Gene Reports最新文献

{"title":"SELEX-based aptamer production: A key step in cholera detection","authors":"Mahboobeh Hasani Fard ,&nbsp;Jafar Amani ,&nbsp;Gholamreza Olad","doi":"10.1016/j.genrep.2025.102265","DOIUrl":"10.1016/j.genrep.2025.102265","url":null,"abstract":"<div><div><em>Vibrio cholerae</em> (<em>V. cholerae</em>) is responsible for the second-highest number of deaths worldwide due to diarrhea. This microorganism is closely associated with cholera outbreaks, both pandemic and epidemic. Therefore, an early rapid detection assay is crucial to prevent the disease's spread. Cholera toxin (Ctx) is a <em>V. cholerae</em> virulence factor that plays a primary and essential role in the pathogenesis of this bacterium. Aptamers, a single-stranded (ss) folded RNA or ssDNA that can bind and detect various nucleic and non-nucleic acid molecules with high affinity and specificity, offer a promising alternative to antibodies in various applications such as biomarker discovery, diagnosis, imaging, and targeted therapy. These aptamers are selected through a process called systematic evolution of ligands by exponential enrichment (SELEX). The present study aimed to produce aptamers by asymmetric PCR, the best conditions obtained for asymmetric PCR included the ratio of 1:80 primers, 20 cycles, and a temperature of 57 °C. After running 11 rounds of SELEX, appropriate aptamers were isolated. The limit of detection (LoD) and dissociation constant (K_D) of the best aptamer for CtxB were calculated for specificity and affinity. The LoD was measured as 100 ± 20 pg/ml, and the K_D was calculated as 320 ± 60 pM.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102265"},"PeriodicalIF":1.0,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144178494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring genetic complexity: Pseudo hypoparathyroidism mimicking cystic fibrosis","authors":"Hima J. Challa,&nbsp;Kalyan Ram Uppaluri,&nbsp;A.Sai. Rishika Gopikar,&nbsp;Anusha Dasari,&nbsp;Sravani Tadikonda,&nbsp;Rebecca Chalcedony,&nbsp;K. Krishna Vardhini,&nbsp;Kalyani Palasamudram,&nbsp;Natya Kanuri,&nbsp;Aswini Korivepi,&nbsp;Sruthi Gadwalker,&nbsp;S. Lokesh Sai Kishore","doi":"10.1016/j.genrep.2025.102266","DOIUrl":"10.1016/j.genrep.2025.102266","url":null,"abstract":"<div><div>Cystic fibrosis (CF) is a genetic disorder caused by pathogenic variants in the <em>CFTR</em> gene, primarily affecting the respiratory, gastrointestinal, and endocrine systems. However, due to overlapping clinical features with other genetic and metabolic disorders, differentiating CF from alternative diagnoses remains challenging. Pseudohypoparathyroidism (PHP), a rare endocrine disorder characterized by parathyroid hormone (PTH) resistance, leading to hypocalcemia, hyperphosphatemia, and skeletal abnormalities, further complicates the process of differentiating CF from other genetic conditions featuring respiratory symptoms.</div><div>We present a 10-year-old male with recurrent respiratory infections, chronic cough, growth impairment, and hypotonia, initially suspected of having CF. Whole-exome sequencing (WES) identified a variant of uncertain significance (VUS) in <em>CFTR</em> (Exon 1, p. Ser4Leu) but a likely pathogenic variant in <em>GNAS</em> (Exon 5, p. Val128Ala), confirming PHP. This case not only highlights the complexity of genetic disorders with overlapping phenotypes but also underscores the need for continuous learning and adaptation in the face of such complexity. The crucial role of next-generation sequencing (NGS) in refining diagnoses further emphasizes this point.</div><div>This case underscores the importance of considering alternative genetic etiologies in patients with CF-like symptoms. A multidisciplinary approach integrating genetic, biochemical, and clinical assessments is essential for accurate diagnosis and optimal management. This case also highlights the need for further research to explore respiratory involvement in PHP, an area that remains largely unexplored.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102266"},"PeriodicalIF":1.0,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144130829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The insertion/deletion gene polymorphism of angiotensin-converting enzyme and its serum level in lupus nephritis among Egyptians","authors":"Shaymaa Abdelraheem Abdelhady ,&nbsp;Eman Abd El Moamen ,&nbsp;Mohamed Fawzy ,&nbsp;Ayman Salem ,&nbsp;Ahmed Maaty ,&nbsp;Maii Abdelraheem ,&nbsp;Salwa Faisal ,&nbsp;Gehan A. Ibrahim","doi":"10.1016/j.genrep.2025.102264","DOIUrl":"10.1016/j.genrep.2025.102264","url":null,"abstract":"<div><h3>Background and objective</h3><div>Systemic lupus erythematosus (SLE) and its complications like lupus nephritis (LN) may be affected by Angiotensin Converting Enzyme (ACE) insertion/deletion (I/D) polymorphism. However, the results of previous studies and meta-analyses didn't find consistent conclusions about the association between LN and ACE alleles. This study aimed to assess the I/D polymorphism of the ACE gene in Egyptian patients with biopsy-confirmed LN.</div></div><div><h3>Methodology</h3><div>This case-control study was conducted on 94 LN patients and 40 healthy controls. LN was diagnosed according to the histopathological findings of the International Society of Nephrology/Renal Pathology Society. The biochemical analysis includes serum creatinine, 24-h proteinuria, anti-nuclear antibodies (ANA), and anti-double-stranded deoxyribonucleic acid (dsDNA) in all patients have been done. Serum ACE levels were measured using an ELISA Kit. ACE I/D genotypes were determined by real-time polymerase chain reaction (RT-PCR).</div></div><div><h3>Results</h3><div>A significant prevalence of DD genotype was observed in LN patients than in healthy participants. Higher serum creatinine was observed with DD genotypes, ACE levels, and proteinuria than the other genotypes. DD genotype has been linked to a higher risk of LN.</div></div><div><h3>Conclusion</h3><div>ACE I/D polymorphism could be associated with lupus nephritis and it can be exploited as a prognostic marker for early LN predisposition.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102264"},"PeriodicalIF":1.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144321253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interplay between the cellular stress pathway, stemness markers, and Helicobacter pylori infection in gastric cancer","authors":"Mehran Gholamin ,&nbsp;Atena Mansouri ,&nbsp;Mohammad Reza Abbaszadegan ,&nbsp;Mohammad Ali Karimi ,&nbsp;Hossein Barzegar ,&nbsp;Fatemeh Fardi Golyan ,&nbsp;Hanie Mahaki ,&nbsp;Hamid Tanzadehpanah ,&nbsp;Reihaneh Alsadat Mahmoudian","doi":"10.1016/j.genrep.2025.102263","DOIUrl":"10.1016/j.genrep.2025.102263","url":null,"abstract":"<div><h3>Background</h3><div>Gastric cancer (GC) remains one of the leading causes of cancer-related mortality worldwide, particularly in regions with a high prevalence of <em>Helicobacter pylori</em> (<em>H. pylori</em>). Chronic <em>H. pylori</em> infection triggers persistent inflammation and cellular stress, both of which play critical roles in the malignant transformation of gastric epithelial cells. This study aimed to investigate the correlation between <em>H. pylori</em> infection, activation of cellular stress pathways, and the expression of stemness markers in GC.</div></div><div><h3>Methods</h3><div>The study analyzed GC tissues and matched adjacent normal tissues from 86 patients who underwent gastrectomy. Total RNA was extracted from these samples and subjected to quantitative real-time PCR to evaluate the mRNA expression profiling of stemness markers (<em>CD44</em> and <em>SALL4</em>) and stress response proteins (<em>DDIT3</em> or <em>CHOP</em> and <em>GRP94</em> or <em>HSP90B1</em>). The presence of <em>H. pylori</em> was confirmed by PCR amplification of specific bacterial genes.</div></div><div><h3>Results</h3><div>The study revealed significant overexpression of <em>CD44</em> (43/86) and <em>SALL4</em> (49/86) in tumor tissues compared to adjacent normal tissues, with expression levels correlating with advanced disease stages (<em>P</em> &lt; 0.05). Elevated expression of <em>DDIT3</em> (32/86) and <em>GRP94</em> (39/86) was also observed, highlighting their roles in apoptosis resistance and increased tumor aggressiveness (<em>P</em> &lt; 0.05). Notably, a significant correlation was found between the co-expression of <em>DDIT3</em>, <em>GRP94</em> (<em>HSP90B1</em>), <em>CD44</em>, and <em>SALL4</em> with each other in relation to certain clinicopathological features in GC specimens (<em>P</em> &lt; 0.05). Furthermore, <em>H. pylori</em> infection was detected in 55.8 % of samples, suggesting a strong association between chronic inflammation and GC progression.</div></div><div><h3>Conclusion</h3><div>These findings highlight the critical role of <em>H. pylori</em>-induced cellular stress in promoting stemness properties within GC cells. The upregulation of stemness markers presents promising potential as prognostic indicators and therapeutic targets. Understanding of these molecular mechanisms could facilitate the development of innovative diagnostic tools and targeted treatments for GC.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102263"},"PeriodicalIF":1.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144147716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular and genetic insights into varicose veins","authors":"V. Naveen Kumar ,&nbsp;V. Chitra ,&nbsp;T. Tamilanban","doi":"10.1016/j.genrep.2025.102260","DOIUrl":"10.1016/j.genrep.2025.102260","url":null,"abstract":"<div><div>Varicose veins are characterized by enlarged, twisted, and tortuous veins in the lower extremities. The identified etiologies of varicose veins include age, sex, orthostasis, and genetics. However, numerous other factors remain undetermined. This review explores the various key elements contributing to the pathogenesis of varicose veins, including integrins, flow-sensitive ion channels (Ca²⁺ and K⁺), angiotensin II type 1 receptor (AT1R), matrix metalloproteinases (MMPs), purinergic receptors, vascular endothelial growth factor (VEGF) and its receptors, elastin, collagen, estrogen, and calcium ions. Also, this review covers the role of vascular cell adhesion molecule-1 (VCAM-1), intercellular adhesion molecule-1 (ICAM-1), endothelial leucocyte adhesion molecule (ELAM-1), and von Willebrand factor on veno-tonicity. Both an invasive and non-invasive therapeutic approach against varicose veins were explored. Research on varicose veins continues to expand in an effort to identify the precise causal factors and underlying mechanisms. The rising incidence of comorbidities also presents an increasing concern for healthcare. These factors highlight the need to define the disease's underlying pathology in order to identify new, more effective drug intervention targets.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102260"},"PeriodicalIF":1.0,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144239405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Start Codon Targeted (SCoT) markers unveiled the genetic diversity of Nelumbo nucifera Gaertn. from Kerala, South India","authors":"Divyashri,&nbsp;B. Vishnu,&nbsp;E.A. Siril","doi":"10.1016/j.genrep.2025.102262","DOIUrl":"10.1016/j.genrep.2025.102262","url":null,"abstract":"<div><div>Start Codon Targeted (SCoT) DNA markers are dominant and commonly used for the evaluation of the genetic diversity of several horticultural crops. <em>Nelumbo nucifera</em> Gaertn. is an important perennial species chiefly valued in horticulture, ornamental, and medicinal uses. In the present study, SCoT markers were used to assess the genetic diversity of <em>N. nucifera</em> accessions from Kerala along with some collections hail from Tamil Nadu, and Andhra Pradesh of India. A total of 94.2 % SCoT alleles were found to be polymorphic amidst 31 accessions. Simultaneously, the polymorphism information content (PIC), heterozygosity, effective multiplex ratio, marker index, discriminating and resolving power values indicated the efficacy of selected primers. Further, midpoint values of diversity indices such as Shannon's information index (0.36), gene diversity (0.23), the effective number of alleles (1.38), and the observed number of alleles (1.94) revealed moderate genetic diversity among the accessions studied. This was also supported by a Dendrogram plotted based on the Unweighted neighbor joining method using Jaccard's similarity coefficient. The arrangement of accessions, regardless of their geographical location, was confirmed by the dendrogram and scatter plot based on the principal coordinate analysis. Relationships established by Andhra Pradesh and Tamil Nadu accessions with the individuals from three political zones of Kerala strengthen the chances of genetic mix-up <em>via</em> migrations. However, conservation strategies have been duly implemented for this species since it faces severe habitat destruction. The study is the first report on the genetic diversity analysis of <em>N. nucifera</em> using highly informative SCoT markers.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102262"},"PeriodicalIF":1.0,"publicationDate":"2025-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144105277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The prevalence of chemokine receptors (CCR5-Δ32, CCR5-m303, CCR2-64I, and SDF1-3'A) in the population with sickle cell anemia","authors":"Motiram Sahu ,&nbsp;Dinesh Kumar ,&nbsp;Somendra Kumar ,&nbsp;Anil Kumar","doi":"10.1016/j.genrep.2025.102261","DOIUrl":"10.1016/j.genrep.2025.102261","url":null,"abstract":"<div><h3>Objective</h3><div>The objective of the present research was to examine the presence of gene polymorphisms within chemokine receptors in a population with Sickle Cell Disease (SCD) and in a group of individuals without health complications. The selected genotypes were the chemokine receptor genes CCR5-Δ32, CCR5-m303, CCR2-64I, and SDF1-3'A.</div></div><div><h3>Methods</h3><div>From Chhattisgarh, India, 2586 individuals were screened for sickle cell anemia, out of which 200 individuals with SCD and 50 as controls were subjected to genotyping of CCR5-Δ32, CCR5-m303, CCR2-64I, and SDF1-3'A gene polymorphisms using RT-qPCR, followed by RFLP. The frequencies of both genotypes and alleles were calculated, and the assessment of Hardy-Weinberg equilibrium was performed using the chi-squared goodness-of-fit test.</div></div><div><h3>Results</h3><div>We report a 10.55 % (HbAs-9.78 % &amp; HbSS-0.77 %) prevalence of sickle cell anemia in Chhattisgarh, India, and the allelic frequencies of CCR5/CCR5 and Δ32/Δ32 as 0.966 and 0.034, respectively (χ2 = 0.3097, P-0.85654). The CCR5-m303 mutation was not detected in any of the individuals, indicating the absence of mutant alleles. The allelic frequencies for the wild-type CCR2-64 V allele and the CCR2-64I variant were calculated at 0.84 and 0.16 (χ2 = 6.9444, <em>P</em> = 0.3105) and the wild-type SDF1 and the 3′A variant were determined as 0.732 and 0.268, respectively (χ2 = 0.9630, P-061783).</div></div><div><h3>Conclusions</h3><div>The present study provides essential insights into the prevalence of chemokine receptor gene polymorphisms in SCD and healthy populations. The findings indicate distinct patterns in the distribution of genotypes and alleles, consistent with Hardy-Weinberg equilibrium. The variant CCR5-Δ32 is found to be helpful in inhibiting inflammation, especially in the SCD population.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102261"},"PeriodicalIF":1.0,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144072562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular cloning and enzymatic characterization of arginine deiminase (LrADI) from Limosilactobacillus reuteri DSM 20016: A candidate for cancer metabolic therapy","authors":"Darshali Pravin Thakker,&nbsp;K.N. Rajnish","doi":"10.1016/j.genrep.2025.102257","DOIUrl":"10.1016/j.genrep.2025.102257","url":null,"abstract":"<div><div>Arginine deiminase (ADI) is an arc-degrading enzyme that hydrolyzes L-arginine into L-citrulline and ammonia through guanidine deamination. It belongs to the guanidino group modifying enzymes (GME) superfamily, which plays a crucial role in the microbial ADI pathway. In this study, the ADI-encoding gene <em>arcA</em> from <em>Limosilactobacillus reuteri</em> DSM 20016 was cloned and expressed. The open reading frame (ORF) comprises 1233 base pairs, encodes a protein of 411 amino acids. A recombinant pET28b-<em>arcA</em> expression vector was constructed and transformed into <em>Escherichia coli</em> BL21 (DE3) for heterologous expression. Protein expression was induced with IPTG, and the recombinant ADI (LrADI) was purified using Ni-NTA histidine-tagged affinity chromatography. Biochemical characterization revealed an optimal reaction temperature of 40 °C and a pH optimum of 6. Kinetic analysis showed a Michaelis constant of 1.63 mM and a maximum reaction velocity (V_max) of 1.08 mM/min. SDS-PAGE confirmed a molecular mass of ~46 kDa. These findings provide insights into the enzymatic properties and potential applications of LrADI in the pharmaceutical industry, particularly in cancer treatment, due to its ability to deplete arginine in arginine-auxotrophic tumors.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102257"},"PeriodicalIF":1.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144125381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DDX6 promotes invasion of hepatocellular carcinoma through CEBPB regulating fatty acid degradation","authors":"Ziyu Wang ,&nbsp;Mengyuan Cui ,&nbsp;Linyue Zhao ,&nbsp;Wen Jiang","doi":"10.1016/j.genrep.2025.102259","DOIUrl":"10.1016/j.genrep.2025.102259","url":null,"abstract":"<div><h3>Background</h3><div>Processing bodies (P-bodies), dynamic cytoplasmic ribonucleoprotein granules, play crucial roles in post-transcriptional regulation and translational control. However, their functional significance in hepatocellular carcinoma (HCC) pathogenesis remains poorly understood.</div></div><div><h3>Methods</h3><div>We systematically analyzed HCC datasets from public repositories using bioinformatics approaches. Cellular phenotypes were assessed through MTT proliferation assays and Transwell migration assays. Molecular mechanisms were investigated using enhanced crosslinking and immunoprecipitation sequencing (eCLIP-seq) for DDX6-RNA interactions and chromatin immunoprecipitation sequencing (ChIP-seq) for CEBPB transcriptional regulation.</div></div><div><h3>Results</h3><div>Clinical bioinformatics revealed that elevated DDX6 expression, a core component of P-body assembly, correlates with adverse prognosis in HCC patients. Functional studies demonstrated that DDX6 knockdown significantly attenuated HCC cell migration capacity. Integrated eCLIP-seq and transcriptomic profiling identified direct binding of DDX6 to CEBPB mRNA, leading to its destabilization and reduced expression. Gene set enrichment analysis (GSEA) uncovered a significant association between CEBPB levels and fatty acid degradation pathways. ChIP-seq validation confirmed that CEBPB binds to the promoter regions of fatty acid degradation (FAD) genes and regulates its expression. Functional validation confirmed that the suppression of CEBPB leads to impaired free fatty acid metabolism.</div></div><div><h3>Conclusions</h3><div>Our findings delineate a novel DDX6/CEBPB/FAD axis in HCC progression, where DDX6 post-transcriptionally suppresses CEBPB through mRNA binding, subsequently impairing FAD gene transcription. This mechanistic insight positions DDX6 as a promising therapeutic target for HCC intervention.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102259"},"PeriodicalIF":1.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144185180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation the forensic efficacy and genetic trait of a Chinese ethnic group by 57 autosomal InDel loci","authors":"Xiaolian Wu ,&nbsp;Qinglin Liang ,&nbsp;Qinglin Liu ,&nbsp;Lisiteng Luo ,&nbsp;Meiming Cai ,&nbsp;Yanfang Liu ,&nbsp;Meisen Shi ,&nbsp;Bofeng Zhu","doi":"10.1016/j.genrep.2025.102253","DOIUrl":"10.1016/j.genrep.2025.102253","url":null,"abstract":"<div><h3>Introduction</h3><div>The 60-Plex InDel panel has recently been developed for forensic individual identification, and has demonstrated high sensitivity, reproducibility, and stability through various validation tests. However, its effectiveness still requires further validation across diverse populations to expand the population genetic database.</div></div><div><h3>Materials and methods</h3><div>In this study, we applied the 60-Plex InDel panel to genotype 190 unrelated healthy individuals from Chinese Manchu group. Through a series of genetic analyses, we evaluated the forensic efficacy of this panel in Chinese Manchu group.</div></div><div><h3>Results</h3><div>The 57 autosomal InDel loci showed high polymorphisms in Chinese Manchu group. The cumulative probability of matching and cumulative power of exclusion values of this panel were 4.4465 × 10^–24 and 0.9999808285 in Chinese Manchu group, respectively. Full sibling identification accuracy reached 82.90 % in Chinese Manchu group with the likelihood ratio limit of 100. Population genetic analyses, including <em>D</em>_<em>A</em> distances, <em>F</em>_<em>ST</em> values, phylogenetic tree construction, principal component analysis and STRUCTURE analysis, revealed that the Chinese Manchu group shared genetic proximity with the East Asian populations. The biogeographic origins of three continental populations (African, East Asian, and European) were inferred with high accuracy using two classification models (Random Forest and Support Vector Machine).</div></div><div><h3>Conclusions</h3><div>The 60 Plex-InDel panel is powerful for individual identification and paternity testing in Chinese Manchu group. It also has potential in inferring the biogeographic origins of individuals from different continents. The Chinese Manchu group is genetically related to East Asian populations, particularly to the Chinese Beijing Han population.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"40 ","pages":"Article 102253"},"PeriodicalIF":1.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144125380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}