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MTHFR Gene Polymorphisms: A Single Gene with Wide-Ranging Clinical Implications—A Review
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Role of MicroRNAs in Acute Myeloid Leukemia
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SYNGAP1 Syndrome and the Brain Gene Registry
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Genetics of Suicide
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Genetic Features of Tumours Arising in the Context of Suspected Hereditary Cancer Syndromes with RAD50, RAD51C/D, and BRIP1 Germline Mutations, Results of NGS-Reanalysis of BRCA/MMR-Negative Families
Journal Description
Genes
Genes
is a peer-reviewed, open access journal of genetics and genomics published monthly online by MDPI. The Spanish Society for Biochemistry and Molecular Biology (SEBBM) is affiliated with Genes and their members receive discounts on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
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- Journal Rank: JCR - Q2 (Genetics and Heredity) / CiteScore - Q2 (Genetics (clinical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 14.6 days after submission; acceptance to publication is undertaken in 2.5 days (median values for papers published in this journal in the first half of 2025).
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Impact Factor:
2.8 (2024);
5-Year Impact Factor:
3.2 (2024)
Latest Articles
Germline and Somatic Changes Associated with the Development of Inherited and De Novo Pediatric Acute Myeloid Leukemia
Genes 2025, 16(7), 798; https://doi.org/10.3390/genes16070798 (registering DOI) - 1 Jul 2025
Abstract
Acute myeloid leukemia (AML) accounts for only about 15–20% of pediatric leukemia and an overall incidence of 1.4 cases per 200,000 children under the age of 15 years. The majority of pediatric AML occurs de novo, often as the result of somatic first
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Acute myeloid leukemia (AML) accounts for only about 15–20% of pediatric leukemia and an overall incidence of 1.4 cases per 200,000 children under the age of 15 years. The majority of pediatric AML occurs de novo, often as the result of somatic first hits in utero. A minority of pediatric AML occurs in response to a predisposition syndrome, such as a bone marrow failure syndrome, or other inherited mutations and copy number changes. While the overall survival of pediatric patients with AML is approximately 70%, survival at the individual level is dependent on the abnormality detected either through cytogenomic analyses or sequencing for mutations in responsible genes. Indeed, de novo infant AML carries a more sobering prognosis than that of pediatric AML. This review describes many of the common genomic abnormalities associated with pediatric AML and characterizes their detection from a laboratory assessment perspective. Pediatric AML is primarily a disease of gene rearrangements rather than of gene mutations, and, as such, clinical cytogenetics takes a primary role.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessArticle
Genetic Factors Associated with Intraocular Inflammation After Brolucizumab Administration in Patients with Exudative Age-Related Macular Degeneration
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Seigo Yoneyama, Yoichi Sakurada, Taiyo Shijo, Yoshiko Fukuda, Yumi Kotoda, Wataru Kikushima, Fumihiko Mabuchi and Kenji Kashiwagi
Genes 2025, 16(7), 797; https://doi.org/10.3390/genes16070797 (registering DOI) - 1 Jul 2025
Abstract
Purpose: We aimed to investigate whether genetic variants susceptible to age-related macular degeneration (AMD) are associated with intraocular inflammation after brolucizumab administration in eyes that have exudative AMD. Methods: A total of 206 eyes from 206 patients (156 men/50 women, 74.0 ± 8.4
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Purpose: We aimed to investigate whether genetic variants susceptible to age-related macular degeneration (AMD) are associated with intraocular inflammation after brolucizumab administration in eyes that have exudative AMD. Methods: A total of 206 eyes from 206 patients (156 men/50 women, 74.0 ± 8.4 years; treatment-naïve, 128 [62.1%]; switching, 78 [37.9%]) were included in this study. All patients were treated with intravitreal brolucizumab at least once. The genotyping of ARMS2 A69S (rs10490924), CFH I62V (rs800292), CFH (rs1329428), SKIV2L (rs429608), C3 (rs2241394), cholesteryl ester transfer protein (CETP) (rs3764261), and ADAMTS9 (rs6795375) was performed using TaqMan technology. Results: Out of the 206 patients who were included, 21 eyes from 21 patients (10.2%) exhibited intraocular inflammation (IOI). Four (19.0%) exhibited severe IOI, including retinal vasculitis and/or retinal vascular occlusion, and 17 (81.0%) showed mild IOI. The frequency of the T allele of the CETP gene was significantly lower in patients who developed IOI compared to patients who did not develop IOI (T allele frequency: 9.5% vs. 23.5%, p = 0.036). After adjusting for confounding factors, the T allele remained significantly associated with protection against IOI (p = 0.028, 95% confidence interval: 0.098–0.88). Conclusions: The T allele of the CETP gene, a risk allele for AMD and the protective allele for atherosclerosis, may be associated with protection against IOI after brolucizumab administration in eyes that have exudative AMD.
Full article
(This article belongs to the Special Issue 15th Anniversary of Genes: Feature Papers in the “Molecular Genetics and Genomics” Section)
Open AccessReview
Molecular and Environmental Modulators of Aging: Interplay Between Inflammation, Epigenetics, and RNA Stability
by
Konstantina Dragoumani, Dimitris Kletsas, George P. Chrousos, Dimitrios Vlachakis and Nikolaos A. A. Balatsos
Genes 2025, 16(7), 796; https://doi.org/10.3390/genes16070796 (registering DOI) - 1 Jul 2025
Abstract
Aging is a complex biological process characterized by the progressive accumulation of cellular and molecular damage, leading to functional decline and increased susceptibility to age-related diseases. Central to this process is cellular senescence, a state of irreversible cell cycle arrest that acts as
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Aging is a complex biological process characterized by the progressive accumulation of cellular and molecular damage, leading to functional decline and increased susceptibility to age-related diseases. Central to this process is cellular senescence, a state of irreversible cell cycle arrest that acts as both a protective mechanism against tumorigenesis and a contributor to tissue degeneration. Herein, we explore the genetic and molecular mechanisms underlying aging, with a focus on telomere dynamics, the Klotho gene, angiotensin-converting enzyme (ACE), and the NF-κB pathway. Telomeres, which serve as protective caps at chromosome ends, shorten with each cell division, leading to replicative senescence, while the enzyme telomerase plays a pivotal role in maintaining telomere length and cellular longevity. The Klotho gene encoding for an aging suppressor influences insulin/IGF-1 signaling and has antioxidant properties that protect against oxidative stress. ACE, through its dual role in regulating blood pressure and degrading amyloid-beta, impacts longevity and age-related pathologies. The NF-κB pathway drives chronic inflammation or “inflammaging,” contributing to the onset of age-related diseases. Understanding these pathways offers promising avenues for therapeutic interventions to extend health span and lifespan. Targeting mechanisms such as telomerase activation, Klotho supplementation, ACE inhibition, and NF-κB modulation hold potential for combating the detrimental effects of aging and promoting healthier aging in the population.
Full article
(This article belongs to the Special Issue Genomic Approaches for Disease Diagnosis and Prognosis)
Open AccessArticle
Cascade Genetic Testing for Hereditary Cancer Predisposition: Characterization of Patients in a Catchment Area of Southern Italy
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Anna Bilotta, Elisa Lo Feudo, Valentina Rocca, Emma Colao, Francesca Dinatolo, Serena Marianna Lavano, Paola Malatesta, Lucia D’Antona, Rosario Amato, Francesco Trapasso, Nicola Perrotti, Giuseppe Viglietto, Francesco Baudi and Rodolfo Iuliano
Genes 2025, 16(7), 795; https://doi.org/10.3390/genes16070795 (registering DOI) - 30 Jun 2025
Abstract
Background: The national guidelines, informed by evidence from the National Institutes of Health (NIH), define the cri-teria for genetic testing of BRCA1/2 and other genes associated with Hereditary Breast and Ovarian Cancer (HBOC) and Lynch Syndrome (LS). When a germline pathogenic variant
[...] Read more.
Background: The national guidelines, informed by evidence from the National Institutes of Health (NIH), define the cri-teria for genetic testing of BRCA1/2 and other genes associated with Hereditary Breast and Ovarian Cancer (HBOC) and Lynch Syndrome (LS). When a germline pathogenic variant (PV) is identified in an index case, clinical recommendations advise informing at-risk relatives about the availability of predictive genetic testing, as early identification of carriers allows for timely implementation of preventive measures. Methods:This retrospective observational study examined data collected between 2017 and 2024 at the Medical Genetics Unit of the “Renato Dulbecco” University Hospital in Catanzaro, Italy. The analysis focused on trends in the identification of individuals carrying PVs in cancer predisposition genes (CPGs) and the subsequent uptake of cascade genetic testing (CGT) among their family members. Results: Over the study period, from 116 probands were performed 257 CGTs on 251 relatives.A notable reduction of approximately ten years in median age was observed, 39% were found to carry familial mutation and were referred to personalized cancer prevention programs. Among these, 62% accessed Oncological Genetic Counselling (CGO) within one year of the proband’s diagnosis, suggesting effective communication and outreach. Conclusions: The findings highlight the critical role of effective CGO and intrafamilial communication in hereditary cancer prevention. The identification of PVs, followed by timely CGTs and implementation of preventive strategies, sig-nificantly contributes to early cancer risk management. Periodic monitoring of CGT uptake and outcome trends, as demonstrated in this study, is essential to refine and optimize genetic services and public health strategies.
Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
Open AccessReview
A Review of the Diagnostic Approaches for the Detection of Antimicrobial Resistance, Including the Role of Biosensors in Detecting Carbapenem Resistance Genes
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Kaily Kao and Evangelyn C. Alocilja
Genes 2025, 16(7), 794; https://doi.org/10.3390/genes16070794 (registering DOI) - 30 Jun 2025
Abstract
Antimicrobial resistance (AMR) is a rapidly growing global concern resulting from the overuse of antibiotics in both agricultural and clinical settings, the lack of surveillance for resistant bacteria, and the low quality of some available antimicrobial agents. Resistant pathogens are no longer susceptible
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Antimicrobial resistance (AMR) is a rapidly growing global concern resulting from the overuse of antibiotics in both agricultural and clinical settings, the lack of surveillance for resistant bacteria, and the low quality of some available antimicrobial agents. Resistant pathogens are no longer susceptible to common clinical antimicrobials, which decreases the effectiveness of medicines used to treat infections caused by these organisms. Carbapenems are an important class of antibiotics due to their broad-spectrum effectiveness in treating infections caused by Gram-positive and Gram-negative organisms. Carbapenem-resistant bacteria have been found not only in healthcare but also in the environment and food supply chain, where they have the potential to spread to pathogens and infect humans and animals. Current methods of detecting AMR genes are expensive and time-consuming. While these methods, like polymerase chain reactions or whole-genome sequencing, are considered the “gold standard” for diagnostics, the development of inexpensive, rapid diagnostic assays is necessary for effective AMR detection and management. Biosensors have shown potential for success in diagnostic testing due to their ease of use, inexpensive materials, rapid results, and portable nature. Biosensors can be combined with nanomaterials to produce sensitive and easily interpretable results. This review presents an overview of carbapenem resistance, current and emerging detection methods of antimicrobial resistance, and the application of biosensors for rapid diagnostic testing for bacterial resistance.
Full article
(This article belongs to the Special Issue Mobile Genetic Elements and Microbial Multidrug Resistance)
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Open AccessArticle
A Genome-Wide Association Study of Anti-Müllerian Hormone (AMH) Levels in Samoan Women
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Zeynep Erdogan-Yildirim, Jenna C. Carlson, Mohanraj Krishnan, Jerry Z. Zhang, Geralyn Lambert-Messerlian, Take Naseri, Satupaitea Viali, Nicola L. Hawley, Stephen T. McGarvey, Daniel E. Weeks and Ryan L. Minster
Genes 2025, 16(7), 793; https://doi.org/10.3390/genes16070793 (registering DOI) - 30 Jun 2025
Abstract
Background/Objectives:The anti-Müllerian hormone (AMH) is a key biomarker of the ovarian reserve, correlating with ovarian follicle count, fertility outcomes, and menopause timing. Understanding its genetic determinants has broad implications for female reproductive health. However, prior genome-wide association studies (GWASs) have focused exclusively
[...] Read more.
Background/Objectives:The anti-Müllerian hormone (AMH) is a key biomarker of the ovarian reserve, correlating with ovarian follicle count, fertility outcomes, and menopause timing. Understanding its genetic determinants has broad implications for female reproductive health. However, prior genome-wide association studies (GWASs) have focused exclusively on women of European ancestry, limiting insights into diverse populations. Methods: We conducted a GWAS to identify genetic loci associated with circulating AMH levels in a sample of 1185 Samoan women from two independently recruited samples. Using a Cox mixed-effects model we accounted for AMH levels below detectable limits and meta-analysed the summary statistics using a fixed-effect model. To prioritize variants and genes, we used FUMA and performed colocalization and transcriptome-wide association analysis (TWAS). We also assessed whether any previously reported loci were replicated in our GWAS. Results: We identified eleven genome-wide suggestive loci, with the strongest signal at ARID3A (19-946163-G-C; p = 2.32 × 10⁻⁷) and replicated rs10093345 near EIF4EBP1. The gene-based testing revealed ARID3A and R3HDM4 as significant genes. Integrating GWAS results with expression quantitative trait loci via TWAS, we detected seven transcriptome-wide significant genes. The lead variant in ARID3A is in high linkage disequilibrium (r² = 0.79) with the known age-at-menopause variant 19-950694-G-A. Nearby KISS1R is a biologically plausible candidate gene that encodes the kisspeptin receptor, a regulator of ovarian follicle development linked to AMH levels. Conclusions: This study expands our understandings of AMH genetics by focusing on Samoan women. While these findings may be particularly relevant to Pacific Islanders, they hold broader implications for reproductive phenotypes such as the ovarian reserve, menopause timing, and polycystic ovary syndrome.
Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
Open AccessArticle
Genetic Effects for Individual Honeybee Grooming Behavior in Response to Varroa Mites and Its Relationship with the Mite Infestation Levels of Honeybee Colonies
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Miguel Enrique Arechavaleta-Velasco, Laura Yavarik Alvarado-Avila, Claudia García-Figueroa, Francisco Javier Ramírez-Ramírez, Vicente Eliezer Vega-Murillo and Moisés Montaño-Bermúdez
Genes 2025, 16(7), 792; https://doi.org/10.3390/genes16070792 (registering DOI) - 30 Jun 2025
Abstract
Background/Objectives: The objectives of this study were to identify the genetic effects involved in the expression of individual honeybee grooming behavior in response to Varroa destructor and to determine if there is an association between the expression of this behavior and the
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Background/Objectives: The objectives of this study were to identify the genetic effects involved in the expression of individual honeybee grooming behavior in response to Varroa destructor and to determine if there is an association between the expression of this behavior and the infestation levels of Varroa in the honeybee colonies. Methods: The study was conducted in a population of 112 colonies composed of six segregating genetic groups that were derived from two honeybee lines that were selected for high and low individual honeybee grooming behavior. The individual honeybee grooming behavior of 3974 workers from the 112 colonies was measured by the time it takes a bee to respond in performing grooming behavior after a mite was placed on her body. The population growth of Varroa in the colonies was measured over a period of six months. Results: Differences between the genetic groups were found in the expression of individual honeybee grooming behavior (p < 0.01). The distribution of means of the genetic groups fits a genetic additive and dominance effects model for the expression of individual honeybee grooming behavior (r2 = 0.95; p < 0.01). Differences between the genetic groups were found in the colony population growth of Varroa over a period of six months (p < 0.01). A positive correlation was found between the mean individual honeybee grooming behavior of the colonies and the Varroa level of infestation in the colonies (r = 0.57; p < 0.01). Conclusions: The results indicate that additive and dominance genetic effects are associated with honeybee individual grooming behavior and that this trait has an effect on the levels of Varroa infestation in the colonies.
Full article
(This article belongs to the Section Animal Genetics and Genomics)
Open AccessArticle
Regulatory RNA Networks in Ovarian Follicular Cysts in Dairy Cows: Implications for Human Polycystic Ovary Syndrome
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Ramanathan Kasimanickam, Vanmathy Kasimanickam, Joao Ferreira, John Kastelic and Fabiana de Souza
Genes 2025, 16(7), 791; https://doi.org/10.3390/genes16070791 (registering DOI) - 30 Jun 2025
Abstract
Background/Objectives: Ovarian follicular cysts (OFCs) in dairy cows represent a significant cause of infertility and share striking similarities with polycystic ovary syndrome (PCOS) in women. This study aimed to elucidate the molecular mechanisms underlying OFCs and their relevance to PCOS by profiling
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Background/Objectives: Ovarian follicular cysts (OFCs) in dairy cows represent a significant cause of infertility and share striking similarities with polycystic ovary syndrome (PCOS) in women. This study aimed to elucidate the molecular mechanisms underlying OFCs and their relevance to PCOS by profiling differentially expressed (DE) microRNAs (miRNAs) and constructing integrative RNA interaction networks. Methods: Expression analysis of 84 bovine miRNAs was conducted in antral follicular fluid from normal and cystic follicles using miScript PCR arrays. Bioinformatic tools including miRBase, miRNet, and STRING were employed to predict miRNA targets, construct protein–protein interaction networks, and perform gene ontology and KEGG pathway enrichment. Network analyses integrated miRNAs with coding (mRNAs) and non-coding RNAs (circRNAs, lncRNAs, snRNAs). Results: Seventeen miRNAs were significantly dysregulated in OFCs, including bta-miR-18a, bta-miR-30e-5p, and bta-miR-15b-5p, which were associated with follicular arrest, insulin resistance, and impaired steroidogenesis. Upregulated miRNAs such as bta-miR-132 and bta-miR-145 correlated with inflammation, oxidative stress, and intrafollicular androgen excess. Key regulatory lncRNAs such as Nuclear Enriched Abundant Transcript 1 (NEAT1), Potassium Voltage-Gated Channel Subfamily Q Member 1 Opposite Strand/Antisense Transcript 1 (KCNQ1OT1), Taurine-Upregulated 1 (TUG1), and X Inactive Specific Transcript (XIST), as well as circRNA/pseudogene hubs, were identified, targeting pathways involved in metabolism, inflammation, steroidogenesis, cell cycle, and apoptosis. Conclusions: The observed transcriptomic changes mirror core features of human PCOS, supporting the use of bovine OFCs as a comparative model. These findings provide novel insights into the regulatory RNA networks driving ovarian dysfunction and suggest potential biomarkers and therapeutic targets for reproductive disorders. This network-based approach enhances our understanding of the complex transcriptomic landscape associated with follicular pathologies in both cattle and women.
Full article
(This article belongs to the Section Animal Genetics and Genomics)
Open AccessArticle
Genome-Wide Analysis of the Typical Thioredoxin Gene Family in Hexaploid Oil-Camellia: Identification, Phylogenetic Analysis, and Gene Expression Patterns
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Lan Wu, Peipei Song, Yifan Xia, Min Min, Tingting Xu, Junyong Cheng, Jihua Cheng and Huaguo Zhu
Genes 2025, 16(7), 790; https://doi.org/10.3390/genes16070790 (registering DOI) - 30 Jun 2025
Abstract
Hioredoxins are small proteins crucial for maintaining cellular redox balance and are involved in various biological processes, including growth, photosynthesis, development, and stress responses. This study aims to conduct a genome-wide analysis of the typical Thioredoxin (TRX) gene family in hexaploid Camellia oleifera
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Hioredoxins are small proteins crucial for maintaining cellular redox balance and are involved in various biological processes, including growth, photosynthesis, development, and stress responses. This study aims to conduct a genome-wide analysis of the typical Thioredoxin (TRX) gene family in hexaploid Camellia oleifera and explore the role of the CoTRX25 gene in flowering. Through bioinformatics approaches, we identified 27 typical TRX gene family members in the C. oleifera genome and analyzed their phylogenetic relationships, gene structures, conserved motifs, and chromosomal distributions. Transcriptomic analysis across different tissues was performed to determine the expression patterns of these genes. Additionally, the CoTRX25 gene was cloned and heterologously overexpressed in Arabidopsis thaliana to investigate its functional role in flowering. The 27 TRX genes were mainly located on 11 chromosomes, with multiple gene duplication events identified, indicating that gene duplication has played a significant role in the expansion of the TRX family. Transcriptomic analysis revealed that most typical TRX genes are highly expressed in embryos, suggesting their potential importance in seed development. Overexpression of CoTRX25 in A. thaliana led to delayed flowering, implying that this gene may be involved in flowering regulation. This study provides a theoretical basis for understanding the functions of typical TRX genes in C. oleifera growth and development, particularly highlighting the role of CoTRX25 in flowering regulation.
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(This article belongs to the Section Plant Genetics and Genomics)
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Open AccessArticle
Comparison of Chloroplast Genome Sequences of Saxifraga umbellulata var. pectinata in Qinghai–Xizang Plateau
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Cui Wang, Kaidi Su, Qiwen Li, Rui Sun, Haoyu Liu, Jingxuan Du, Jinping Li and Likuan Liu
Genes 2025, 16(7), 789; https://doi.org/10.3390/genes16070789 (registering DOI) - 30 Jun 2025
Abstract
Background: Saxifraga umbellulata var. pectinata (Saxifragaceae) is recognized as a genuine medicinal material from the Qinghai–Tibet Plateau in China. This paper presents the chloroplast (cp) genome of S. umbellulata var. pectinata, marking the first report for this genus. The Tibetan medicinal
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Background: Saxifraga umbellulata var. pectinata (Saxifragaceae) is recognized as a genuine medicinal material from the Qinghai–Tibet Plateau in China. This paper presents the chloroplast (cp) genome of S. umbellulata var. pectinata, marking the first report for this genus. The Tibetan medicinal plants documented in ‘Chinese Medicinal Plant Resources’ are associated with their chloroplast genomes and medicinal mechanisms. Objective: In order to resolve any potential ambiguity in conventional classifications, this study reconstructs the evolutionary position of S. umbellulata var. pectinata within the genus by comparing its chloroplast genetic information with that of other groupings. Methods: The chloroplast genome of S. umbellulata var. pectinata was sequenced using the Illumina NovaSeq 6000 platform. Subsequent sequence assembly, annotation, and characterization were performed using bioinformatics analysis. The NJ phylogenetic tree was constructed using MEGA 7.0 software. Results: The complete chloroplast genome of S. umbellulata var. pectinata is 146,549 bp in length, comprising four subregions: a large single-copy (LSC) region of 79,318 bp and a small single-copy (SSC) region of 16,390 bp, separated by a pair of inverted repeat (IR) regions each 25,421 bp long. This cp genome contains 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 38.1%. Phylogenetic analysis based on 20 cp genomes indicates that S. umbellulata var. pectinata is closely related to Saxifraga sinomontana and Saxifraga stolonifera.
Full article
(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)
Open AccessArticle
Screening and Validation of Reference Genes for Normalization of qRT-PCR in Rice BLB Pathogen Xanthomonas oryzae pv. oryzae Under Tetramycin Stress
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Feiyan Fang, Xinli Miao, Tong Mou, Zian Wang, Yanhe Guo, Yingfen Yang, Shunyu Gao, Zhenji Wang, Chengdong Xu and Jun Yang
Genes 2025, 16(7), 788; https://doi.org/10.3390/genes16070788 (registering DOI) - 30 Jun 2025
Abstract
Background: Xanthomonas oryzae pv. oryzae (Xoo) causes rice leaf blight (BLB) and poses a major threat to global rice production. In rice production, tetramycin agents provide good control of rice leaf blight, while the standardization of the reference genes of Xoo
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Background: Xanthomonas oryzae pv. oryzae (Xoo) causes rice leaf blight (BLB) and poses a major threat to global rice production. In rice production, tetramycin agents provide good control of rice leaf blight, while the standardization of the reference genes of Xoo under tetramycin stress has not been reported. The aim of this study was to identify the most stable reference genes for quantitative PCR analysis of Xoo under tetramycin stress. Methods: Six candidate reference genes, gyrB (RNA polymerase β gene), GADPH (glyceraldehyde-3-phosphate dehydrogenase gene), recA (recombinase A gene), gyrA (citrate synthase encoding gene), dnaK (molecular chaperone protein gene), and 16S rRNA (16S ribosomal RNA gene) were selected and their expression stability was assessed under tetramycin stress conditions using real-time quantitative PCR (qRT-PCR). GeNorm, NormFinder, BestKeeper and RefFinder were used to assess the expression stability, the relative expression values of the eight genes involved QS (Quorum sensing) pathway under tetramycin stress were used to validate by the rpf (regulation of pathogenic factors) gene family. Results: 16S rRNA expression was most stable under tetracycline stress, whereas GADPH was the least. The rpf gene family showed a highly stable expression level, confirming the reliability of 16S r RNA as a reference gene in the study of Xoo under tetramycin stress. Conclusions: 16S rRNA was identified as the best reference gene for Xoo gene expression analysis under tetramycin stress. It provides a reliable support for the molecular research on the control strategy of rice BLB.
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(This article belongs to the Section Genes & Environments)
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Open AccessArticle
Selection and Validation of Stable Reference Genes for RT-qPCR Analyses of Rumex patientia (Polygonaceae) Under Four Abiotic Stresses
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Qian Yang, Xiaoli Li, Rongju Qu, Yuping Liu, Xu Su, Jiarui Jin, Mingjun Yu, Zhaxi Cairang, Penghui Zhang, Yinghui Zheng, Xuanlin Gao and Marcos A. Caraballo-Ortiz
Genes 2025, 16(7), 787; https://doi.org/10.3390/genes16070787 (registering DOI) - 30 Jun 2025
Abstract
Background: Rumex patientia (Polygonaceae), a perennial herbaceous species predominantly found in northern temperate regions, has been historically utilized in traditional Chinese medicine for its hematological regulatory properties, including blood cooling, hemostasis, and detoxification. Despite the pharmacological value of this species, unvalidated reference genes
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Background: Rumex patientia (Polygonaceae), a perennial herbaceous species predominantly found in northern temperate regions, has been historically utilized in traditional Chinese medicine for its hematological regulatory properties, including blood cooling, hemostasis, and detoxification. Despite the pharmacological value of this species, unvalidated reference genes compromise precise gene expression profiling. Methods: We initially selected eight candidate genes (ACT, GAPDH, YLS, SKD1, UBQ, UBC, EF-1α, TUA) from R. patientia transcriptomes and then assessed their transcriptional stability using RT-qPCR across root, stem, and leaf tissues under four abiotic stresses: cold, drought, salinity, and heavy metal exposure. Results: ACT emerged as the most stable reference gene in three specific scenarios: root/leaf tissues under cold stress, stems during drought exposure, and roots subjected to salt treatment, revealing distinct tissue–stress response patterns. TUA emerged as the most stable reference in cold- and salt-challenged stems, while SKD1 exhibited superior stability in drought-affected roots/leaves, heavy-metal-stressed tissues, and salt-treated leaves. Validation via the drought-inducible MYB transcription factor confirmed reference gene reliability. Conclusions: This work pioneers a standardized reference gene framework for R. patientia under multi-stress conditions, offering essential methodological foundations for subsequent molecular research in this medicinal plant.
Full article
(This article belongs to the Section Plant Genetics and Genomics)
Open AccessArticle
Genetic Variants in BIRC5 (rs8073069, rs17878467, and rs9904341) Are Associated with Susceptibility in Mexican Patients with Breast Cancer: Clinical Associations and Their Analysis In Silico
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María Renee Jiménez-López, César de Jesús Tovar-Jácome, Alejandra Palacios-Ramírez, Martha Patricia Gallegos-Arreola, Teresa Giovanna María Aguilar-Macedo, Rubria Alicia González-Sánchez, Efraín Salas-González, José Elías García-Ortiz, Clara Ibet Juárez-Vázquez and Mónica Alejandra Rosales-Reynoso
Genes 2025, 16(7), 786; https://doi.org/10.3390/genes16070786 (registering DOI) - 30 Jun 2025
Abstract
Background/Objectives: Breast cancer (BC) is a multifactorial disease, with genetic alterations in cell proliferation and migration pathways being significant risk factors. This study examines the association between three variants in the BIRC5 gene (rs8073069, rs17878467, and rs9904341) and breast cancer (BC) susceptibility. Methods:
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Background/Objectives: Breast cancer (BC) is a multifactorial disease, with genetic alterations in cell proliferation and migration pathways being significant risk factors. This study examines the association between three variants in the BIRC5 gene (rs8073069, rs17878467, and rs9904341) and breast cancer (BC) susceptibility. Methods: Peripheral blood DNA samples were collected from 423 women (221 BC patients and 202 healthy controls). Genotyping was performed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) methodology. Associations were calculated using odds ratios (OR), with p-values adjusted by the Bonferroni test (significance at p ≤ 0.016). In silico analyses were conducted to predict the functional impact of the analyzed variants. Results: Patients carrying the C/C genotype for the rs8073069 variant showed increased susceptibility to BC with early TNM (tumor-node-metastasis classification) stage and Luminal A subtype (OR > 2.00; p ≤ 0.004). For the rs17878467 variant, patients with the C/T or T/T genotype exhibited a higher susceptibility to developing breast cancer (BC), particularly at early TNM stages or with a histological lobular type (OR > 2.00; p ≤ 0.012). Regarding the rs9904341 variant, patients with the G/C or C/C genotype had a higher susceptibility to breast cancer. Notably, G/C genotype carriers with Luminal A and B subtypes, and C/C genotype carriers who had TNM stages II and III, and Luminal A, Luminal B, and HER2 subtypes demonstrated increased risk (OR > 2.00; p ≤ 0.009). The C-T-C haplotype (rs8073069–rs17878467–rs9904341) was significantly associated with BC (OR = 4.20; 95% CI = 2.38–7.41; p ≤ 0.001). In silico analysis using CADD indicated a low probability of deleterious effects. Conclusions: The results suggest that the rs8073069, rs17878467, and rs9904341 variants in BIRC5 have a significant influence on breast cancer susceptibility.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
Genome-Wide Identification of the ABF/AREB/ABI5 Gene Family in Ziziphus jujuba cv. Dongzao and Analysis of Its Response to Drought Stress
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Zhikai Zhang, Xiaoming Liu, Yu Wang, Jun Zhou, Zhongwu Wan, Xin Zhang, Jing Wang, Binbin Si, Lan Luo and Wendi Xu
Genes 2025, 16(7), 785; https://doi.org/10.3390/genes16070785 (registering DOI) - 30 Jun 2025
Abstract
Abscisic acid (ABA), a pivotal phytohormone regulating plant growth and stress adaptation, orchestrates abiotic stress responses through the ABA-responsive element-binding factors ABF/AREB/ABI5. Nevertheless, the functional characterization of ABF/AREB/ABI5 homologs in Z. jujuba cv. Dongzao remains unexplored. In this study, we identified seven ZjABF
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Abscisic acid (ABA), a pivotal phytohormone regulating plant growth and stress adaptation, orchestrates abiotic stress responses through the ABA-responsive element-binding factors ABF/AREB/ABI5. Nevertheless, the functional characterization of ABF/AREB/ABI5 homologs in Z. jujuba cv. Dongzao remains unexplored. In this study, we identified seven ZjABF genes distributed across five chromosomes. Domain analyses revealed high structural conservation, particularly within the basic leucine zipper (bZIP) DNA-binding domain. Subcellular localization confirmed nuclear targeting of all seven ZjABF proteins. Phylogenetic classification resolved these factors into three clades (A–C). Cis-regulatory element profiling implicated the involvement of the ZjABFs in hormone signaling, abiotic stress transduction, and photoregulatory pathways. Synteny analyses identified three segmental duplication events within the gene family. Tissue-specific expression patterns indicated critical roles for ZjABF2 and ZjABF3 in fruit maturation, and most of the ABF/AREB/ABI5 genes were highly expressed in the root. Under drought stress, four ZjABF genes exhibited differential expression, with ZjABF2 demonstrating pronounced sensitivity. These findings establish a molecular framework for understanding ZjABF-mediated abiotic stress responses in non-model woody perennials.
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(This article belongs to the Section Plant Genetics and Genomics)
Open AccessArticle
Comparative Transcriptome and Metabolome Analyses Provide New Insights into the Molecular Mechanisms Underlying Taproot Development and Bioactive Compound Biosynthesis in Ficus hirta vahl
by
Meiqiong Tang, Chunying Liang, Yude Peng, Hong He, Fan Wei, Ying Hu, Yang Lin, Chunfeng Tang, Gang Li and Linxuan Li
Genes 2025, 16(7), 784; https://doi.org/10.3390/genes16070784 (registering DOI) - 30 Jun 2025
Abstract
Background: F. hirta vahl is a famous Chinese medicinal plant. The root is the main organ accumulating bioactive compounds, and its development is directly related to the yield and quality of the harvested F. hirta. However, the molecular mechanisms underlying the bioactive compound
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Background: F. hirta vahl is a famous Chinese medicinal plant. The root is the main organ accumulating bioactive compounds, and its development is directly related to the yield and quality of the harvested F. hirta. However, the molecular mechanisms underlying the bioactive compound biosynthesis occurring during the root development of F. hirta are unknown. Method: Transcriptome and widely targeted metabolome analyses were performed to investigate gene expression and metabolite variation during the development of F. hirta taproots. Results: A total of 3792 differentially expressed genes (DEGs) were identified between the one- and three-year-old F. hirta taproots; they are related to circadian rhythm–plant, phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant–pathogen interaction pathways. In total, 119 differentially accumulated metabolites (DAMs) were identified between the one- and three-year-old F. hirta taproots, including flavonols, phenolic acids, and coumarins compounds. Integrative transcriptome and metabolome analyses revealed a significant correlation between 172 DEGs and 21 DAMs; they were predominantly enriched for processes associated with phenylpropanoid biosynthesis, flavonoid biosynthesis, plant hormone signal transduction, and stilbenoid, diarylheptanoid, and ginerol biosynthesis. In addition, 26 DEGs were identified to be significantly correlated with the DAMs that accumulated in the phenylpropanoid biosynthesis pathway, and these DEGs may be the key genes for the biosynthesis of F. hirta active compounds. Conclusions: The phenylpropanoid biosynthesis pathway plays a dual role in both development and bioactive compound synthesis in F. hirta taproots. These findings provide a molecular regulatory network in the relationships between F. hirta taproot development and the accumulation of secondary metabolites. The identification of candidate genes and pathways provides a genetic resource for quality control and future molecular breeding in F. hirta.
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(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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Open AccessArticle
Identification of Immune Hub Genes in Obese Postmenopausal Women Using Microarray and Single-Cell RNA Seq Data
by
Fu-Rong Zhang, Xuan Lu, Jia-Li Li, Yu-Xin Li, Wei-Wei Pang, Ning Wang, Kun Liu, Qian-Qian Zhang, Yun Deng, Qin Zeng, Xiao-Chao Qu, Xiang-Ding Chen, Hong-Wen Deng and Li-Jun Tan
Genes 2025, 16(7), 783; https://doi.org/10.3390/genes16070783 (registering DOI) - 30 Jun 2025
Abstract
Background: Obesity is characterized by a chronic state of low-grade inflammation. Investigating immune-critical genes and their biological functions in the adipose tissue of postmenopausal obese women is crucial for elucidating the underlying mechanisms of immune dysregulation associated with obesity. Methods: In this study,
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Background: Obesity is characterized by a chronic state of low-grade inflammation. Investigating immune-critical genes and their biological functions in the adipose tissue of postmenopausal obese women is crucial for elucidating the underlying mechanisms of immune dysregulation associated with obesity. Methods: In this study, microarray (GSE151839) and single-cell RNA-seq (GSE176171) datasets were obtained from the Gene Expression Omnibus (GEO). For microarray data analysis, weighted gene co-expression network analysis (WGCNA), protein–protein interaction network (PPI) analysis, and immune infiltration analysis (ssGSEA) were employed to identify obesity-related immune-critical genes. Subsequently, the candidate genes were validated using scRNA-seq data to explore their expression patterns at the single-cell level. Finally, the expression levels of these immune-critical genes were experimentally verified in adipose tissue from obese and control zebrafish models using RT-qPCR. Results: Analysis of microarray data through WGCNA, PPI and ssGSEA identified 16 obesity-related immune-critical genes, including IL7R, CD3E, CD2, CCR5, CD3D, MS4A1, TRAT1, SLAMF8, CCL3L1, SPP1, CCL5, IL2RG, CD3G, TLR8, ITK, and CCL3. Differential expression of SPP1, ITK and CCL5 was confirmed in scRNA-seq data, with ITK and CCL5 showing distinct expression patterns in natural killer (NK) cells. Furthermore, RT-qPCR analysis revealed upregulation of SPP1 and ITK in adipose tissue of obese zebrafish compared to lean controls. Conclusions: This study identifies SPP1, ITK and CCL5 as key immune hub genes in the adipose tissue of postmenopausal obese women, with NK cells playing a significant role in adipose tissue inflammation through the expression of these genes. These findings provide novel insights into potential therapeutic targets for the prevention and treatment of obesity in postmenopausal women.
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(This article belongs to the Section RNA)
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Open AccessReview
Intron Retention and Alzheimer’s Disease (AD): A Review of Regulation Genes Implicated in AD
by
Ayman El-Seedy and Véronique Ladevèze
Genes 2025, 16(7), 782; https://doi.org/10.3390/genes16070782 (registering DOI) - 30 Jun 2025
Abstract
Determining the genetic variations of candidate genes in affected subjects will help identify early pathological biomarkers of Alzheimer’s disease (AD) and develop effective treatments. It has recently been found that some genes that are linked share an increase in intron retention (IR). In
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Determining the genetic variations of candidate genes in affected subjects will help identify early pathological biomarkers of Alzheimer’s disease (AD) and develop effective treatments. It has recently been found that some genes that are linked share an increase in intron retention (IR). In this review, we discuss a few instances of mRNA-IR in various genes linked to AD, including APOE, MAPT-Tau, Psen2, Farp1, Gpx4, Clu, HDAC4, Slc16a3, and App genes. These genes are vulnerable to IR, encompassing additional crucial proteins for brain functionality, but they are frequently involved in pathways linked to the control of mRNA and protein homeostasis. Despite the advancements in human in vivo RNA therapy, as far as we know, there are no reports of data generated regarding artificial in vivo splicing in either animal models or humans. To prevent genetic variations and improve or repair errors in expression of desired genes, humans have adopted new gene editing techniques like CRISPR-Cas9 and RNAi modalities. Ultimately, IR could be utilized as a therapeutic potential biomarker for disorders related to intronic expansion.
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(This article belongs to the Special Issue Study on Genotypes and Phenotypes of Neurodegenerative Diseases—2nd Edition)
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Open AccessArticle
Effects of Stems and Leaves of Panax notoginseng on mRNA Expression of TLR Signaling Pathway in Hepatic Tissue of Duzang Pigs
by
Na Zhang, Lanlan Yi, Yuxiao Xie, Huijin Jia, Guangyao Song, Wenjie Cheng, Wenzhe Shi, Junhong Zhu and Sumei Zhao
Genes 2025, 16(7), 781; https://doi.org/10.3390/genes16070781 (registering DOI) - 30 Jun 2025
Abstract
Background/Objectives: Panax notoginseng stems and leaves (PNSLs) have shown limited adoption as a forage component in commercial livestock operations due to low utilization rates. Methods: This study was designed to add 10% and 20% PNSLs in the diet of Duzang pigs.
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Background/Objectives: Panax notoginseng stems and leaves (PNSLs) have shown limited adoption as a forage component in commercial livestock operations due to low utilization rates. Methods: This study was designed to add 10% and 20% PNSLs in the diet of Duzang pigs. Hepatic tissues were collected to investigate the expression levels of Toll-like receptor (TLR), MyD88, TRIF genes, and downstream cytokines within the TLR signaling pathway. Results: 10% and 20% PNSLs in the diet significantly up-regulated mRNA expression levels of TLR3, TLR6, TLR7, TLR8, TRIF, IL-10, IFN-α and IFN-β, while they down-regulated TLR5, TLR9, TNF-α and IL-1β in Duzang pigs. No significant effects were observed on the expression of TLR2 and IL-6. Conclusions: Different amounts of PNSLs modulated the TLR signaling pathway mRNA expression levels in the hepatic tissues of Duzang pigs.
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(This article belongs to the Section Animal Genetics and Genomics)
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Open AccessReview
Cytogenetics and Cytogenomics in Clinical Diagnostics: Genome Architecture, Structural Variants, and Translational Applications
by
Concetta Federico, Desiree Brancato, Francesca Bruno, Elvira Coniglio, Valentina Sturiale and Salvatore Saccone
Genes 2025, 16(7), 780; https://doi.org/10.3390/genes16070780 (registering DOI) - 30 Jun 2025
Abstract
The spatial organization of the genome within the nucleus is a fundamental regulator of gene expression, genome stability, and cell identity. This review addresses the central question of how nuclear genome architecture contributes to disease mechanisms and diagnostics, and how technological advances enable
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The spatial organization of the genome within the nucleus is a fundamental regulator of gene expression, genome stability, and cell identity. This review addresses the central question of how nuclear genome architecture contributes to disease mechanisms and diagnostics, and how technological advances enable its clinical exploration. We first outline the principles of nuclear genome architecture, including chromosome territories, replication timing, and 3D domains, and their role in gene regulation and disease. We then explore the mechanisms and consequences of chromosomal rearrangements, and how replication dynamics intersect with epigenetic regulation and genome stability. Diagnostic tools are presented in chronological progression, from conventional cytogenetics to high-resolution genomic and single-cell techniques. A dedicated section focuses on cancer cytogenomics and its clinical implications. We further highlight emerging technologies for 3D genome and epigenome profiling and their integration into diagnostic workflows. Finally, we discuss current challenges, such as standardization and cost, and the transformative potential of multi-omics and artificial intelligence for future precision diagnostics. Overall, we provide a comprehensive overview of how cytogenetics and cytogenomics contribute to the understanding and clinical diagnosis of genetic and neoplastic diseases.
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(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
Open AccessArticle
Development and Evaluation of a Molecular Test for Monkeypox Virus in the Federal District, Brazil
by
Lucas Pereira da Silva, Fabián Andrés Hurtado, Aline Belmok, Rafael Correa, Claudia F. Sousa, Gislene P. Gil, Lara Velasco, Rafael H. Jácomo, Lídia F. Nery, Maria Tereza de Oliveira Rodrigues, Miguel S. Andrade and Rosângela Vieira de Andrade
Genes 2025, 16(7), 779; https://doi.org/10.3390/genes16070779 (registering DOI) - 30 Jun 2025
Abstract
Background: Monkeypox virus, the etiological agent of Mpox, is a double-stranded DNA virus belonging to the Orthopoxvirus genus that has attracted increasing attention due to sporadic outbreaks in humans. In 2022, it was responsible for the largest Mpox outbreak outside the African continent,
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Background: Monkeypox virus, the etiological agent of Mpox, is a double-stranded DNA virus belonging to the Orthopoxvirus genus that has attracted increasing attention due to sporadic outbreaks in humans. In 2022, it was responsible for the largest Mpox outbreak outside the African continent, infecting over 117,000 individuals worldwide. In Brazil, since the first confirmed case in June 2022, more than 13,000 people have been diagnosed with the virus. Methods: In July 2022, we developed the first molecular test for the detection of monkeypox virus in the Midwest region of the country, allowing the diagnosis of the disease in various patients, mainly residents of the Federal District. Thus, in this work, we present the validation of a laboratory-developed qPCR test (LDT) for monkeypox virus detection, as well as a retrospective epidemiological analysis based on laboratory results. Results: The developed qPCR test demonstrated 100% accuracy, with a detection limit of 21.25 copies per reaction, and was validated for samples from swabbed pustule exudates and lesion crusts. To date, 295 tests have been conducted, with 88 (30%) returning positive. The positivity rate was 41.15% in male patients and 2.41% in female patients. A peak in positivity was observed in August 2022. From 2023 to 2024, there was a marked decline in test demand with occasional positive results. Conclusions: The rapid implementation of the test by our laboratory allowed for an immediate response to patients and provided important data for understanding the dynamics of monkeypox virus spread in Brazil, particularly in the Midwest region.
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(This article belongs to the Special Issue Molecular Assays for Mutation and Infectious Agent Detection)
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