Clinical Genetic Research Research Articles

SV4GD: a comprehensive structural variation database specially for genetic diseases.

Structural variations (SVs) contribute to a large extent to genomic diversity and are highly relevant for various human genetic diseases. The sensitivity and specificity of SV identification have significantly improved with the development and widespread application of high-throughput sequencing, making clinical diagnosis and treatment more accurate. Therefore, the SV4GD (Structural Variation for Genetic Diseases, https://bio-computing.hrbmu.edu.cn/SV4GD/), a manually curated database, was constructed to provide a comprehensive, standardized and user-friendly data resource for selective batch browsing, searching, downloading and comparing those genetic disease-relevant SVs. This database compiles 10 305 records of germline structural variants from 58 human neoplastic diseases and 232 non-neoplastic genetic diseases, including 2695 disease-related SVs, and other 7610 pending research SVs detected from patients. SV4GD provides a browser and search engine to query for the detailed information of SVs, human genetic diseases and the clinical information of patients, providing an easy-to-use online tool for clinical and molecular genetics research.

Short Tandem Repeats in the era of next-generation sequencing: from historical loci to population databases.

In this study, we explore the landscape of short tandem repeats (STRs) within the human genome through the lens of evolving technologies to detect genomic variations. STRs, which encompass approximately 3% of our genomic DNA, are crucial for understanding human genetic diversity, disease mechanisms, and evolutionary biology. The advent of high-throughput sequencing methods has revolutionized our ability to accurately map and analyze STRs, highlighting their significance in genetic disorders, forensic science, and population genetics. We review the current available methodologies for STR analysis, the challenges in interpreting STR variations across different populations, and the implications of STRs in medical genetics. Our findings underscore the urgent need for comprehensive STR databases that reflect the genetic diversity of global populations, facilitating the interpretation of STR data in clinical diagnostics, genetic research, and forensic applications. This work sets the stage for future studies aimed at harnessing STR variations to elucidate complex genetic traits and diseases, reinforcing the importance of integrating STRs into genetic research and clinical practice.

Twinning for the Armenian research infrastructure on cancer research

The incidence of cancer is expected to rise globally, with low-and middle-income countries affected disproportionally. One of those countries, Armenia, also faces the challenge of exhibiting one of the lowest research and scientific publication rates within Europe on cancer research. This report presents the experiences of the Twinning for the Armenian Research Infrastructure on Cancer Research (ARICE) program, funded by the European Commission from 2019 – 2024. The project brought together experts from three leading research-intensive, cancer centres: the Medical University of Graz, Austria; the Charles University, Czechia; and the International Agency for Research on Cancer, World Health Organization (IARC/WHO), in partnership with the Yerevan State Medical University. The aim was to enhance the research capacity in Armenia in the field of infrastructure development for clinical genetic research, in particular targeting the collection and use of biological materials, and the data integration for downstream analyses in relation to chronic, non-communicable diseases such as cancer. To this end, training initiatives and educational programmes were developed throughout the duration of the grant and are discussed within their local context.

РАСПРЕДЕЛЕНИЕ ГЕНОТИПОВ ГЕНА SLC2A9, УРОВЕНЬ МОЧЕВОЙ КИСЛОТЫ И МЕТАБОЛИТЫ ПУРИНОВОГО ОБМЕНА У ПАЦИЕНТОВ С АРТЕРИАЛЬНОЙ ГИПЕРТЕНЗИЕЙ И ФИБРИЛЛЯЦИЕЙ ПРЕДСЕРДИЙ

The aim is to investigate the frequency of genotypes and alleles of the SLC2A9 gene rs734553 polymorphism, the level of serum uric acid (sUA) and metabolites of purine metabolism in patients with arterial hypertension (AH) and atrial fibrillation (AF), as well as in healthy individuals. Material and methods. The study included 154 patients: 50 were healthy individuals (group 0), of which 22 (44%) were men and 28 (56%) were women aged 50 [45;53] years and 104 were patients with AH and AF (main group), of which 94 (90.4%) were men and 10 (9.6%) were women aged 55 [45; 61] years. The main group was divided into subgroups: subgroup I – patients with AF without a history of AH and other rhythm disorders (n=13); subgroup II – patients with AH in combination with AF (n=68); subgroup III – patients with AH without a history of AF or other rhythm disturbances (n=23). Hyperuricemia was detected in 34 (22.1%) patients, normal uric acid levels were revealed in 120 (77.9%) patients. All patients were studied using clinical, laboratory, instrumental and molecular genetic research methods. The level of sUA was determined by the enzymatic colorimetric method. Serum xanthine oxidase was measured using a method based on a solid phase sandwich-type enzyme-linked immunosorbent assay. Metabolites of purine metabolism in blood plasma were measured using the method of high-performance liquid chromatography. The SLC2A9 gene rs734553 polymorphism was determined using the polymerase chain reaction with real-time detection of results. Results. The patients with AH and AF, as compared to healthy individuals, had more severe disturbances of purine metabolism, characterized by higher concentration of sUA (330 [283; 412] µmol/l and 197 [161; 229] µmol/l (p<0.001), respectively). Also, in contrast to the group of healthy individuals, the group of patients with AH and AF demonstrated an increase in the level of adenosine (p=0.001), and a decrease in the levels of hypoxanthine and xanthine (p<0.001). There were no statistically significant differences in xanthine oxidase activity level (p>0.05), however, in 54% of patients in the main group it was higher than normal values. The dominant allele A and the dominant genotype A/A of the SLC2A9 gene rs734553 polymorphism (75%, p=0.005; 64%, p=0.001, respectively) occurred significantly more often in healthy individuals, while the recessive allele C and the heterozygous genotype A/C were found significantly more often in the group of patients with AH and AF (41.3%, p=0.005; 48.1%, p=0.003, respectively). The C/C genotype (41.7%, p=0.001) was significantly more common in patients with AH in combination with AF and hyperuricemia, compared to patients with AH combined with AF without hyperuricemia as well as healthy individuals (6.8%; 14%, p=0.001, respectively). Patients with AH in combination with AF and the C/C genotype were characterized by a significantly higher level of sUA (p=0.003) compared to patients with the A/A genotype. Conclusions. A statistically significant predominance of the recessive allele C of the SLC2A9 gene rs734553 polymorphism was established in patients with AH and AF compared with healthy individuals (p=0.005). In patients with AH in combination with AF and hyperuricemia, the C/C genotype was significantly more common (41.7%, p=0.001). Patients with AH in combination with AF and the C/C genotype were characterized by a significantly higher level of sUA (p=0.003) compared to patients with the A/A genotype.

Патогенез и морфогенез хронического асептического остеомиелита

Chronic nonbacterial (recurrent) osteomyelitis is a rare inflammatory disease of the musculoskeletal system with unknown etiology described in 1972 by A. Gidion et al. as subacute or chronic symmetrical osteomyelitis. This article reviews literature on pathogenesis and morphology of the disease and studies balance violation of pro- and anti-inflammatory cytokines and its association with osteolysis. Morphological manifestations in bone biopsies are given. We describe necrosis and thinning of trabeculae in combination with sclerosis of intertrabecular spaces and pronounced lymphohistiocytic infiltration with a large number of osteoclasts. Due to the absence of specific signs, the necessity of clinical and morphological correlations and genetic research in differential diagnosis is emphasized. Keywords: chronic nonbacterial osteomyelitis, chronic recurrent osteomyelitis, autoinflammatory disease

Unraveling the Complexity of Apert Syndrome: Genetics, Clinical Insights, and Future Frontiers.

Apert syndrome (AS), also known as type I acrocephalosyndactyly, is a rare congenital condition characterized by craniosynostosis resulting from missense mutations in the fibroblast growth factor receptor 2 (FGFR2) gene. This comprehensive review delves into AS, covering its clinical manifestations, genetics, diagnosis, medical management, psychosocial considerations, and future research directions. AS presents with distinct features, including a brachycephalic skull, midface hypoplasia, and limb anomalies such as syndactyly. It follows an autosomal dominantinheritance pattern with mutations in the FGFR2 gene. Prenatal diagnosis is possible through advanced imaging techniques and molecular testing. The multidisciplinary approach to AS management involves surgical interventions, orthodontics, and psychological support. Although no curative treatment exists, early interventions can significantly improve function and aesthetics. The quality of life for AS patients is influenced by psychosocial factors, necessitating comprehensive support for both patients and their families. Future research directions include gene therapy, understanding cellular responses to FGFR2 mutations, and addressing genetic heterogeneity. Collaborative efforts are vital to advancing knowledge about AS and its genetic underpinnings. Overall, this review serves as a valuable resource for healthcare professionals, educators, and researchers, contributing to a deeper understanding of AS and facilitating advancements in diagnosis and treatment.

Prediction of neuropathologic lesions from clinical data.

Post-mortem analysis provides definitive diagnoses of neurodegenerative diseases; however, only a few can be diagnosed during life. This study employed statistical tools and machine learning to predict 17 neuropathologic lesions from a cohort of 6518 individuals using 381 clinical features (Table S1). The multisite data allowed validation of the model's robustness by splitting train/test sets by clinical sites. A similar study was performed for predicting Alzheimer's disease (AD) neuropathologic change without specific comorbidities. Prediction results show high performance for certain lesions that match or exceed that of research annotation. Neurodegenerative comorbidities in addition to AD neuropathologic change resulted in compounded, but disproportionate, effects across cognitive domains as the comorbidity number increased. Certain clinical features could be strongly associated with multiple neurodegenerative diseases, others were lesion-specific, and some were divergent between lesions. Our approach could benefit clinical research, and genetic and biomarker research by enriching cohorts for desired lesions.

Doubly bi-allelic variants of MTHFR and MTHFD1 in a Chinese patient with hyperhomocysteinemia and failure of folic acid therapy.

Background: Hyperhomocysteinemia (HHcy) is a risk factor for thromboembolic disease. Defects in one-carbon metabolism (1-CM)-related genes, such as methylenetetrahydrofolate reductase (MTHFR), methylenetetrahydrofolate dehydrogenase, cyclohydrolase, and formyltetrahydrofolate synthetase 1 (MTHFD1), can cause HHcy and may also affect the efficacy of folic acid therapy. The details of mechanisms are yet to be further investigated. Method: We described a Chinese family with hereditary HHcy. The proband suffered from severe thromboembolic disease and experienced failure of folic acid therapy. Two sons of the proband were also diagnosed with HHcy but were sensitive to folic acid therapy. Whole-exome sequencing (WES) was conducted to evaluate the genetic lesion of this family. Results: Compound heterozygous variants (a common polymorphism, p. A222V, and a novel variant, p. C631*fs*1) of the MTHFR gene and a homozygous missense variant (p. K134R) of the MTHFD1 gene were identified in the proband. The two sons, with successful intervention, only harbored the homozygous p. A222V variant of the MTHFR gene. Conclusion: The clinical manifestations and genetic research synergistically confirmed the diagnosis of HHcy and clarified the failure of folic acid therapy in the proband caused by doubly bi-allelic variants of the MTHFR and MTHFD1 genes. Our study increased our understanding of the molecular basis of 1-CM-related gene defects on folic acid therapy in HHcy.

Update Research in Psoriasis

Psoriasis is now more recognized as a chronic-lymphocyte mediated inflammatory and proliferous skin disease. In European countries, the prevalence of psoriasis is 1%~3%, so the study of psoriasis is very important. With the study of immune pathogenesis and the progress of genetic engineering technology, it has been gradually developed a wide range of biological agents, And achieved good results in clinical trials or clinical treatment. This paper discusses the typical clinical manifestations, genetic research and treatment of psoriasis.

Successful integration of newborn genetic testing into UK routine screening using prospective consent to determine eligibility for clinical trials

ObjectiveINGR1D (INvestigating Genetic Risk for type 1 Diabetes) was a type 1 diabetes (T1D) genetic screening study established to identify participants for a primary prevention trial (POInT, Primary Oral Insulin...

The cannabinoid antagonist, AM251 attenuates ataxia related deficiencies in a cerebellar ataxic model

Aim: Disruption in cerebellar inputs, as well as dysfunction of Purkinje cells (PCs), causes a change in the timing of electrical signaling in the cerebellum resulting in disorders such as cerebellar ataxia. Although much clinical and molecular genetics research has been conducted to understand this disorder, there is no specific treatment for cerebellar ataxia. As cannabinoid type 1 receptors (CB1Rs) are highly expressed in the cerebellum and have been suggested as a therapeutic strategy, we determined whether AM251, a cannabinoid receptor antagonist, was neuroprotective of PCs in a rat cerebellar ataxic model.Materials and methods: To this end, we conducted behavioral and histological tests in the 3-acetylpyridine (3AP) rat cerebellar ataxia model, to explore whether AM251 was protective against induction of ataxia and cell death.Results: Rats with chemical degeneration of the inferior olive induced by 3AP (55 mg/kg, i.p.) clearly showed cerebellar ataxic symptoms. The locomotor activity and motor coordination of the ataxic animals were clearly disrupted compared to the control group. Further, histological analysis showed cell death and PCs degenerated with loss of cell membrane integrity associated with 3AP. Pre-treatment by AM251 improved the locomotor activity of the ataxic animals, and AM251 almost prevented PCs neuronal degeneration.Conclusion: Our data which show protection of cerebellar PCs and motor improvement in the ataxic rat model by treatment with AM251 suggests that targeting cannabinoid receptors should be considered for therapeutic intervention in cerebellar ataxia. HIGHLIGHTS: AM251 was protective against induction of ataxia and cell death. CBR antagonist typically ameliorated 3AP induced Ataxia. AM251 affected explorative and gait disturbances induced by 3AP. CBR antagonist improved impairments of anxiety-like behaviors following 3AP

FVC as an adaptive and accurate method for filtering variants from popular NGS analysis pipelines

The quality control of variants from whole-genome sequencing data is vital in clinical diagnosis and human genetics research. However, current filtering methods (Frequency, Hard-Filter, VQSR, GARFIELD, and VEF) were developed to be utilized on particular variant callers and have certain limitations. Especially, the number of eliminated true variants far exceeds the number of removed false variants using these methods. Here, we present an adaptive method for quality control on genetic variants from different analysis pipelines, and validate it on the variants generated from four popular variant callers (GATK HaplotypeCaller, Mutect2, Varscan2, and DeepVariant). FVC consistently exhibited the best performance. It removed far more false variants than the current state-of-the-art filtering methods and recalled ~51-99% true variants filtered out by the other methods. Once trained, FVC can be conveniently integrated into a user-specific variant calling pipeline.

Results and lessons from dual extraction of DNA and RNA from formalin-fixed paraffin-embedded breast tumor tissues for a large Cancer epidemiologic study

BackgroundThe use of archived formalin-fixed paraffin-embedded (FFPE) tumor tissues has become a common practice in clinical and epidemiologic genetic research. Simultaneous extraction of DNA and RNA from FFPE tissues is appealing but can be practically challenging. Here we report our results and lessons learned from processing FFPE breast tumor tissues for a large epidemiologic study.MethodsQiagen AllPrep DNA/RNA FFPE kit was adapted for dual extraction using tissue punches or sections from breast tumor tissues. The yield was quantified using Qubit and fragmentation analysis by Agilent Bioanalyzer. A subset of the DNA samples were used for genome-wide DNA methylation assays and RNA samples for sequencing. The QC metrices and performance of the assays were analyzed with pre-analytical variables.ResultsA total of 1859 FFPE breast tumor tissues were processed. We found it critical to adjust proteinase K digestion time based on tissue volume to achieve balanced yields of DNA and RNA. Tissue punches taken from tumor-enriched regions provided the most reliable output. A median of 1475 ng DNA and 1786 ng RNA per sample was generated. The median DNA integrity number (DIN) was 3.8 and median DV200 for RNA was 33.2. Of 1294 DNA samples used in DNA methylation assays, 97% passed quality check by qPCR and 92% generated data deemed high quality. Of the 130 RNA samples with DV200 ≥ 20% used in RNA-sequencing, all but 5 generated usable transcriptomic data with a mapping rate ≥ 60%.ConclusionsDual DNA/RNA purification using Qiagen AllPrep FFPE extraction protocol is feasible for clinical and epidemiologic studies. We recommend tissue punches as a reliable source material and fine tuning of proteinase K digestion time based on tissue volume.ImpactOur protocol and recommendations may be adapted by future studies for successful extraction of archived tumor tissues.

Publication trends of research on conjunctival melanoma during 1997-2022: A 25-year bibliometric study.

BackgroundConjunctival melanoma (CM) is a life-threatening ocular tumor with a high rate of local recurrence and metastasis. Our objective is to analyze research trends in CM field and compare contributions from different countries, institutions and authors.MethodsWe extracted all CM-related publications published from 1997 to 2022 from the Web of Science database and applied Microsoft Excel and VOSviewer to review publication data, analyze publication trends, and visualize relevant data.ResultsA total of 708 publications were identified. The United States contributed the most publications (280) and citations (8,781 times) with the highest H-index value (47). The Ophthalmic Plastic and Reconstructive Surgery, British Journal of Ophthalmology, American Journal of Ophthalmology and Cornea were the most productive journal concerning CM, and Shields CL, Shields JA, Jager MJ as well as Finger PT had published the most papers in the field. Keywords were classified into three clusters: clinical research, management-related research and genetic research. The keywords “primary acquired melanosis”, “metastasis” and “BRAF mutations” were most frequently emerged. According to the average appearing year (AAY), targeted therapy (AAY of 2019.0) and nivolumab (AAY of 2018.7) were identified as the main focuses of the field in the near future.ConclusionIn the past 25 years, the United States, Germany, England and the Netherlands held the leading position in the CM research. A group of scholars made important contributions to CM research and will continue to guide cutting-edge research. Treatments that have been shown to be effective for advanced cutaneous melanoma, such as targeted therapy and immunotherapy, are potential focuses for future CM research.

Clinical manifestations of Angelman syndrome in children

Angelman syndrome is a genetic disorder characterized by mental retardation and severe speech delay, movement disorders and ataxia, dysmorphic features, and behavioral disorders. Angelman syndrome is caused by the loss of the 15q11.2-q13 region of chromosome 15 received from the mother, which leads to a violation of the expression of the UBE3A gene.Purpose. To analyze clinical manifestations in children with Angelman syndrome to identify early-onset and characteristic clinical signs.Characteristics of children and research methods. The study included 60 children. In all cases, Angelman syndrome was diagnosed on the basis of international clinical criteria and the results of genetic testing. The researchers used clinical, functional and molecular genetic research methods.Results. 80-100% of children demonstrated delayed mental and motor development, lack of speech, affective behavior, ataxia, hand stereotypes, apraxia of hand movements, strabismus, sialorrhea. 72% of children had epileptic seizures; all patients (regardless of the presence / absence of epilepsy) had a pattern characteristic of Angelman syndrome on the electroencephalogram. Differential diagnosis was based on the gene / chromosomal syndromes characterized by similar clinical signs.Conclusion. The combination of such most frequent, early clinical symptoms as difficulties in feeding, strabismus, impaired muscle tone, delayed motor and psycho-speech development, affective behavior with frequent laughter, and sleep disorders may indicate Angelman syndrome in a child.

Launching the Newfoundland and Labrador Health Research Ethics Authority Act and Reflections on its Current Status

The Health Research Ethics Authority (HREA) Act was established to ensure that research ethics review of all human health research in the province of Newfoundland and Labrador is conducted by a local, in-province, Research Ethics Board (REB). The HREA Act arose as a result of complaints by patients and family members enrolled in a clinical genetics research study being conducted by a team of researchers from outside the province who failed to provide appropriate clinical follow-up. This review provides a record of the steps taken to draft the legislation and prepare for proclamation and includes information on the key stakeholders involved in the process. The review also provides a brief commentary on the HREA, and the newly formed Health Research Ethics Board, in the years following proclamation and how the HREA aligns with national interests for harmonizing research ethics review across multiple REBs. At the outset, the process was envisioned as simply moving to a provincially legislated research ethics board; however, the actual task involved establishing a new entity to oversee research ethics review and expanding or enhancing the office required to manage this research ethics review oversight. The task for the working committees involved in establishing the legislation was more complex than envisioned by the partner organizations, the government of Newfoundland and Labrador, Memorial University of Newfoundland and the Eastern Health Authority, and the workload and time to establish and proclaim the legislation was more involved than anticipated.

Ethical, Legal, and Social Issues (ELSI) in Clinical Genetics Research.

ELSI (Ethical, Legal, and Social Issues) is a widely used acronym in the bioethics literature that encompasses a broad range of research examining the various impacts of science and technology on society. In Canada, GE3LS (Genetics, Ethical, Economic, Environmental, Legal, Social issues) is the term used to describe ELSI studies in the context of genetics and genomics research. It is intentionally more expansive in that GE3LS explicitly brings economic and environmental issues under its purview. ELSI/GE3LS research is increasingly relevant in recent years as there has been a greater emphasis on "translational research" that moves genomic discoveries from the bench to the clinic. The purpose of this chapter is to outline a range of ELSI-related work that might be conducted as part of a large scale genetics or genomics research project, and to provide some practical insights on how a scientific research team might incorporate a strong and effective ELSI program within its broader research mandate. We begin by describing the historical context of ELSI research and the development of GE3LS research in the Canadian context. We then illustrate how some ELSI research might unfold by outlining a variety of GE3LS research questions or content domains and the methodologies that might be employed in studying them. We conclude with some practical suggestions about how to build an effective ELSI/GE3LS team and focus within a broader scientific research program.

Application Value of Blood Types Gene Detection in Blood Transfusion of Patients with ABO Blood Type Identification Difficulty

The human red blood cell blood group system plays an extremely important role in blood transfusion medicine and the ABO blood group system is of great significance in clinical blood transfusion, organ transplantation, forensic medicine and genetics research. The aim of this study was to study the application of genotyping technology in difficult ABO blood types identification. A total of 12 patients were selected in our hospital from August 2019 to August 2020. Among them, 1 patient with peptic ulcer, 1 patient with chronic kidney disease stage V, 2 patients with diabetes, 1 patient with infertility, 3 patients with anemia, 1 patient with primary liver cancer, 2 patients with leukemia and 1 patient with systemic lupus erythematosus. Polymerase chain reaction-sequence specific primers genotyping method was used to detect these patients with difficult ABO blood type antigens and statistical method was used to analyze the correlation of ABO genotypes and difficult ABO blood types. The specific distribution of ABO genotypes in 12 patients were detected as follows: 6 cases of A/B, 3 cases of A/O and 3 cases of B/O. The genotype detected by polymerase chain reaction-sequence specific primers was consistent with serological phenotype. As an auxiliary method, ABO genotyping can be used to detect difficult ABO blood types.

The Impact of African Ancestry on Prostate Cancer Disparities in the Era of Precision Medicine.

Prostate cancer disproportionately affects men of African ancestry at nearly twice the rate of men of European ancestry despite the advancement of treatment strategies and prevention. In this review, we discuss the underlying causes of these disparities including genetics, environmental/behavioral, and social determinants of health while highlighting the implications and challenges that contribute to the stark underrepresentation of men of African ancestry in clinical trials and genetic research studies. Reducing prostate cancer disparities through the development of personalized medicine approaches based on genetics will require a holistic understanding of the complex interplay of non-genetic factors that disproportionately exacerbate the observed disparity between men of African and European ancestries.

Genetic screening for monogenic hypertension in hypertensive individuals in a clinical setting

BackgroundMonogenic hypertension describe a series of hypertensive syndromes that are inherited by Mendelian laws. Sometimes genetic testing is required to provide evidence for their diagnoses, precise classification and targeted treatment....