1.Liuwei Dihuangwan Promote Mitophagy to Modulate Neuroinflammation and Behavioral Impairments in Rat Model of Autism Spectrum Disorder (ASD)
Pengjue HUANG ; Mingyue JIANG ; Ji WU ; Niya YIN ; Lei OUYANG ; Qinquan ZHU ; Di ZHANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(2):52-60
ObjectiveTo observe the effect of Liuwei Dihuangwan on behavioral impairments in the rat model of autism spectrum disorder (ASD) and explore the mechanism of action. MethodsTwelve SD pregnant rats were intraperitoneally injected with valproic acid (VPA) (10 rats) or normal saline (2 rats), and male offspring were selected to establish the model of ASD and the control rats. Rats were randomly assigned into model, low-dose (0.75 g·kg-1) and high-dose (1.5 g·kg-1) Liuwei Dihuangwan, vitamin D (positive drug, 3.7×10-5 g·kg-1), and blank groups. Each group was administrated with the corresponding concentration of drugs or the same volume of normal saline by gavage for 2 weeks. After the intervention, the three-chamber social test was conducted to evaluate social interaction and social preference. The open field test was carried out to observe spontaneous behavior and anxiety state. Hematoxylin-eosin staining (HE) was used to observe the pathological changes of the prefrontal tissue. Transmission electron microscopy was employed to observe the ultrastructure of mitochondria in prefrontal neurons. Immunofluorescence was used to detect the expression of ionized calcium-binding adapter molecule-1 (Iba-1) in the prefrontal tissue. Enzyme-linked immunosorbent assay (ELISA) was adopted to measure the levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6). Western blot was employed to assess the expression differences of phosphorylated adenosine monophosphate-activated protein kinase (p-AMPK), adenosine monophosphate-activated protein kinase (AMPK), phosphorylated Unc-51-like autophagy-activating kinase 1 (p-ULK1), Unc-51-like autophagy-activating kinase 1 (ULK1), and FUN14 domain-containing protein 1 (FUNDC1). ResultsCompared with the blank group, the model group spent less time sniffing stranger 1 and stranger 2 in the three-chamber social test (P<0.01) and showed reductions in the total distance traveled, average speed, distance traveled in the central area, and time spent in the central area in the open field test (P<0.01). In addition, the model group showed extensive apoptosis of neurons, with shrunken nuclei and red-stained cytoplasm, and extensive necrosis of neurons in the prefrontal tissue, mitochondrial swelling, decreased matrix density, disrupted cristae, and autophagic lysosomes in neurons, increases in the rate of Iba-1 positive cells in the prefrontal area (P<0.01) and the levels of TNF-α and IL-6 (P<0.01), and down-regulation in the expression of p-AMPK/AMPK, p-ULK1/ULK1, and FUNDC1 (P<0.01). Compared with the model group, low-dose and high-dose Liuwei Dihuangwan and the vitamin D prolonged the time spent sniffing stranger 1 and stranger 2 in the three-chamber social test (P<0.05, P<0.01), increased the total distance traveled, average speed, distance traveled in the central area, and time spent in the central area in the open field test (P<0.05, P<0.01), restored the morphology of neurons in the prefrontal tissue, decreased the number of apoptotic cells, alleviated the swelling of mitochondria in neurons, increased the matrix density, mitigated the fragmentation and disorder of cristae, and increased the number of autophagosomes. Moreover, the drugs decreased the rate of Iba-1 positive cells in the prefrontal area (P<0.01), lowered the levels of TNF-α and IL-6 (P<0.01), and up-regulated the expression of p-AMPK/AMPK, p-ULK1/ULK1, and FUNDC1 (P<0.01). ConclusionLiuwei Dihuangwan ameliorate autism-like behaviors and reduce neuronal apoptosis and neuroinflammatory damage in the rat model of ASD by promoting mitophagy mediated by the AMPK/ULK1/FUNDC1 pathway.
2.Mechanism prediction and verification of Xihuang pill against diffuse large B-cell lymphoma
Ruyi HUANG ; Jinyu LI ; Wenqi LIN ; Xin JIANG ; Yanling CHEN ; Weikun HUANG ; Lin YANG
China Pharmacy 2026;37(2):161-167
OBJECTIVE To investigate the mechanism of Xihuang pill (XHP) against diffuse large B-cell lymphoma (DLBCL). METHODS The active ingredients of XHP and potential therapeutic targets for DLBCL were identified using TCMSP, GeneCards and DisGeNET databases. Protein-protein interaction networks were constructed using the String database and Cytoscape software to screen core components and core targets. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were then performed. The clinical relevance of core targets was analyzed using the GEPIA and PanCanSurvPlot databases. Molecular docking and molecular dynamics (MD) simulation were conducted to verify the interactions between core components and core targets, and the binding free energy was calculated using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The effects of XHP on DLBCL and the related molecular mechanisms were validated using CCK-8 assay, flow cytometry and Western blot. RESULTS Network pharmacology analysis identified 108 active ingredients of XHP and 410 potential therapeutic targets for DLBCL. Six core components (e.g., 17 beta-estradiol, quercetin) and ten core targets [e.g., tumor protein 53 (TP53), proto-oncogene tyrosine-protein kinase Src (SRC)] were obtained. Enrichment analysis indicated that the anti-DLBCL effects of XHP were primarily associated with the apoptotic signaling pathway, the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway and so on. Clinical correlation analysis revealed that TP53 and SRC expression were significantly up-regulated in DLBCL tissues and associated with poor patient prognosis (P<0.05). Molecular docking, MD simulations and MM-PBSA calculations confirmed that the SRC-quercetin complex had a mail:stronger and more stable binding affinity. In vitro experiments demonstrated that XHP concentration-dependently inhibited the proliferation of DLBCL cells; compared with control group, XHP medium- and high-dose groups could significantly induce the apoptosis of SU-DHL2 and SU-DHL4 cells, and significantly down- regulated the expressions of SRC protein, phosphorylated (p)-PI3K/PI3K and p-Akt/Akt in SU-DHL4 cells (P<0.05). CONCLUSIONS XHP may inhibit the proliferation and induce the apoptosis of DLBCL cells by regulating the SRC/PI3K/Akt signaling pathway.
3.Staged Efficacy of Qijia Rougan Prescription Combined with Entecavir for Chronic Hepatitis B-related Hepatic Fibrosis with Qi Deficiency and Collateral Stasis Syndrome Based on "Zhu Ke Jiao" Theory
Baixue LI ; Xin WANG ; Jibin LIU ; Li WEN ; Cen JIANG ; Wenjun WU ; Dong WANG ; Shuwan LIU ; Huabao LIU ; Yongli ZHENG ; Liang HUANG ; Yue SU ; Song ZHANG ; Yanan SHANG ; Hang ZHOU ; Quansheng FENG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(9):180-188
ObjectiveThis paper aims to investigate and evaluate the staged efficacy and safety of the representative empirical prescription of the “Zhu Ke Jiao” theory, Qijia Rougan prescription, combined with entecavir in the treatment of hepatic fibrosis in chronic hepatitis B. MethodsA multicenter randomized controlled clinical study was conducted, and 101 patients diagnosed with chronic hepatitis B-related hepatic fibrosis (CHB-HF) who met the diagnosis and inclusion criteria were randomly assigned to an observation group (Qijia Rougan prescription + entecavir) and a control group (entecavir). The treatment duration was 24 weeks. Liver stiffness measurement (LSM), fibrosis-4 index (FIB-4), portal vein diameter, hepatitis B serology, biochemical indicators, hepatic fibrosis markers in serum [hyaluronic acid (HA), laminin (LN), procollagen Ⅲ peptide (PⅢP), and type Ⅳ collagen (Ⅳ-C)], and traditional Chinese medicine syndrome scores were used as efficacy evaluation indicators. Efficacy assessments and explorations of different staged subgroups of Qijia Rougan prescription were conducted according to LSM values based on the Metavir pathological staging standard. ResultsA total of 98 cases were included for statistical analysis, with 49 cases in the observation group and 49 in the control group. The general data of the patients in both groups were comparable. Compared with the same group before treatment, the observation group showed a significant reduction in LSM and FIB-4 (P<0.01), as well as notable improvements in LN, Ⅳ-C, and various TCM syndrome scores (P<0.05, P<0.01). When compared to the control group after treatment, the observation group demonstrated significant improvements in LSM, FIB-4, and various TCM syndrome score indicators (P<0.05, P<0.01), indicating that the observation group performed better than the control group. Subgroup analysis of the regression of hepatic fibrosis stages showed that compared to the same group before treatment, the observation group had better improvement in regression of stages F2 and F3 (P<0.05). When compared to the control group after treatment, the observation group exhibited superior improvement in regression of stage F3 (P<0.05). No adverse events occurred in either group during the treatment period. ConclusionCompared with entecavir alone, the combination of Qijia Rougan prescription and entecavir significantly improves the degree of hepatic fibrosis and clinical TCM symptoms in patients. The optimal intervention period is primarily during stage F3, which is a potential “interception” point of the “Zhu Ke Jiao” theory.
4.Transcriptome-based Mining of Genes Involved in Regulation of Cyclopeptide B Synthesis in Pseudostellaria heterophylla
Qingsu ZHOU ; Yishu HUANG ; Xiuwen WANG ; Jiao XU ; Xiaohong OU ; Hua HE ; Weike JIANG ; Tao ZHOU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(9):224-230
ObjectiveThe biosynthesis of heterophyllin B (HB), a cyclopeptide from Pseudostellaria heterophylla, is regulated by various abiotic stresses. Elucidating the transcriptional regulatory mechanism underlying HB biosynthesis is of great guiding significance for the directional improvement of P. heterophylla varieties and the enhancement of HB content. MethodsBased on transcriptome data from different tissues of P. heterophylla, transcription factors (TFs) specifically upregulated and highly expressed in the phloem of tuberous roots were screened through a combination of Mfuzz time-series clustering, transcription factor family prediction, and correlation analysis. Quantitative real-time polymerase chain reaction (Real-time PCR) was employed to analyze expression patterns of candidate TFs under abscisic acid (ABA) induction, and the dual-luciferase reporter assay was applied to verify their regulatory effects on HB precursor genes. ResultsContent determination showed that HB accumulated at the highest in the phloem of P. heterophylla tuberous roots (34 μg
5.Regulatory Pathways of Cell Apoptosis in Diabetic Kidney Disease and Intervention by Traditional Chinese Medicine: A Review
Yunjie YANG ; Mingqian JIANG ; Chen QIU ; Yaqing RUAN ; Senlin CHEN ; Wenxin HUANG ; Hangbin ZHENG ; Yi WEI ; Pengfei LI ; Xueqin LIN ; Jing WU ; Shiwei RUAN ; Jianting WANG ; Yuliang QIU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(9):294-306
Diabetic kidney disease(DKD) is a chronic kidney structural and functional disorder caused by diabetes. With the global prevalence of diabetes continuing to rise, DKD has gradually become a major cause of chronic kidney disease and end-stage renal disease(ESRD), posing a serious threat to patients' quality of life and long-term health outcomes. Studies have shown that apoptosis plays a pivotal role in the development and progression of DKD, with its mechanisms involving abnormal activation of multiple signaling pathways such as Toll-like receptor 4(TLR4)/nuclear transcription factor-κB(NF-κB)/B-cell lymphoma-2(Bcl-2)/cysteinyl aspartate-specific proteinase(Caspase)-3, protein kinase R-like endoplasmic reticulum kinase(PERK)/eukaryotic initiation factor 2α(eIF2α)/activating transcript factor 4(ATF4)/CCAAT enhancer-binding protein homologous protein(CHOP), phosphatidylinositol 3-kinase(PI3K)/protein kinase B(Akt)/glycogen synthase kinase-3β(GSK-3β), Janus kinase 2(JAK2)/signal transducer and activator of transcription 3(STAT3), adenosine monophosphate-activated protein kinase(AMPK)/mammalian target of rapamycin(mTOR) and silent information regulator 1(SIRT1)/tumor suppressor protein 53(p53), thereby accelerating renal pathological damage in DKD. Extensive evidence-based medical studies have confirmed that traditional Chinese medicine(TCM), leveraging its unique therapeutic advantages of multi-target, multi-component and multi-pathway approaches, has demonstrated remarkable efficacy and favorable safety profiles in treating DKD. Recent studies have demonstrated that active components of TCM can specifically target and modulate key effectors in apoptotic signaling pathways. Meanwhile, traditional compound formulations exert synergistic effects through multiple approaches such as replenishing deficiency and activating blood circulation, detoxifying and dredging collaterals, tonifying kidney essence, and removing stasis and purging turbidity, thereby comprehensively regulating critical pathological processes including endoplasmic reticulum stress and mitochondrial apoptosis pathways. This combined therapeutic approach of molecular targeting and holistic regulation provides novel strategies for delaying the progression of DKD. Based on this, this paper provides an in-depth analysis of key apoptotic signaling pathways and their regulatory mechanisms, while systematically summarizing recent research advances regarding the therapeutic effects of TCM active components, compound formulations, and proprietary Chinese medicines on DKD through modulation of these pathways, with particular emphasis on their underlying molecular mechanisms. These findings not only elucidate the modern scientific connotation and theoretical basis of TCM in treating DKD but also establish a solid theoretical and practical foundation for promoting the wider clinical application and further research of TCM in the field of DKD treatment.
6.Analyses of the epidemiological characteristics of multiple pathogens in people aged 14 years and above with acute respiratory infection in Huangpu District of Shanghai from 2015 to 2024
Yun ZHANG ; Yinzi CHEN ; Zhenzi ZUO ; Yu WANG ; Fujie SHEN ; Yuliang HUANG ; Qiang GAO ; Chenyan JIANG ; Yijun WANG
Shanghai Journal of Preventive Medicine 2026;38(2):116-121
ObjectiveTo analyze the epidemiological characteristics of 8 major respiratory pathogens in influenza-like illness (ILI) cases with acute respiratory infections at fever clinics in Huangpu District, Shanghai from 2015 to 2024, and to provide a scientific basis for the prevention and treatment of respiratory diseases. MethodsA retrospective study was conducted in Huangpu District. Individuals meeting the case definition of ILI from 2015 to 2024 was registered. Their nasopharyngeal swabs were collected for pathogen detection. A total of 8 respiratory viruses were tested, including Influenza A virus (Flu A), Influenza B virus (Flu B), adenovirus (ADV), enterovirus/human rhinovirus (EV/HRV), human parainfluenza virus (HPIV), human coronavirus (HCoV), respiratory syncytial virus (RSV), and human metapneumovirus (HMPV). ResultsFrom 2015 to 2019, a total of 344 ILI cases were tested, of which 192 out of 344 cases (55.81%) were tested positive for single respiratory pathogen. From 2023 to 2024, 1 557 ILI cases were tested, with 572 out of 1 557 cases (36.74%) being positive for single pathogen. From 2023 to 2024, the positive rate of single pathogen in ILI cases was significantly lower than that in 2015‒2019 (χ2=42.66, P<0.001). Specifically, the positive rate of Flu A (χ2=74.43, P<0.001) decreased, while that of HPIV (χ2=8.66, P=0.003) increased, both with statistically significant differences. According to the seasonal pattern, the epidemic intensity of Flu A decreased in summer, while that of HPIV increased in summer and autumn. Demographic results showed statistically significant differences in the positive rates of EV/HRV between genders (χ2=22.38, P<0.001), with males exhibiting a higher positive rate than females. No statistically significant differences were identified in the positive rates of single pathogen among different age groups (χ2=4.42, P=0.110). Nevertheless, statistically significant differences were noted when comparing the positive rates of EV/HRV, Flu A, Flu B and HPIV across different age groups (P<0.05). EV/HRV was more commonly detected in the 15‒<25 age group (10.93%), while Flu A and HPIV had the highest positive rates in the ≥60 age group (21.24% and 4.77%). Flu B had the highest positive rate in the 25‒<60 age group (11.26%). 52.63% of cases with co-infections occurred during winter, with the primary pathogens involved being EV/HRV (9 cases) and HCoV (6 cases). The most prevalent combination of co-infection was Flu A with EV/HRV. ConclusionThe prevalence of respiratory pathogens among ILI cases from 2023 to 2024 exhibited notable fluctuations compared to that from 2015 to 2019. Therefore, influenza surveillance should be strengthened, and attention should also be paid to the prevalence of respiratory pathogens such as HPIV. These findings have profound implications for future research, surveillance, vaccine planning, and public health policy making.
7.Integrating Transcriptomics and 3D Organoids to Investigate Mechanism of Periplaneta americana Extract Against Lung Adenocarcinoma
Qiong MA ; Chunxia HUANG ; Jiawei HE ; Yuting BAI ; Xingyue LIU ; Yuxuan XIONG ; Yang ZHONG ; Hengzhou LAI ; Yuling JIANG ; Xueke LI ; Qian WANG ; Yifeng REN ; Xi FU ; Funeng GENG ; Taoqing WU ; Ping XIAO ; Fengming YOU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(11):124-132
ObjectiveTo evaluate the antitumor activity of Periplaneta americana extract(PAE) against human-derived lung adenocarcinoma organoids(LUAD-PDOs) and to elucidate its potential mechanism based on transcriptomics. MethodsFresh tumor and adjacent normal tissues from patients with LUAD were collected to construct LUAD-PDOs and normal lung organoid(Nor-PDOs) models using 3D organoid culture technology. The effective intervention concentration of PAE was determined using the cell counting kit-8(CCK-8) assay. Experimental groups included the model group(LUAD-PDOs), normal group, model administration group(LUAD-PDOs+PAE), and normal administration group(Nor-PDOs+PAE). Hematoxylin-eosin(HE) staining was used to observe the pathological structures of PDOs, immunohistochemistry(IHC) was performed to detect the expressions of the proliferation marker Ki-67 and lung adenocarcinoma differentiation markers cytokeratin-7(CK-7) and Napsin A, TUNEL staining was applied to detect cell apoptosis. RNA sequencing(RNA-Seq) was conducted to identify differentially expressed genes(DEGs), followed by Gene Ontology(GO), Kyoto Encyclopedia of Genes and Genomes(KEGG), and Gene Set Enrichment Analysis(GSEA), alongside protein-protein interaction(PPI) network analysis to screen core mechanisms. Finally, key targets were validated by integrating external database analysis with immunofluorescence(IF). ResultsNor-PDOs and LUAD-PDOs that highly recapitulated the pathological characteristics of the primary tissues were successfully established. The CCK-8 assay determined that the effective intervention concentration of PAE was 16 g·L-1. Morphological observation showed that Nor-PDOs exhibited lumen-forming structures, whereas LUAD-PDOs displayed dense, solid structures. CCK-8 and TUNEL assays revealed that, compared with the model group, PAE intervention inhibited the proliferation of LUAD-PDOs and promoted apoptosis in LUAD cells, while showing no significant effect on the viability of Nor-PDOs. Transcriptomic analysis identified 719 DEGs that were significantly reversed after PAE intervention(347 up-regulated and 372 down-regulated)(P<0.05). GO enrichment analysis indicated that DEGs in the model administration group were significantly enriched in biological processes related to cell cycle regulation compared to the model group. KEGG pathway analysis revealed that PAE affected pathways related to proliferation and metabolism, including pathways in cancer and the p53 signaling pathway. GSEA further confirmed that PAE significantly enhanced the activity of the p53 signaling pathway(P<0.05). PPI network analysis indicated that breast cancer type 1 susceptibility protein(BRCA1) and checkpoint kinase 1(CHEK1) were the core down-regulated targets in the p53 pathway. IF verified the high expression of BRCA1 and CHEK1 in LUAD-PDOs and their significant downregulation after PAE intervention(P<0.05). Furthermore, survival analysis based on The Cancer Genome Atlas(TCGA) database indicated that low expression of BRCA1 and CHEK1 was significantly associated with prolonged overall survival in patients with LUAD(P<0.05). ConclusionPAE effectively inhibits proliferation of LUAD-PDOs and promotes their apoptosis, its anti-tumor mechanism is potentially associated with the activation of the p53 signaling pathway, with BRCA1 and CHEK1 genes likely serving as key downstream targets for the effects of PAE.
8.From Cathartic Colon to Cathartic-dependent Constipation: Diagnostic-therapeutic Strategies from Integrative Medicine Perspective
Youcheng HE ; Fengru JIANG ; Yanru WANG ; Minghan HUANG ; Yue WU ; Chunyu ZHOU ; Lian MO ; Lifeng WEI ; Keyi PAN ; Shuyu CAI ; Jianye YUAN
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(11):162-172
Both cathartic colon (CC) and cathartic-dependent constipation (CDC) are caused by the abuse of stimulant laxatives, while their concepts are not completely the same.Starting from the disease name of CC, this article traced the origin and evolution of the concept of CC, summarizes and compared the similarities and differences between CC, CDC, and slow transit constipation (STC), and called for strict differentiation among the three.Furthermore, this article explored the specific contents of Western medicine clinical subtypes and traditional Chinese medicine (TCM) syndrome differentiation of CDC and delved into the TCM pathogenesis of CDC according to both literature and clinical practice.The relationship between clinical subtypes and TCM syndromes was established, and the syndrome characteristics of CDC of different clinical subtypes and TCM syndromes were summarized.The recommended prescriptions for corresponding syndromes were listed.A systematic CDC diagnosis and treatment approach of "clinical subtypes-syndrome differentiation-syndrome characteristics-recommended prescriptions" was thus formed.Additionally, the paper provides an overview of current research on CDC in both Western medicine and TCM contexts, identifies future research directions, and suggests research pathways for refining and advancing CDC studies.
9.Animal Models of Functional Constipation: A Review
Youcheng HE ; Shijin LIN ; Fengru JIANG ; Sihan LI ; Xiao KE ; Wenrong WANG ; Jianye YUAN ; Minghan HUANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(11):196-209
Functional constipation (FC) is a clinically common functional bowel disorder characterized by a protracted course and associations with various chronic disorders and psychological abnormalities. Although not life-threatening, FC significantly impairs patients' quality of life. FC subtypes include slow-transit constipation (STC), defecatory disorder (DD), and normal-transit constipation (NTC). The pathological mechanisms underlying FC have not been fully elucidated, and overall clinical efficacy remains unsatisfactory. Animal models of FC serve as essential tools for the study of disease mechanisms and the development of novel therapeutics. This article systematically reviews the current state of research on the animal models of FC and identifies that rodents, particularly rats and mice, are the most commonly used species. Dogs and pigs are also employed in complex intervention studies due to their physiological similarities to humans, though their use is limited by housing challenges and ethical considerations. Induction methods vary across different FC subtypes. STC models are primarily established with chemical agents such as loperamide or compound diphenoxylate. DD modeling often involves low-fiber diets combined with methylene blue injection or rectal narrowing. NTC modeling mainly relies on low-fiber dietary interventions. In addition, disease-syndrome combination models based on traditional Chinese medicine (TCM) theory have been developed, encompassing excess patterns such as heat accumulation, cold accumulation, and Qi stagnation, as well as deficiency patterns including Qi deficiency, blood deficiency, Yin deficiency, and Yang deficiency. These are achieved through an approach of disease model + syndrome induction, enabling the integration of mechanisms from both Western and TCM perspectives. Models are evaluated from two aspects: disease and syndrome manifestations (e.g., colonic transit, secretory function, and TCM syndrome indicators such as mental state and body weight) and disease mechanisms (e.g., enteric nervous system, interstitial cells of Cajal, smooth muscle cells, gut microbiota, and metabolites). However, current research still faces challenges such as poor consistency in some models, non-specific interference in mechanism interpretation, insufficient studies on NTC, and lack of TCM tongue and pulse diagnosis in evaluation. Future efforts should focus on optimizing model stability and specificity to provide a more reliable experimental basis for investigating the pathological mechanisms of FC and developing therapeutic agents.
10.Assessing High-density Y-SNP Panels for Paternal Haplogroup Assignment in Forensic Practice
De-Qin ZHANG ; Chun-Nian WANG ; Lin-Lin LOU ; Meng NI ; Jing GAO ; Jiang HUANG ; Li JIANG
Progress in Biochemistry and Biophysics 2026;53(2):458-469
ObjectiveThe accuracy of Y-chromosome haplogroup assignment is crucial for tracing paternal lineage in male samples. With the advancement of high-throughput sequencing technologies, high-density Y-SNP genotyping from whole-genome or array-based data has become a standard method for determiningY-chromosome haplogroups. This study systematically evaluated the performance of 4 commonly used high-density SNP genotyping systems—namely, the Global Screening Array (GSA), Chinese Genotyping Array (CGA), Affymetrix array, and the 1240K capture panel—for haplogroup assignment. This work provides a reference for data comparison across different systems. MethodsWe extracted genotype data for the 4 Y-SNP panels from 30× whole-genome sequencing (WGS) data of 1 590 male samples from the 1000 Genomes Project. Additionally, GSA array genotype data from 384 relative pairs (spanning 1st- to 12th-degree relationships) from 109 Chinese Han families were collected. Haplogroup assignment was performed using Y-LineageTracker v1.3.0 software. We assessed the concordance and resolution of haplogroup assignments between the four Y-SNP panels and the WGS data. The consistency and resolution of haplogroup assignments were also evaluated for both the 1000 Genomes Project samples and the 109 family samples collected in this study. Furthermore, the impact of varying numbers of Y-SNPs on haplogroup assignment was examined. ResultsThe GSA and CGA panels demonstrated superior resolution and discrimination of haplogroup subclades compared with the other two panels. The haplogroup assignments from the GSA, CGA, and 1240K panels showed high concordance with WGS data, with consistency rates exceeding 88.70%, whereas the Affymetrix platform exhibited a significantly lower consistency rate of 61.89%. Specifically, the GSA and CGA panels consistently demonstrated superior performance compared with the other two panels in the assignment of haplogroups O-M175 and H-L901, achieving complete concordance (100%) for both haplogroups. In contrast, the Affymetrix panel erroneously assigned all individuals belonging to haplogroup O-M175 to haplogroup K2-M526. Furthermore, its accuracy for haplogroup H-L901 was exceedingly low, at merely 1.41%. This poor performance was characterized by the misassignment of 98.59% of H-L901 samples—specifically, 1.41% to J-M304 and a predominant 97.18% to F-M89. For haplogroup R-M207, all four panels exhibited uniformly high levels of consistency, with concordance values exceeding 94.00%. Notably, for haplogroup E-M96, the 1240K and Affymetrix panels outperformed the GSA and CGA panels in terms of concordance, representing the first instance in which these two panels surpassed the latter. Conversely, for haplogroups J-M304, Q-M242, and I-M170, all 4 panels showed relatively elevated misclassification rates, with the Affymetrix array demonstrating the poorest overall performance. None of the four panels showed any discordant haplogroup assignments among the familial relative pairs analyzed. A positive correlation was observed between the number of Y-SNPs (ranging from 1 000 to 10 000) and classification consistency; however, classification consistency plateaued when the number of Y-SNPs exceeded 10 000. Furthermore, a random sampling analysis conducted on the GSA and CGA panels demonstrated that the haplogroup misclassification rate exhibited negligible fluctuation across the Y-SNP range of 500 to 1 000. Conversely, a marked enhancement in classification consistency was observed as the number of markers increased from 1 000 to 5 000, ultimately reaching a plateau within the interval of 5 000 to 8 000 markers. ConclusionThese findings indicate that the GSA and CGA panels provide high resolution and concordance, delivering reliable Y-haplogroup assignment for forensic investigations.

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