptron, XG Boost, and ADA Boost to analyze multi-omics data, incorporating ROC-AUC score comparisons for various diseases and feature combinations. Additionally, we train Cox proportional hazard models for each disease to perform survival analysis. Although the integration of multi-omics data significantly improves risk prediction for 8 diseases, we find that the contribution of metabolomic data is marginal when compared to standard demographic, genetic, and biomarker features. Nonetheless, we see that metabolomics is a useful replacement for the standard biomarker panel when it is not readily available.

Distinct roles of CD244 expression in cancer diagnosis and prognosis: A pan-cancer analysis

The abnormal expression of tumor associated genes in pan-cancer is closely related to the clinicopathological features of distinct cancer types. Thus, identifying the role of specific genes in pan-cancer is needed for developing effective anti-cancer strategies. However, the function of CD244 in pan-cancer has not been fully understood. In this study, we explored the CD244 expression profile across 33 tumor types based on The Cancer Genome Atlas project, the Gene Expression Omnibus database, and other bioinformatics tools. We found down-regulated expression levels in seven tumor types and up-regulated expression levels in two tumor types. We subsequently explored the relationship between survival rate and CD244 expression, and found the positive relationship in patients with adrenocortical carcinoma (ACC), head and neck squamous cell carcinoma (HNSC), skin cutaneous melanoma (SKCM), and uterine corpus endometrial carcinoma (UCEC). We further investigated the association between CD244 expression and tumor-infiltrating immune cells, and discovered their positive correlation in different tumors. We found that CD244 expression level was higher in normal samples than in UCEC samples, and was positively associated with CD8+ T cells infiltrating. The mutation status, promoter methylation, CD244-related molecules and signaling pathways were also employed to study the potential function of CD244 in tumor initiation and progression. Our study offers a comprehensive overview of CD244 in human tumors, revealing CD244 as a potential prognostic biomarker and immunotherapeutic target in cancers.

Ultra-stable threose nucleic acid-based biosensors for rapid and sensitive nucleic acid detection and in vivo imaging

The human genome's nucleotide sequence variation, such as single nucleotide mutations, can cause numerous genetic diseases. However, detecting nucleic acids accurately and rapidly in complex biological samples remains a major challenge. While natural deoxyribonucleic acid (DNA) has been used as biorecognition probes, it has limitations like poor specificity, reproducibility, nuclease-induced enzymatic degradation, and reduced bioactivity on solid surfaces. To address these issues, we introduce a stable and reliable biosensor called graphene oxide (GO)- threose nucleic acid (TNA). It comprises chemically modified TNA capture probes on GO for detecting and imaging target nucleic acids in vitro and in vivo, distinguishing single nucleobase mismatches, and monitoring dynamic changes in target microRNA (miRNA). By loading TNA capture probes onto the GO substrate, the GO-TNA sensing platform for nucleic acid detection demonstrates a significant 88-fold improvement in the detection limit compared to TNA probes alone. This platform offers a straightforward preparation method without the need for costly and labor-intensive isolation procedures or complex chemical reactions, enabling real-time analysis. The stable TNA-based GO sensing nanoplatform holds promise for disease diagnosis, enabling rapid and accurate detection and imaging of various disease-related nucleic acid molecules at the in vivo level. STATEMENT OF SIGNIFICANCE: The study's significance lies in the development of the GO-TNA biosensor, which addresses limitations in nucleic acid detection. By utilizing chemically modified nucleic acid analogues, the biosensor offers improved reliability and specificity, distinguishing single nucleobase mismatches and avoiding false signals. Additionally, its ability to detect and image target nucleic acids in vivo facilitates studying disease mechanisms. The simplified preparation process enhances practicality and accessibility, enabling real-time analysis. The biosensor's potential applications extend beyond healthcare, contributing to environmental analysis and food safety. Overall, this study's findings have substantial implications for disease diagnosis, biomedical research, and diverse applications, advancing nucleic acid detection and its impact on various fields.

Most Monogenic Disorders Are Caused by Mutations Altering Protein Folding Free Energy

Revealing the molecular effect that pathogenic missense mutations have on the corresponding protein is crucial for developing therapeutic solutions. This is especially important for monogenic diseases since, for most of them, there is no treatment available, while typically, the treatment should be provided in the early development stages. This requires fast targeted drug development at a low cost. Here, we report an updated database of monogenic disorders (MOGEDO), which includes 768 proteins and the corresponding 2559 pathogenic and 1763 benign mutations, along with the functional classification of the corresponding proteins. Using the database and various computational tools that predict folding free energy change (ΔΔG), we demonstrate that, on average, 70% of pathogenic cases result in decreased protein stability. Such a large fraction indicates that one should aim at in silico screening for small molecules stabilizing the structure of the mutant protein. We emphasize that knowledge of ΔΔG is essential because one wants to develop stabilizers that compensate for ΔΔG, but do not make protein over-stable, since over-stable protein may be dysfunctional. We demonstrate that, by using ΔΔG and predicted solvent exposure of the mutation site, one can develop a predictive method that distinguishes pathogenic from benign mutations with a success rate even better than some of the leading pathogenicity predictors. Furthermore, hydrophobic-hydrophobic mutations have stronger correlations between folding free energy change and pathogenicity compared with others. Also, mutations involving Cys, Gly, Arg, Trp, and Tyr amino acids being replaced by any other amino acid are more likely to be pathogenic. To facilitate further detection of pathogenic mutations, the wild type of amino acids in the 768 proteins mentioned above was mutated to other 19 residues (14,847,817 mutations), the ΔΔG was calculated with SAAFEC-SEQ, and 5,506,051 mutations were predicted to be pathogenic.

Consanguineous Marriage and Its Association With Genetic Disorders in Saudi Arabia: A Review

Consanguineous marriages, where spouses are related by blood, have been a longstanding practice in human history. The primary medical concern with consanguineous marriages is the increased risk of genetic disorders. When closely related individuals reproduce, there is a higher probability that both parents carry the same genetic mutation. In Arab countries, especially Saudi Arabia, the rate of consanguineous marriage is high compared with Western European and Asian countries. This high rate is directly proportionate with elevated risk of genetic disorders, including congenital heart diseases, renal diseases, and rare blood disorders. Additionally, it was noted that the rate of negative postnatal outcomes is higher in consanguineous marriages compared with the general population. These observations indicate the necessity of tackling this area and highlighting the consequences of this practice. In this review, we aim to discuss the current evidence regarding the association between consanguineous marriages and genetic disorders in Saudi Arabia.

Systematic analysis and evaluation of chromosome aberrations in major birth defects associated with infertility

Previous studies have indicated an elevated risk of infertility in certain birth defects, including congenital heart disease (CHD), hypospadias, cryptorchidism, and disorders of sexual development (DSD). Although the identification of chromosomal abnormalities or chromosomal aberrations (CAs) is crucial for the diagnosis of these conditions, the assessment of CAs in these disorders remains unclear, and few large-scale studies have been conducted at multiple centers. The aim of the current study was to systematically evaluate the prevalence of CAs in CHD, hypospadias, cryptorchidism, and DSD. Studies reporting CAs in these birth defects were retrospectively analyzed from 1991- 2023, using online databases such as PubMed and Google scholar as well as preprints and references from related literature. Comprehensive screening, data acquisition, and systematic assessments of the identified literature were performed. Ultimately, searches yielded a total of 7,356 samples from 14 published articles on CHD, 298 hypospadias cases from 4 published articles, 1,681 cryptorchidism cases from 4 published articles, and 2,876 DSD cases from 7 published articles. Carrier rates of CAs varied widely among these studies and conditions. A retrospective analysis revealed that CHD was associated with the highest carrier rate (26%) for CAs, followed by DSD (21%), hypospadias (9%), and cryptorchidism (5%). A subtype analysis of CAs indicated a higher prevalence of numerical abnormalities among the reported cases. Therefore, considering CAs in birth defects associated with infertility is imperative. This provides a foundation for the further clinical implementation of chromosomal screening and enhancing high-risk screening for individuals in the real world.

Lipid nanoparticles: The game-changer in CRISPR-Cas9 genome editing

The steady progress in genome editing, especially genome editing based on the use of clustered regularly interspaced short palindromic repeats (CRISPR) and programmable nucleases to make precise modifications to genetic material, has provided enormous opportunities to advance biomedical research and promote human health. However, limited transfection efficiency of CRISPR-Cas9 poses a substantial challenge, hindering its wide adoption for genetic modification. Recent advancements in nanoparticle technology, specifically lipid nanoparticles (LNPs), offer promising opportunities for targeted drug delivery. LNPs are becoming popular as a means of delivering therapeutics, including those based on nucleic acids and mRNA. Notably, certain LNPs, such as Polyethylene glycol-phospholipid-modified cationic lipid nanoparticles and solid lipid nanoparticles, exhibit remarkable potential for efficient CRISPR-Cas9 delivery as a gene editing instrument. This review will introduce the molecular mechanisms and diverse applications of the CRISPR/Cas9 gene editing system, current strategies for delivering CRISPR/Cas9-based tools, the advantage of LNPs for CRISPR-Cas9 delivery, an overview of strategies for overcoming off-target genome editing, and approaches for improving genome targeting and tissue targeting. We will also highlight current developments and recent clinical trials for the delivery of CRISPR/Cas9. Finally, future directions for overcoming the limitations and adaptation of this technology for clinical trials will be discussed.

RLP system: A single-tube two-step approach with dual amplification cascades for rapid identification of EGFR T790M

BACKGROUND

The detection of cancer gene mutations in biofluids plays a pivotal role in revolutionizing disease diagnosis. The presence of a large background of wild-type sequences poses a challenge to liquid biopsy of tumor mutation genes. Suppressing the detection of wild-type sequences can reduce their interference, however, due to the minimal difference between mutant and wild-type sequences (such as single nucleotide variants differing by only one nucleotide), how to suppress the detection of wild-type sequences to the greatest extent without compromising the sensitivity of mutant sequence detection remains to be explored.

SIGNIFICANCE

The RLP system addresses the incompatibility between RPA and RT-PCR reactions through a physical separation strategy. Besides, due to the remarkable flexibility of locked nucleic acid probes, the RLP system emerges as a potent tool for detecting mutations across diverse genes. It excels in sensitivity and speed, tolerates plasma matrix, and is cost-effective. This bodes well for advancing the field of precision medicine.

RESULTS

The recombinase-assisted locked nucleic acid (LNA) probe-mediated dual amplification biosensing platform (namely RLP), which combines recombinase polymerase amplification (RPA) and LNA clamp PCR method in one tube, enabling highly sensitive and selective detection of EGFR T790M mutation under the help of well-designed LNA probes. This technique can quantify DNA targets with a limit of detection (LoD) at the single copy level and identify point mutation with mutant allelic fractions as low as 0.007 % in 45 min. Moreover, RLP has the potential for the direct detection of plasma samples without the need for nucleic acid extraction and the cost of a single test is less than 1USD. Furthermore, the RLP system is a cascading dual amplification reaction conducted in a single tube, which eliminates the risk of cross-contamination associated with opening multiple tubes and ensures the reliability of the results.

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup

OBJECTIVE

Given the importance AI in genomics and its potential impact on human health, the American Medical Informatics Association-Genomics and Translational Biomedical Informatics (GenTBI) Workgroup developed this assessment of factors that can further enable the clinical application of AI in this space.

PROCESS

A list of relevant factors was developed through GenTBI workgroup discussions in multiple in-person and online meetings, along with review of pertinent publications. This list was then summarized and reviewed to achieve consensus among the group members.

CONCLUSIONS

Substantial informatics research and development are needed to fully realize the clinical potential of such technologies. The development of larger datasets is crucial to emulating the success AI is achieving in other domains. It is important that AI methods do not exacerbate existing socio-economic, racial, and ethnic disparities. Genomic data standards are critical to effectively scale such technologies across institutions. With so much uncertainty, complexity and novelty in genomics and medicine, and with an evolving regulatory environment, the current focus should be on using these technologies in an interface with clinicians that emphasizes the value each brings to clinical decision-making.

Human DNA Mutations and their Impact on Genetic Disorders

DNA is a remarkably precise medium for copying and storing biological information. It serves as a design for cellular machinery that permits cells, organs, and even whole organisms to work. The fidelity of DNA replication results from the action of hundreds of genes involved in proofreading and damage repair. All human cells can acquire genetic changes in their DNA all over life. Genetic mutations are changes to the DNA sequence that happen during cell division when the cells make copies of themselves. Mutations in the DNA can cause genetic illnesses such as cancer, or they could help humans better adapt to their environment over time. The endogenous reactive metabolites, therapeutic medicines, and an excess of environmental mutagens, such as UV rays all continuously damage DNA, compromising its integrity. One or more chromosomal alterations and point mutations at a single site (monogenic mutation) including deletions, duplications, and inversions illustrate such DNA mutations. Genetic conditions can occur when an altered gene is inherited from parents, which increases the risk of developing that particular condition, or some gene alterations can happen randomly. Moreover, symptoms of genetic conditions depend on which gene has a mutation. There are many different diseases and conditions caused by mutations. Some of the most common genetic conditions are Alzheimer's disease, some cancers, cystic fibrosis, Down syndrome, and sickle cell disease. Interestingly, scientists find that DNA mutations are more common than formerly thought. This review outlines the main DNA mutations that occur along the human genome and their influence on human health. The subject of patents pertaining to DNA mutations and genetic disorders has been brought up.

Genetic counselling considerations with genetic/genomic testing in Neonatal and Pediatric Intensive Care Units: A scoping review

Genetic and genomic technologies can effectively diagnose numerous genetic disorders. Patients benefit when genetic counselling accompanies genetic testing and international guidelines recommend pre- and post-test genetic counselling with genome-wide sequencing. However, there is a gap in knowledge regarding the unique genetic counselling considerations with different types of genetic testing in the Neonatal Intensive Care Unit (NICU) and the Pediatric Intensive Care Unit (PICU). This scoping review was conducted to identify the gaps in care with respect to genetic counselling for infants/pediatric patients undergoing genetic and genomic testing in NICUs and PICUs and understand areas in need of improvement in order to optimize clinical care for patients, caregivers, and healthcare providers. Five databases (MEDLINE [Ovid], Embase [Ovid], PsycINFO [Ebsco], CENTRAL [Ovid], and CINHAL [Ebsco]) and grey literature were searched. A total of 170 studies were included and used for data extraction and analysis. This scoping review includes descriptive analysis, followed by a narrative account of the extracted data. Results were divided into three groups: pre-test, post-test, and comprehensive (both pre- and post-test) genetic counselling considerations based on indication for testing. More studies were conducted in the NICU than the PICU. Comprehensive genetic counselling was discussed in only 31% of all the included studies demonstrating the need for both pre-test and post-test genetic counselling for different clinical indications in addition to the need to account for different cultural aspects based on ethnicity and geographic factors.

The Impact of Increased Homozygosity on Human Fertility: A Comprehensive Review

This comprehensive review explores the multifaceted relationship between increased homozygosity and human fertility, delving into the genetic, ethical, cultural, and public health dimensions of this complex phenomenon. Homozygosity, characterized by identical alleles at specific gene loci, can result from consanguineous marriages, genetic drift, and population isolation. The review highlights key findings, including the heightened risk of recessive genetic disorders, the implications for immune system diversity, and the influence on complex traits and diseases. It underscores the critical role of genetic counseling in addressing these consequences, considering the ethical implications, and respecting cultural practices. The delicate balance between genetic diversity and cultural norms is emphasized, calling for increased awareness and community engagement. Looking ahead, the review suggests emerging technologies, longitudinal studies, and interdisciplinary research as crucial avenues for further exploration, with the ultimate goal of informing effective public health policies and interventions that safeguard genetic diversity and cultural traditions for future generations.

Relation of Life's Essential 8 to the genetic predisposition for cardiovascular outcomes and all-cause mortality: results from a national prospective cohort

AIMS

To evaluate the independent, mediating, interactive, and associated effects of Life's Essential 8 (LE8) and genetic predisposition on the risk of cardiovascular outcomes and all-cause mortality.

METHODS AND RESULTS

We retrieved a total of 254 783 individuals from the UK Biobank. LE8 was determined by eight metrics (nicotine exposure, physical activity, diet, sleep, body mass index, blood pressure, blood glucose, and blood lipids), and was characterized as low, moderate, and high cardiovascular health (CVH). Genetic predisposition was estimated using the polygenic risk score (PRS). Cox regressions were performed to evaluate the associations between LE8, PRS, and outcomes. During a median follow-up of 12.53 years, all-cause mortality occurred in 10 257 of 197 473 participants, cardiovascular mortality in 2074 of 215 675, and incident cardiovascular disease (CVD) in 71 774 of 215 675. Individuals with moderate or high CVH experienced a lower risk [hazard ratios (HRs) 0.33 to 0.81] of adverse health outcomes compared with their counterparts with low CVH. A substantial proportion (16.1∼69.8%) of health outcomes could be attributable to moderate or high LE8, and up to 51.2% of the associations between PRS and adverse outcomes were mediated by LE8. In high PRS group, individuals with high CVH had lower CVD mortality (HR: 0.26, 95% confidence interval: 0.18, 0.39), compared to those with low CVH.

CONCLUSION

Ideal CVH was associated with lower risks of cardiovascular outcomes and all-cause mortality, with a more pronounced association observed in individuals with high PRS for CVD. Improving CVH according to LE8 guidelines should be encouraged, especially for those with PRS that indicate high CVD risk.

The downstream bioprocess toolbox for therapeutic viral vectors

Viral vectors are poised to acquire a prominent position in modern medicine and biotechnology owing to their role as delivery agents for gene therapies, oncolytic agents, vaccine platforms, and a gateway to engineer cell therapies as well as plants and animals for sustainable agriculture. The success of viral vectors will critically depend on the availability of flexible and affordable biomanufacturing strategies that can meet the growing demand by clinics and biotech companies worldwide. In this context, a key role will be played by downstream process technology: while initially adapted from protein purification media, the purification toolbox for viral vectors is currently undergoing a rapid expansion to fit the unique biomolecular characteristics of these products. Innovation efforts are articulated on two fronts, namely (i) the discovery of affinity ligands that target adeno-associated virus, lentivirus, adenovirus, etc.; (ii) the development of adsorbents with innovative morphologies, such as membranes and 3D printed monoliths, that fit the size of viral vectors. Complementing these efforts are the design of novel process layouts that capitalize on novel ligands and adsorbents to ensure high yield and purity of the product while safeguarding its therapeutic efficacy and safety; and a growing panel of analytical methods that monitor the complex array of critical quality attributes of viral vectors and correlate them to the purification strategies. To help explore this complex and evolving environment, this study presents a comprehensive overview of the downstream bioprocess toolbox for viral vectors established in the last decade, and discusses present efforts and future directions contributing to the success of this promising class of biological medicines.

Most monogenic disorders are caused by mutations altering protein folding free energy

Revealing the molecular effect that pathogenic missense mutations cause on the corresponding protein is crucial for developing therapeutic solutions. This is especially important for monogenic diseases since, for most of them, there is no treatment available, while typically, the treatment should be provided in the early development stages. This requires fast, targeted drug development at a low cost. Here, we report a database of monogenic disorders (MOGEDO), which includes 768 proteins, the corresponding 2559 pathogenic and 1763 benign mutations, along with the functional classification of the corresponding proteins. Using the database and various computational tools that predict folding free energy change (ΔΔG), we demonstrate that, on average, 70% of pathogenic cases result in decreased protein stability. Such a large fraction indicates that one should aim at in-silico screening for small molecules stabilizing the structure of the mutant protein. We emphasize that knowledge of ΔΔG is essential because one wants to develop stabilizers that compensate for ΔΔG but not to make protein over-stable since over-stable protein may be dysfunctional. We demonstrate that using ΔΔG and predicted solvent exposure of the mutation site; one can develop a predictive method that distinguishes pathogenic from benign mutation with a success rate even better than some of the leading pathogenicity predictors. Furthermore, hydrophobic-hydrophobic mutations have stronger correlations between folding free energy change and pathogenicity compared with others. Also, mutations involving Cys, Gly, Arg, Trp and Tyr amino acids being replaced by any other amino acid are more likely to be pathogenic. To facilitate further detection of pathogenic mutations, the wild type of amino acids in the 768 proteins mentioned above was mutated to other 19 residues (14,847,817 mutations), and the ΔΔG was calculated with SAAFEC-SEQ, and 5,506,051 mutations were predicted to be pathogenic.

da Silva C, de Castro Michelassi G, Brentani H, Nunes FL, Machado-Lima A. Computer aided diagnosis of neurodevelopmental disorders and genetic syndromes based on facial images - A systematic literature review

Neurodevelopment disorders can result in facial dysmorphisms. Therefore, the analysis of facial images using image processing and machine learning techniques can help construct systems for diagnosing genetic syndromes and neurodevelopmental disorders. The systems offer faster and cost-effective alternatives for genotyping tests, particularly when dealing with large-scale applications. However, there are still challenges to overcome to ensure the accuracy and reliability of computer-aided diagnosis systems. This article presents a systematic review of such initiatives, including 55 articles. The main aspects used to develop these diagnostic systems were discussed, namely datasets - availability, type of image, size, ethnicities and syndromes - types of facial features, techniques used for normalization, dimensionality reduction and classification, deep learning, as well as a discussion related to the main gaps, challenges and opportunities.

DisVar: an R library for identifying variants associated with diseases using large-scale personal genetic information

Background

Genetic variants may potentially play a contributing factor in the development of diseases. Several genetic disease databases are used in medical research and diagnosis but the web applications used to search these databases for disease-associated variants have limitations. The application may not be able to search for large-scale genetic variants, the results of searches may be difficult to interpret and variants mapped from the latest reference genome (GRCH38/hg38) may not be supported.

Methods

In this study, we developed a novel R library called "DisVar" to identify disease-associated genetic variants in large-scale individual genomic data. This R library is compatible with variants from the latest reference genome version. DisVar uses five databases of disease-associated variants. Over 100 million variants can be simultaneously searched for specific associated diseases.

Results

The package was evaluated using 24 Variant Call Format (VCF) files (215,054 to 11,346,899 sites) from the 1000 Genomes Project. Disease-associated variants were detected in 298,227 hits across all the VCF files, taking a total of 63.58 m to complete. The package was also tested on ClinVar's VCF file (2,120,558 variants), where 20,657 hits associated with diseases were identified with an estimated elapsed time of 45.98 s.

Conclusions

DisVar can overcome the limitations of existing tools and is a fast and effective diagnostic and preventive tool that identifies disease-associated variations from large-scale genetic variants against the latest reference genome.

Documentation and prevalence of prenatal and neonatal outcomes in a cohort of individuals with KBG syndrome

Ankyrin Repeat Domain 11 (ANKRD11) gene mutations are associated with KBG syndrome, a developmental disability that affects multiple organ systems. The function of ANKRD11 in human growth and development is not clear, but gene knockout or mutation are lethal in mice embryos and/or pups. In addition, it plays a vital role in chromatin regulation and transcription. Individuals with KBG syndrome are often misdiagnosed or remain undiagnosed until later in life. This is largely due to KBG syndrome's varying and nonspecific phenotypes as well as a lack of accessible genetic testing and prenatal screening. This study documents perinatal outcomes for individuals with KBG syndrome. We obtained data from 42 individuals through videoconferences, medical records, and emails. 45.2% of our cohort was born by C-section, 33.3% had a congenital heart defect, 23.8% were born prematurely, 23.8% were admitted to the NICU, 14.3% were small for gestational age, and 14.3% of the families had a history of miscarriage. These rates were higher in our cohort compared to the overall population, including non-Hispanic and Hispanic populations. Other reports included feeding difficulties (21.4%), neonatal jaundice (14.3%), decreased fetal movement (7.1%), and pleural effusions in utero (4.7%). Comprehensive perinatal studies about KBG syndrome and updated documentation of its phenotypes are important in ensuring prompt diagnosis and can facilitate correct management.