Journal Description
Genes
Genes
is a peer-reviewed, open access journal of genetics and genomics published monthly online by MDPI. The Spanish Society for Nitrogen Fixation (SEFIN) 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.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, PubAg, and other databases.
- 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).
- Recognition of Reviewers: Reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
2.8 (2024);
5-Year Impact Factor:
3.2 (2024)
Latest Articles
Cardiac Phenotypes in Fabry Disease: Genetic Variability and Clinical Severity Staging Correlation in a Reference Center Cohort
Genes 2025, 16(9), 1086; https://doi.org/10.3390/genes16091086 - 15 Sep 2025
Abstract
Background/Objectives: Anderson–Fabry disease (AFD) presents with a wide spectrum of clinical manifestations, influenced by the underlying GLA genotype. While classical variants are typically associated with early-onset, multisystemic involvement, late-onset mutations and variants of uncertain significance (VUS) often display predominantly cardiac phenotypes. This study
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Background/Objectives: Anderson–Fabry disease (AFD) presents with a wide spectrum of clinical manifestations, influenced by the underlying GLA genotype. While classical variants are typically associated with early-onset, multisystemic involvement, late-onset mutations and variants of uncertain significance (VUS) often display predominantly cardiac phenotypes. This study aimed to explore the relationship between GLA variant class, cardiovascular severity, and clinical outcomes using validated staging systems and real-world data. Methods: In this single-centre retrospective study, we evaluated 42 patients with genetically confirmed AFD, stratified into classical, late-onset, and VUS categories. Cardiovascular involvement was assessed using three standardized staging tools—Del Franco, Meucci, and MSSI—and correlated with the occurrence and burden of major adverse cardiovascular events (MACE). Multivariable analyses were performed to adjust for age, sex, and treatment status. Results: Classical variants were strongly associated with more advanced cardiac staging (Del Franco, Meucci) and higher MSSI scores, reflecting systemic disease severity. These patients experienced significantly more frequent and severe MACE (p = 0.022), confirming the prognostic relevance of genotypic stratification. In contrast, carriers of late-onset mutations and VUS exhibited milder phenotypes and lower event rates. Importantly, genotype remained an independent predictor of cardiovascular risk in adjusted models, suggesting a direct contribution to disease progression beyond demographic or therapeutic factors. Conclusions: This study highlights the role of GLA genotype in shaping cardiovascular risk and clinical trajectory in AFD. Integrating genetic classification with clinical staging provides a powerful, multimodal approach to risk stratification and supports the move toward genotype-informed, personalized management strategies in AFD.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessReview
Genetic and Epigenetic Factors in Ulcerative Colitis: A Narrative Literature Review
by
Lavinia Caba, Andreea Florea, Petru Cianga, Vasile Drug, Roxana Popescu, Catalina Mihai, Cristian-Gabriel Ciobanu, Vlad Victor Iacob, Laura Florea and Eusebiu Vlad Gorduza
Genes 2025, 16(9), 1085; https://doi.org/10.3390/genes16091085 - 15 Sep 2025
Abstract
Background/Objectives: Ulcerative colitis is a chronic inflammatory bowel disease whose incidence is steadily growing worldwide. The interactions between host genetic susceptibility, gut microbiota and environmental factors determine the onset and relapsing evolution of ulcerative colitis, making it a multifactorial disorder. Methods: A narrative
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Background/Objectives: Ulcerative colitis is a chronic inflammatory bowel disease whose incidence is steadily growing worldwide. The interactions between host genetic susceptibility, gut microbiota and environmental factors determine the onset and relapsing evolution of ulcerative colitis, making it a multifactorial disorder. Methods: A narrative review was conducted to synthesize the available literature on the genes and mechanisms related to ulcerative colitis. Results: The most important independent risk factor is genetics and the candidate genes are associated with inflammation, immune regulation and epithelial permeability. Multiple GWAS have already identified candidate genes and their polymorphisms implicated in ulcerative colitis pathogenesis. Genetic susceptibility is conferred by predisposing variants influencing disease onset and progression, as well as by epigenetic modifications (DNA methylation, microRNAs). Conclusions: This review summarizes the interactions between the functional products encoded by genes linked to ulcerative colitis and immunological factors revealing their common mechanisms.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
Halotolerant Mycorrhizal Symbiosis Enhances Tolerance in Limonium Species Under Long-Term Salinity
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Catarina Gomes-Domingues, Isabel Marques, Maria Cristina Simões Costa and Ana D. Caperta
Genes 2025, 16(9), 1084; https://doi.org/10.3390/genes16091084 - 15 Sep 2025
Abstract
To survive in saline environments, plants establish complex symbiotic relationships with soil microorganisms, including halotolerant arbuscular mycorrhizal fungi (AMF). The main objective of this study was to uncover how inoculation with a consortium of halotolerant AMF influences recretohalophyte Limonium species tolerance to long-term
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To survive in saline environments, plants establish complex symbiotic relationships with soil microorganisms, including halotolerant arbuscular mycorrhizal fungi (AMF). The main objective of this study was to uncover how inoculation with a consortium of halotolerant AMF influences recretohalophyte Limonium species tolerance to long-term salinity, at physiological and molecular levels. In this study, the physiological performance, ultrastructure of leaf epidermal cells, and expression of seven genes involved in salinity response were studied in Limonium daveaui and Limonium algarvense plants exposed to 200 mM NaCl and inoculated with an AMF consortium, dominated by Rhizoglomus invernaius. An isohydric response was observed for both species after one year in salinity. Inoculation with AMF led to higher stomatal conductance for plants in non-saline conditions and improved photosystem II efficiency under salinity. In L. algarvense, inoculation enhanced stomata and salt gland epidermal area under tap water. While salinity significantly increased salt gland, stomata and pavement cells areas but not cell size. In L. daveaui, AMF led to an increased salt gland density as well as salt gland size under saline conditions. In both species, salinity increased the expression of Na+/H+ antiporter AtSOS1, aquaporin TIP5, and salt gland development related genes LbTRY, Lb7G34824 and Lb4G22721GIS2. The expression of such genes was significantly reduced in AMF-inoculated plants under salinity. Besides, higher levels of gene expression were observed in L. algarvense than in L. daveaui. Overall, our findings highlight the protective role of halotolerant AMF and emphasize their potential as sustainable effective bio-inoculants for enhancing plant salinity tolerance.
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(This article belongs to the Section Plant Genetics and Genomics)
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Open AccessReview
Evidence-Based Reporting in Preimplantation Genetic Testing (PGT)
by
Maurizio Poli, Ludovica Picchetta, Laura Siciliani and Antonio Capalbo
Genes 2025, 16(9), 1083; https://doi.org/10.3390/genes16091083 - 15 Sep 2025
Abstract
Preimplantation genetic testing (PGT) reports play a decisive role in determining the fate of IVF-generated embryos. The identification of a chromosomal or genetic abnormality that could impact the health of the resulting newborn often leads to embryo disposal or indefinite storage in cryogenic
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Preimplantation genetic testing (PGT) reports play a decisive role in determining the fate of IVF-generated embryos. The identification of a chromosomal or genetic abnormality that could impact the health of the resulting newborn often leads to embryo disposal or indefinite storage in cryogenic containers. As a growing proportion of IVF cycles include PGT assessment, greater scrutiny is being placed on its clinical validity. Initially developed to detect monogenic disorders (PGT-M) and later expanded to identify full chromosomal aneuploidies, PGT is primarily used to identify embryos unlikely to implant (aneuploid), those that would lead to miscarriage, or those causing chromosomal syndromes or monogenic conditions. Advancements in genetic analysis now allow for the assessment of more complex traits and chromosomal features from a trophectoderm biopsy, including segmental aneuploidies, chromosomal mosaicism, and polygenic conditions. However, as technology pushes the limits of biological resolution, questions arise regarding the accuracy, clinical utility, and representativeness of these findings for the entire embryo. This article reviews the gold standards for validating clinical findings and reporting strategies, aiming to maximize diagnostic utility while minimizing false positives towards appropriately defined reproductive outcomes and phenotypes.
Full article
(This article belongs to the Special Issue Current Advances and Future Perspectives on Preimplantation Genetic Testing)
Open AccessArticle
Repeats Influence Structural DNA Properties Around Functional Annotations Associated with 3D Organization and Transcription
by
Aaron Sievers, Michael Hausmann and Georg Hildenbrand
Genes 2025, 16(9), 1082; https://doi.org/10.3390/genes16091082 - 15 Sep 2025
Abstract
Background: While the fundamental principles of chromatin 3D organization and its interplay with transcriptional regulation are still not completely understood, increasing evidence suggests a considerable role of DNA repeats. Considering the influence of DNA repeats on local dinucleotide contents, the influence of dinucleotide
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Background: While the fundamental principles of chromatin 3D organization and its interplay with transcriptional regulation are still not completely understood, increasing evidence suggests a considerable role of DNA repeats. Considering the influence of DNA repeats on local dinucleotide contents, the influence of dinucleotide contents on the structural properties of DNA, their influence on histone affinity, and the influence of histone occupancy on chromatin, an indirect influence of repeats on 3D organization, seems worth testing. Methods: In this study, we search for global correlations between annotations associated with transcription and 3D organization, dinucleotide contents, DNA properties, and repeats in human and mouse. In a second step, we search for local peaks in DNA properties around those annotations and derive the influences of the dinucleotide and repeat contents (including tandem repeats (TRs) and transposons). Results: We identify several strong and significant associations between annotations and DNA properties, which are influenced by a variety of different repeats. Consistent with former findings, the Roll property is found to be especially sensitive to the sequence context. Conclusions: Our results suggest a significant effect of repeats on DNA properties and thus an indirect effect on histone occupancy and 3D chromatin organization.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessArticle
Novel Biallelic INTS1 Variants May Expand the Phenotypic Spectrum of INTS1-Related Disorders—Case Report and Literature Review
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Aleksandra Wnuk-Kłosińska, Anna Sowińska-Seidler, Michał Piechota and Aleksander Jamsheer
Genes 2025, 16(9), 1081; https://doi.org/10.3390/genes16091081 - 15 Sep 2025
Abstract
Background/Objectives: Neurodevelopmental disorders (NDDs) are genetically heterogeneous conditions with a complex molecular etiology involving numerous genes. Biallelic pathogenic variants in INTS1 cause a rare autosomal recessive NDD characterized by congenital cataracts, growth retardation, facial dysmorphism, and global developmental delay. To date, the clinical
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Background/Objectives: Neurodevelopmental disorders (NDDs) are genetically heterogeneous conditions with a complex molecular etiology involving numerous genes. Biallelic pathogenic variants in INTS1 cause a rare autosomal recessive NDD characterized by congenital cataracts, growth retardation, facial dysmorphism, and global developmental delay. To date, the clinical description of this disorder has been based solely on individual case reports, and its phenotypic spectrum remains incompletely defined. Methods: A 9-year-old female proband was evaluated for developmental delay, multiple congenital anomalies, and distinctive craniofacial features. Whole-exome sequencing (WES) was performed, followed by Sanger validation and segregation analysis. Variant pathogenicity was assessed using in silico prediction tools and 3D protein structural modeling. Results: Whole-exome sequencing identified two novel compound heterozygous missense variants in INTS1, c.1145G>A (p.Arg382Gln) and c.1195G>A (p.Gly399Ser), both located in exon 9. Segregation analysis showed that c.1145G>A was inherited from the father and c.1195G>A from the mother, and both variants are extremely rare in population databases. Conclusions: We report a patient carrying novel biallelic INTS1 variants, whose clinical presentation differs from previously reported cases, including those with milder phenotypes characterized by preserved speech development and absence of intellectual disability. This observation broadens the clinical spectrum of INTS1-related disease and underscores its phenotypic heterogeneity.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
Sex-Specific Polygenic Risk Scores and Replication in a Model-Free Analysis of Schizophrenia Data
by
Anna Ott and Jurg Ott
Genes 2025, 16(9), 1080; https://doi.org/10.3390/genes16091080 - 15 Sep 2025
Abstract
Background/Objectives: While single variants may have only small effects on common heritable traits like schizophrenia, methods for combining such effects over multiple variants have been proposed for more than 30 years. The currently favored approaches are polygenic risk scores. Their main aim is
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Background/Objectives: While single variants may have only small effects on common heritable traits like schizophrenia, methods for combining such effects over multiple variants have been proposed for more than 30 years. The currently favored approaches are polygenic risk scores. Their main aim is the genetic prediction of phenotypes. Methods: To accommodate the inherent genetic heterogeneity between males and females, we separated them into two independent datasets and in each developed allelic polygenic risk scores. We focused on variants with high predictability rather than high statistical significance and derived a statistical test to assess the significance of results obtained in one sex and replicated in the other sex. Results: As few as 5000 highly predictive variants achieved accuracy exceeding 95% in each of males and females, and only 2.8% and 3.3% of cases and controls were misclassified in females and males, respectively. Conclusions: Our allelic polygenic risk scores are based on individual genotypes rather than summary statistics and produce highly accurate, cross-validated phenotype predictions. Although variants were originally selected as being highly predictive rather than statistically significant, 544 disease-associated variants were shown to be significantly shared between males and females, which represents a replication in an independent dataset.
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(This article belongs to the Section Bioinformatics)
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Open AccessSystematic Review
Physical Performance and Sports Genetics: A Systematic Review of Candidate Gene Polymorphisms Involved in Team Sports
by
Raluca Mijaica, Dragoș Ioan Tohănean, Dan Iulian Alexe and Lorand Balint
Genes 2025, 16(9), 1079; https://doi.org/10.3390/genes16091079 - 15 Sep 2025
Abstract
Background/Objectives: This systematic review aimed to gather the most recent evidence regarding the link between genetic polymorphisms and physical performance in team sports, with a focus on the practical utility of this information for athlete selection, training personalization, and injury prevention. Methods
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Background/Objectives: This systematic review aimed to gather the most recent evidence regarding the link between genetic polymorphisms and physical performance in team sports, with a focus on the practical utility of this information for athlete selection, training personalization, and injury prevention. Methods: Sixteen studies published between 2018 and 2025 were analyzed and selected from six international databases, in accordance with the PRISMA guideline. Only English-language studies were included, which evaluated active athletes in team sports and investigated associations between genetic variations, such as Actinin Alpha 3 (ACTN3 R577X), Angiotensin I Converting Enzyme (ACE I/D), Peroxisome Proliferator-Activated Receptor Alpha (PPARA), Interleukin 6 (IL6), and Nitric Oxide Synthase 3 (NOS3), and physical performance parameters. The methodological quality of the studies was assessed using the Q-Genie tool, with all studies scoring over 45 across all 11 items, indicating high quality. Results: The ACTN3 and ACE genes stood out due to their consistent association with traits such as strength, speed, endurance, and recovery capacity. Other genes, such as PPARA, Fatty Acid Amide Hydrolase (FAAH), Angiotensinogen (AGT), and NOS3, complemented this genetic profile by being involved in the regulation of energy metabolism and injury predisposition. An increasing number of studies have begun to adopt cumulative genotype scores, suggesting a shift from a monogenic approach to complex predictive models. Conclusions: The integration of genetic profiling into the evaluation and management of athletes in team sports is becoming increasingly relevant. Although current evidence supports the applicability of these markers, robust future research conducted under standardized conditions is necessary to validate their use in sports practice and to ensure sound ethical standards.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
APOL1-Risk Genotype Induces Inflammatory and Hypoxic Gene Expression in Donor Kidneys
by
Meghan Unes, Sree Kolli, Shaurya Mehta, Chandrashekhara Manithody, Jonathan Bruno, Krista L. Lentine, Ajay Jain, Mustafa Nazzal and Yasar Caliskan
Genes 2025, 16(9), 1078; https://doi.org/10.3390/genes16091078 - 15 Sep 2025
Abstract
Background/Objectives: APOL1 renal-risk variants (RRVs) are of increasing relevance to kidney disease and transplant outcomes. It is currently understood that the presence of RRVs in donors negatively impacts kidney allograft survival in an autosomal recessive pattern of inheritance. Less well known is the
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Background/Objectives: APOL1 renal-risk variants (RRVs) are of increasing relevance to kidney disease and transplant outcomes. It is currently understood that the presence of RRVs in donors negatively impacts kidney allograft survival in an autosomal recessive pattern of inheritance. Less well known is the interplay between ischemia and alternative allograft preservation methods, such as normothermic machine perfusion (NMP), on APOL1 gene expression. To investigate this, we examined the effects of APOL1 RRVs on APOL1 gene expression in ischemic donor kidneys and compared the differences in cytokine and APOL1 expression patterns between the alternative preservation methods, static cold storage (CS) and NMP. Methods: Non-utilized deceased donor kidney pairs from donors of African ancestry were procured from Mid-America Transplant after being deemed unsuitable for kidney transplant. Samples were collected from each donor kidney pair and DNA was extracted for APOL1 genotyping. APOL1 RRVs G1 (rs73885319) (rs60910145) and G2 (rs71785313) were identified by Sanger sequencing. From each pair, one kidney underwent 6 h NMP (n = 3) and the contralateral kidney 6 h of CS (n = 3) following the initial CS. Renal perfusion and biochemical, and histologic parameters were recorded. NMP was directly compared with CS using paired donor kidneys using NMP with allogeneic red blood cells, followed by assessment of perfusion, biochemical, and histologic parameters, in addition to gene expression. Results: Donor genotyping identified kidney pairs as heterozygous for the G1 RRV (G1/G0), homozygous for the G0 allele (G0/G0), and homozygous for the G2 RRV (G2/G2), respectively. All kidneys were successfully reperfused, with mRNA transcript levels of APOL1-related genes subsequently measured. Significant differences in APOL1 gene expression were observed among all three groups of kidneys. In paired kidneys from baseline to hour 6 of NMP, mRNA expression varied significantly between G1/G0 and G2/G2 homozygous pairs (p = 0.002) as well as between the G0/G0 and G2/G2 pairs (p = 0.002). APOL1 expression shifted by a significantly higher-fold change of 2.4 under NMP conditions in the G2/G2 genotype (p < 0.001). The inflammatory cytokine marker IFN-γ was also significantly upregulated in the G2/G2 genotype kidney, in both CS and NMP groups (p = 0.001). Other related genes such as KIM-1 were upregulated by a change of 3.9-fold in the NMP group for the G2/G2 kidney. Conclusion: Donor kidney pairs with the high-risk APOL1 genotype, especially G2/G2, show increased APOL1 expression and inflammation, particularly under NMP conditions. NMP enables detection of genotype-specific molecular changes in an ischemic reperfusion injury model, supporting its potential to improve donor kidney assessment before transplantation.
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(This article belongs to the Special Issue From Genetic to Molecular Basis of Kidney Diseases)
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Open AccessArticle
Novel ATP7A Splice-Site Variant Causing Distal Motor Neuropathy and Occipital Horn Syndrome: Two Siblings and Literature Review
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Karin Writzl, Maruša Škrjanec Pušenjak, Matevž Jus, Aleš Maver, Nuška Pečarič Meglič, Borut Peterlin and Lea Leonardis
Genes 2025, 16(9), 1077; https://doi.org/10.3390/genes16091077 - 15 Sep 2025
Abstract
Background: Pathogenic hemizygous variants in ATP7A most commonly cause Menkes disease or occipital horn syndrome (OHS), whereas ATP7A-related distal hereditary motor neuropathy (dHMN) is rarely reported. Here, we describe two adult brothers with an overlapping dHMN/OHS phenotype caused by a novel ATP7A
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Background: Pathogenic hemizygous variants in ATP7A most commonly cause Menkes disease or occipital horn syndrome (OHS), whereas ATP7A-related distal hereditary motor neuropathy (dHMN) is rarely reported. Here, we describe two adult brothers with an overlapping dHMN/OHS phenotype caused by a novel ATP7A splice-site variant and review the clinical and genetic features of previously published patients with ATP7A-related dHMN. Methods: We performed detailed clinical, electrophysiological, and genetic evaluations of both siblings, including exome sequencing and RNA analysis. Additionally, we reviewed the clinical, electrophysiological, and genetic data of previously reported patients with ATP7A-related dHMN. Results: We identified a novel hemizygous ATP7A splice-site variant (NM_000052.7:c.1544-2A>T) in both brothers. The younger brother, who exhibited a more severe phenotype, presented in early childhood with mild global developmental delay, intellectual disability, and chronic diarrhea, while the older brother had childhood-onset chronic diarrhea without cognitive impairment. Both developed distal hereditary motor neuropathy later in life, and imaging revealed occipital horns. Serum copper and ceruloplasmin levels were mildly reduced. RNA sequencing revealed two aberrant transcript isoforms resulting from the splice-site variant, one of which may produce a partially functional protein. Review of previously reported patients shows that ATP7A-related dHMN may occur isolated or with overlapping features of OHS. In patients with the overlapping phenotype, chronic diarrhea was often the first symptom, followed by slowly progressive dHMN. Conclusions: Previously reported ATP7A-related dHMN has been mostly associated with missense variants. Our findings expand the mutational spectrum by identifying a splice-site variant. In patients with an overlapping OHS/dHMN phenotype, diagnosis was typically delayed for decades, suggesting this presentation remains underdiagnosed.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessArticle
The ACTN3 R577X Nonsense Allele Is Underrepresented in Professional Volleyball Players and Associated with an Increased Risk of Muscle Injury in Female Players
by
Mesut Cerit, Selin Yıldırım Tuncer, Muhammed Mustafa Piri, Murat Anılır, George John, Ekaterina A. Semenova, Andrey K. Larin, Edward V. Generozov, Ildus I. Ahmetov, Korkut Ulucan and Attila Szabo
Genes 2025, 16(9), 1076; https://doi.org/10.3390/genes16091076 - 13 Sep 2025
Abstract
Background: Muscle injuries pose a significant challenge in sports, leading to decreased performance and shortened career longevity. Individuals homozygous for the nonsense X allele of the ACTN3 rs1815739 (R577X) polymorphism, characterized by a complete absence of α-actinin-3, have been associated with reduced power
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Background: Muscle injuries pose a significant challenge in sports, leading to decreased performance and shortened career longevity. Individuals homozygous for the nonsense X allele of the ACTN3 rs1815739 (R577X) polymorphism, characterized by a complete absence of α-actinin-3, have been associated with reduced power performance and may have an increased injury risk. This study aimed to investigate the association between the ACTN3 R577X polymorphism and both volleyball player status and the risk of non-contact musculoskeletal injuries in female volleyball players. Methods: The study included 5382 Turkish and Russian subjects of European descent (187 professional volleyball players and 5195 controls), of whom 50 female players provided injury data. Sport-related injury information was obtained from medical records maintained by team physicians and physiotherapists. Results: A pooled analysis of the two cohorts demonstrated that the frequency of the ACTN3 X allele was significantly lower in volleyball players than in controls, with an odds ratio of 0.763 (95% CI: 0.61–0.95, p = 0.02). In the pre-specified recessive contrast (XX vs. RR + RX) among 50 players, exact methods indicated higher injury odds for the XX genotype (OR = 7.87, 95% CI: 0.94–374.58; p = 0.0366), which was classified as borderline/exploratory. Penalized (Firth) regression produced estimates of a similar magnitude after adjustment for age and playing position (adjusted OR = 5.92, 95% CI: 1.12–60.98), although confidence intervals remained wide. Conclusions: The ACTN3 X allele is underrepresented in professional volleyball players, and it is associated with an increased risk of muscle injury in female players.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessArticle
Evaluation of Long-Read RNA Sequencing Procedures for Novel Isoform Identification and Quantification in Human Whole Blood
by
Hikari Okada, Alessandro Nasti, Yoshio Sakai, Yumie Takeshita, Sadahiro Iwabuchi, Ho Yagi, Tomomi Hashiba, Noboru Takata, Taka-Aki Sato, Takeshi Urabe, Seiji Nakamura, Toshinari Takamura, Taro Yamashita, Takuro Tamura, Kenichi Matsubara and Shuichi Kaneko
Genes 2025, 16(9), 1075; https://doi.org/10.3390/genes16091075 - 12 Sep 2025
Abstract
Background/Objectives: Blood flows through the body and reaches all tissues, contributing to homeostasis and physiological functions. Providing information and understanding on how the transcriptome of whole blood behaves in response to physiological or pathological stimuli is critical. Methods: We collected blood from four
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Background/Objectives: Blood flows through the body and reaches all tissues, contributing to homeostasis and physiological functions. Providing information and understanding on how the transcriptome of whole blood behaves in response to physiological or pathological stimuli is critical. Methods: We collected blood from four healthy individuals and performed long-read RNA sequencing (lrRNA-seq) for the precise identification and expression quantification of RNA variants. Moreover, we compared two genome references: the Genome Reference Consortium Human Build 38 (GRCh38) and the Telomere-to-Telomere (T2T) assembly of the CHM13 cell line (T2T-CHM13). Results: With GRCh38, we could identify an average of about 46,000 genes, 1.3-fold more genes than T2T-CHM13. Similarly, we identified about 185,000 isoforms with GRCh38 and 140,000 with T2T-CHM13, finding similar differences for full splice match (FSM) and incomplete splice match (ISM) transcript isoforms. There were about 90,000 novel isoforms for GRCh38 and 70,000 for T2T-CHM13, 47% and 50% of the total number of identified isoforms, respectively. Differences in isoform numbers between GRCh38 and T2T-CHM13 were identified for the subcategories “Genic Genomic”, “Intergenic”, and “Genic Intron”. Using GRCh38, we generally identified a higher number of non-coding isoforms, as well as a higher number of isoforms aligning within intron and intergenic regions. Nonetheless, GRCh38 might incur false positive results, and T2T-CHM13 is likely more accurate for genome sequences in the repetitive regions. Conclusions: LrRNA-seq is a valid method for the identification of novel isoforms in blood, and this study is a first step toward the creation of a comprehensive database of the structure and expression of transcript isoforms for optimized predictive medicine.
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(This article belongs to the Section RNA)
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Open AccessArticle
Forensic DNA Recovery from FFPE Tissue Using the Maxwell® RSC Xcelerate Kit: Optimization, Challenges, and Limitations
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Dagmara Lisman, Andrzej Ossowski, Aleksandra Tołoczko-Grabarek, Mateusz Kozłowski and Aneta Cymbaluk-Płoska
Genes 2025, 16(9), 1074; https://doi.org/10.3390/genes16091074 - 12 Sep 2025
Abstract
Background/Objectives: Obtaining reliable DNA profiles from archival tissue preserved as formalin-fixed, paraffin-embedded (FFPE) samples remains a major challenge in both forensic and medical evaluations. The quality of DNA isolated from FFPE material is frequently compromised due to formalin-induced fragmentation and chemical modifications. These
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Background/Objectives: Obtaining reliable DNA profiles from archival tissue preserved as formalin-fixed, paraffin-embedded (FFPE) samples remains a major challenge in both forensic and medical evaluations. The quality of DNA isolated from FFPE material is frequently compromised due to formalin-induced fragmentation and chemical modifications. These limitations are particularly relevant in cases of suspected medical malpractice related to cancer diagnosis or treatment, where retrospective molecular analyses may provide critical evidence. The aim of this study was to evaluate the performance of the Maxwell® RSC Xcelerate DNA FFPE Kit (Promega) in generating DNA profiles from archival FFPE tissue blocks of endometrial cancer and to identify the limitations associated with this approach. Methods: Archival FFPE blocks of endometrial cancer were analyzed using the Maxwell® RSC Xcelerate DNA FFPE Kit. DNA yield, purity, and degradation indices were assessed using standard real-time PCR-based quantification methods. Short tandem repeat (STR) profiling was performed with forensic genotyping kits, and the completeness, allele balance, and reliability of obtained profiles were evaluated. The obtained results were compared with reference quality thresholds commonly used in forensic practice. Results: The Maxwell® RSC Xcelerate Kit allowed for recovery of relatively high DNA yields with consistently low degradation indices, confirming good extraction efficiency from FFPE samples. Nevertheless, despite favorable quantitative values, the generation of complete STR profiles was often unsuccessful. Partial or incomplete profiles were frequent, characterized by allele dropout and imbalance, which substantially reduced their evidentiary value. These findings suggest that DNA fragmentation and fixation-related artifacts impair amplification efficiency and limit the usefulness of STR analysis. Conclusions: This study emphasizes the persistent challenges of DNA profiling from FFPE tissue in forensic-medical contexts. Although the Maxwell® RSC Xcelerate Kit demonstrated effective DNA recovery, the ability to generate complete and interpretable STR profiles remained limited. Further refinement of extraction protocols, as well as improved interpretative strategies, are required to enhance the reliability and evidentiary significance of molecular analyses based on archival FFPE material.
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(This article belongs to the Special Issue Advanced Research in Forensic Genetics)
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Open AccessBrief Report
Rapid Documentation of Possible Semen Stains for Forensic DNA Profiling
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Zhonghui Thong, Audrey Ping Jue Wee, Baoqiang Heng and Christopher Kiu Choong Syn
Genes 2025, 16(9), 1073; https://doi.org/10.3390/genes16091073 - 12 Sep 2025
Abstract
The acid phosphatase (AP) test is widely utilised in forensic biology laboratories to examine for the presence of semen on crime evidence. If semen is present, the AP-positive areas are marked on the exhibit to indicate the precise location of the semen stain.
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The acid phosphatase (AP) test is widely utilised in forensic biology laboratories to examine for the presence of semen on crime evidence. If semen is present, the AP-positive areas are marked on the exhibit to indicate the precise location of the semen stain. However, documenting AP-positive areas with a crayon is time-consuming and laborious. In this proof-of-concept study, we evaluated the use of Saral Wax-Free Transfer Taper (TP) as an alternative tool for tracing the boundaries of AP-positive areas. We demonstrated that the TP pigment did not inhibit PCR amplification, as indicated by consistent internal PCR control (IPC) CT values during real-time DNA quantification. While a reduction in DNA yield was observed under stress-test conditions, where TP pigment was intentionally included in the samples, complete STR profiles were still recovered with no allele dropout. Importantly, the documenting time for AP mapping was reduced by approximately five-fold with TP compared to crayon, underscoring its potential to enhance efficiency in forensic laboratory workflows.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessArticle
Genome-Wide Identification of TPL/TPR Gene Family in Ten Cotton Species and Function Analysis of GhTPL3 Involved in Salt Stress Response
by
Ganggang Zhang, Jianguo Gao, Faren Zhu, Kailu Chen, Jiliang Fan, Lu Meng, Zihan Li, Shandang Shi and Hongbin Li
Genes 2025, 16(9), 1072; https://doi.org/10.3390/genes16091072 - 12 Sep 2025
Abstract
Background/Objectives: The TOPLESS (TPL) and TOPLESS-related (TPR) proteins represent a highly conserved class of transcriptional co-repressors in plants, playing pivotal roles in modulating growth, development, and stress responses through the repression of key transcriptional regulators. However, a comprehensive genome-wide analysis of the TPL
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Background/Objectives: The TOPLESS (TPL) and TOPLESS-related (TPR) proteins represent a highly conserved class of transcriptional co-repressors in plants, playing pivotal roles in modulating growth, development, and stress responses through the repression of key transcriptional regulators. However, a comprehensive genome-wide analysis of the TPL/TPR gene family and its involvement in stress responses remains unexplored in cotton. Methods: In this study, 60 TPL/TPR genes were identified from the genomes of ten Gossypium species via bioinformatics approaches, and their protein physicochemical properties, gene structures, phylogenetic relationships, cis-regulatory elements, and expression profiles were characterized. Results: Chromosomal localization and collinearity analyses revealed that segmental duplication events have contributed to the expansion of the TPL/TPR gene family. Further examination of exon–intron architectures and conserved motifs highlighted strong evolutionary conservation within each TPL/TPR subgroup. Expression profiling demonstrated that TPL/TPR genes exhibit tissue-specific expression patterns, with particularly high transcript abundance in floral organs (e.g., petals and stigmas). Cis-element analysis suggested their potential involvement in multiple stress-responsive pathways. Notably, GhTPL3 showed high constitutive expression across various tissues and under stress conditions, with the most pronounced up-regulation under salt stress. Functional validation via Virus-Induced Gene Silencing (VIGS) confirmed that GhTPL3 silencing significantly impairs cotton salt stress tolerance, underscoring its critical role in abiotic stress adaptation. Conclusions: Our findings provide novel insights into the functional diversification and regulatory mechanisms of the TPL/TPR family in cotton, offering a valuable genetic resource for breeding stress-resilient cotton varieties.
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(This article belongs to the Special Issue Physiological and Molecular Mechanisms of Plant Stress Response)
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Open AccessArticle
Retinoic Acid-Regulated Epigenetic Marks Identify Alx1 as a Direct Target Gene Required for Optic Cup Formation
by
Marie Berenguer and Gregg Duester
Genes 2025, 16(9), 1071; https://doi.org/10.3390/genes16091071 - 11 Sep 2025
Abstract
Background/Objectives: Retinoic acid (RA) is a transcriptional control agent that regulates several aspects of eye development including invagination of the optic vesicle to form the optic cup, although a target gene for this role has not been previously identified. As loss of RA
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Background/Objectives: Retinoic acid (RA) is a transcriptional control agent that regulates several aspects of eye development including invagination of the optic vesicle to form the optic cup, although a target gene for this role has not been previously identified. As loss of RA synthesis in Rdh10 knockout embryos affects the expression levels of thousands of genes, a different approach is needed to identify genes that are directly regulated by RA. Methods: Here, we combined ChIP-seq for the H3K27ac epigenetic mark with RNA-seq on optic field tissue from E10 wild-type and Rdh10−/− embryos that exhibit failure in optic cup formation. Results: We identified a small number of genes with decreased expression when RA is absent that also have a decreased presence of a nearby epigenetic gene activation mark (H3K27ac). One such gene was Alx1 that also has an RA response element (RARE) located near the RA-regulated H3K27ac mark, providing evidence that RA directly activates Alx1. In situ hybridization studies showed that Rdh10−/− embryos exhibit a large decrease of Alx1 expression in the optic field. CRISPR/Cas9 knockout of Alx1 resulted in a defect in optic cup formation due to a failure of perioptic mesenchyme to migrate and separate the optic cup epithelium from the forebrain neuroepithelium. Conclusions: Our studies support a model in which RA functions to directly activate Alx1 in perioptic mesenchyme to stimulate an early stage of eye development during which the optic vesicle folds into an optic cup that forms the retina.
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(This article belongs to the Special Issue Genetics and Genomics of Retinal Development and Diseases)
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Open AccessArticle
JCHAIN: A Prognostic Marker Based on Pan-Cancer Analysis to Inhibit Breast Cancer Progression
by
Jinfeng Zhao, Wanquan Chen, Longpeng Li, Zhibin Zhang and Yaxin Wang
Genes 2025, 16(9), 1070; https://doi.org/10.3390/genes16091070 - 11 Sep 2025
Abstract
Background/Objectives: The JCHAIN (immunoglobulin-linked chain) is a multimeric IgA and IgM-linked chain whose involvement in oncogenesis and immunomodulation is unknown. The goal of this work was to conduct a comprehensive pan-cancer analysis of the JCHAIN to determine its expression profile, prognostic significance, immune
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Background/Objectives: The JCHAIN (immunoglobulin-linked chain) is a multimeric IgA and IgM-linked chain whose involvement in oncogenesis and immunomodulation is unknown. The goal of this work was to conduct a comprehensive pan-cancer analysis of the JCHAIN to determine its expression profile, prognostic significance, immune infiltration, and function in diverse malignancies. Methods: We performed pan-cancer analysis of gene expression data and protein expression data of JCHAIN using multiple databases, and analysed the prognostic significance of JCHAIN in a variety of cancers using univariate Cox analysis and Kaplan–Meier tools. The relationship between JCHAIN and immune cell infiltration was analysed via the TISIDB and TIMER websites, while single-cell and spatial transcriptomic analyses were performed to analyse the relationship between JCHAIN and the immune microenvironment. Mutations in the JCHAIN and their connection with methylation were then investigated using the cBioPortal and UALCAN websites. Afterwards, the function of JCHAIN was analysed by KEGG as well as GSEA, and the function of JCHAIN in breast cancer cells was verified by in vitro experiments. Results: The expression of the JCHAIN gene shows significant differences in most cancers, and its high expression is associated with a favourable prognosis. In most cancers, JCHAIN gene expression is closely linked to immune-related genes, immune cells, and methylation, as well as to being affected by mutations. In breast cancer, we found that the JCHAIN was negatively correlated with cellular stemness. Enrichment analysis indicated that the JCHAIN was involved in immune responses, B cell activation, and JAK-STAT signalling pathways. Functional experiments showed that overexpression of the JCHAIN inhibited tumour migration and invasion, which may be closely related to the activation of the IL-2/STAT4 signalling pathway. Conclusions: We found that JCHAIN can be used as a diagnostic and prognostic marker for a variety of cancers by pan-cancer analysis and verified that JCHAIN affects breast cancer cell progression through IL-2/STAT4 by in vitro experiments.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessCase Report
Mitochondrial Complex IV Deficiency Nuclear Type 11 Caused by a Novel Start-Lost Variant in the COX20 Gene
by
Anna Kuchina, Artem Borovikov, Olga Sidorova, Maria Orlova, Oxana Ryzhkova, Igor Zaigrin and Aysylu Murtazina
Genes 2025, 16(9), 1069; https://doi.org/10.3390/genes16091069 - 11 Sep 2025
Abstract
Background: The COX20 gene encodes a critical assembly factor for cytochrome C oxidase (complex IV), and biallelic loss-of-function variants in this gene cause mitochondrial complex IV deficiency, typically presenting in infancy or childhood with hypotonia, ataxia, neuropathy, or dystonia. Methods: This study
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Background: The COX20 gene encodes a critical assembly factor for cytochrome C oxidase (complex IV), and biallelic loss-of-function variants in this gene cause mitochondrial complex IV deficiency, typically presenting in infancy or childhood with hypotonia, ataxia, neuropathy, or dystonia. Methods: This study describes an adult male patient with a broad clinical spectrum of central and peripheral nervous system involvement. Different medical genetic tests were performed for the patient, and only whole-genome trio sequencing identified pathogenic variants in the COX20 gene. A review of previously reported cases was conducted to compare clinical and imaging findings. Results: Two compound heterozygous COX20 variants in were identified: a known missense variant (c.41A>G; p.Lys14Arg) disrupting splicing, and a novel start-loss variant (c.2T>C; p.Met1?). The patient exhibited progressive ataxia, pyramidal signs, and peripheral neuropathy, accompanied by cervical spinal cord atrophy on spinal cord MRI and lower leg muscle fat infiltration on muscle MRI, an imaging feature not previously emphasized in COX20-related disease. Conclusions: A review of previously reported cases underscores broad clinical variability of the COX20-associated disorder, which may contribute to a prolonged diagnostic odyssey.
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(This article belongs to the Collection Genetics and Genomics of Rare Disorders)
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Open AccessArticle
Genome-Wide Association Study of Chlorophyll Fluorescence and Hyperspectral Indices in Drought-Stressed Young Plants in Maize
by
Lovro Vukadinović, Vlatko Galić, Maja Mazur, Antun Jambrović and Domagoj Šimić
Genes 2025, 16(9), 1068; https://doi.org/10.3390/genes16091068 - 11 Sep 2025
Abstract
Background/Objectives: Global maize production is considerably affected by drought aggravated by climate change. No genome-wide association study (GWAS) or candidate gene analysis has been performed using chlorophyll fluorescence (ChlF) and hyperspectral (HS) indices measured in young plants challenged by a water deficit. Our
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Background/Objectives: Global maize production is considerably affected by drought aggravated by climate change. No genome-wide association study (GWAS) or candidate gene analysis has been performed using chlorophyll fluorescence (ChlF) and hyperspectral (HS) indices measured in young plants challenged by a water deficit. Our objective was to conduct a GWAS of nine ChlF and HS indices measured in a diversity panel of drought-stressed young plants grown in a controlled environment using a maize single nucleotide polymorphism (SNP) 50k chip. Methods: A total of 165 inbred lines were genotyped using the Infinium Maize50K SNP array and association mapping was carried out using a mixed linear model. Results: The GWAS detected 37 respective SNP markers significantly associated with the maximum quantum yield of the primary photochemistry of a dark-adapted leaf (Phi_Po), the probability that a trapped exciton moves an electron into the electron transport chain further than QA (Psi_o), the normalized difference vegetation index (NDVI), the Zarco–Tejada and Miller Index (ZMI), greenness, modified chlorophyll absorption in reflectance (MCARI), modified chlorophyll absorption in reflectance 1 (MCARI1), and Gitelson and Merzlyak indices 1 and 2 (GM1 and GM2). Conclusions: Our results contribute to a better understanding of the genetic dissection of the ChlF and HS indices, which is directly or indirectly related to physiological processes in maize, supporting the use of HS imaging in the context of maize breeding.
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(This article belongs to the Special Issue Molecular Breeding and Genetics of Plant Drought Resistance)
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Open AccessArticle
Exceptions to Broad Tissue-Specific Transcriptomic Interdependence: Searching for Independence in Expression of Genes
by
Mikołaj Danielewski, Jarosław Walkowiak, Karolina Wielgus and Jan Krzysztof Nowak
Genes 2025, 16(9), 1067; https://doi.org/10.3390/genes16091067 - 10 Sep 2025
Abstract
Background: Correlation of genes within tissues has attracted much attention. In contrast, genes that are INDependent In Expression (INDIE) remain poorly understood, even though they may represent tissue admixtures, reflect new regulatory mechanisms, either transcriptional or post-transcriptional, and contribute to biomarkers or machine
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Background: Correlation of genes within tissues has attracted much attention. In contrast, genes that are INDependent In Expression (INDIE) remain poorly understood, even though they may represent tissue admixtures, reflect new regulatory mechanisms, either transcriptional or post-transcriptional, and contribute to biomarkers or machine learning algorithms. We hypothesised that INDIE genes can be found, may remain uncorrelated across tissues, and replicate within tissues in external datasets. Methods: Biweight midcorrelation was calculated for each gene against all other genes with sufficiently high expression in the given tissue from the GTEx dataset v8, along with the means of absolute values of obtained correlation coefficients. The threshold for gene designation as INDIE was both absolute (r) and relative (Z-score), while the threshold for external validation in the whole blood (four datasets) and the ileum (two datasets) was relative. Results: Only one gene, RPL13P12, was INDIE in all the analysed GTEx tissues, but it did not replicate in the external datasets. In contrast, HIST1H2AD and TMEM176B were not only INDIE in GTEx whole blood but also replicated in all four external datasets, despite their heterogeneity. Moreover, ACAT2 replicated in both external ileal datasets. The haemoglobin gene HBB belonged to most widespread INDIE genes in various GTEx tissues and was validated in an external ileal dataset, pointing towards the importance of tissue heterogeneity in bulk samples. Conclusions: A set of genes exhibiting independent expression patterns across various tissues of GTEx was described. Results for each tissue are made available. Even though many findings can be explained by tissue heterogeneity, some results point towards interesting mechanisms of gene expression regulation.
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(This article belongs to the Section Molecular Genetics and Genomics)
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