1.Neuroprotective Mechanism of Yifei Xuanfei Jiangzhuo Prescription on VaD Rats Based on NF-κB/NLRP3 Signaling Pathway
Bingmao YUAN ; Wei CHEN ; Xiu LAN ; Lingfei JIANG ; Lin WU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(3):88-96
ObjectiveTo investigate the molecular mechanism by which Yifei Xuanfei Jiangzhuo prescription regulates the nuclear factor-κB (NF-κB)/NOD-like receptor protein 3 (NLRP3) signaling pathway to improve neuronal function in vascular dementia (VaD) rats. MethodsA VaD model was established by intermittently clamping the bilateral common carotid arteries (CCA) combined with bilateral vascular occlusion (2-VO). Eighty-four SD rats were randomly divided into a blank group, sham group, model group, piracetam group (0.2 g·kg-1), and low-, medium-, and high-dose Yifei Xuanfei Jiangzhuo prescription groups (6.09, 12.18, and 24.36 g·kg-1). Drug administration began on day 7 after surgery, once daily for 28 consecutive days. Behavioral experiments were used to evaluate learning and spatial memory. Hematoxylin-eosin (HE) staining was applied to observe pathological morphological changes in the CA1 region of the hippocampus. Transmission electron microscopy was used to examine the ultrastructure of hippocampal neurons. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) was used to detect neuronal apoptosis in the CA1 region. Immunohistochemistry was performed to determine the positive expression rate of neuronal nuclear antigen (NeuN). Immunofluorescence single staining was used to assess nuclear expression of NF-κB p65 in brain tissue. Western blot was used to detect the protein expression levels of inhibitor of κB kinase (IKK), NF-κB p65, NLRP3, Caspase-1, apoptosis-associated speck-like protein (ASC), and interleukin-1β (IL-1β). ResultsCompared with the blank group, the model group showed a significant reduction in platform-crossing frequency (P0.01), aggravated hippocampal injury, a significant increase in neuronal apoptosis (P0.05), decreased NeuN positivity in the CA1 region (P0.05), increased nuclear expression of NF-κB p65 (P0.05), and significantly elevated expression of p-IKK, p-NF-κB p65, NLRP3, cleaved Caspase-1, ASC, and cleaved IL-1β (P0.05). Compared with the model group, all drug-treated groups improved learning and spatial memory in VaD rats, alleviated hippocampal pathological injury and neuronal apoptosis, and protected neuronal ultrastructure. Yifei Xuanfei Jiangzhuo prescription at doses of 12.18 and 24.36 g·kg-1 reduced hippocampal expression levels of p-IKK, p-NF-κB p65, NLRP3, Caspase-1, ASC, and cleaved IL-1β in VaD rats (P0.05), showing dose-dependent inhibition of the NF-κB/NLRP3 signaling pathway. ConclusionYifei Xuanfei Jiangzhuo prescription may exert neuroprotective effects by regulating the NF-κB/NLRP3 signaling pathway, thereby reducing neuroinflammation and inhibiting hippocampal neuronal apoptosis.
2.Neuroprotective Mechanism of Yifei Xuanfei Jiangzhuo Prescription on VaD Rats Based on NF-κB/NLRP3 Signaling Pathway
Bingmao YUAN ; Wei CHEN ; Xiu LAN ; Lingfei JIANG ; Lin WU
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(3):88-96
ObjectiveTo investigate the molecular mechanism by which Yifei Xuanfei Jiangzhuo prescription regulates the nuclear factor-κB (NF-κB)/NOD-like receptor protein 3 (NLRP3) signaling pathway to improve neuronal function in vascular dementia (VaD) rats. MethodsA VaD model was established by intermittently clamping the bilateral common carotid arteries (CCA) combined with bilateral vascular occlusion (2-VO). Eighty-four SD rats were randomly divided into a blank group, sham group, model group, piracetam group (0.2 g·kg-1), and low-, medium-, and high-dose Yifei Xuanfei Jiangzhuo prescription groups (6.09, 12.18, and 24.36 g·kg-1). Drug administration began on day 7 after surgery, once daily for 28 consecutive days. Behavioral experiments were used to evaluate learning and spatial memory. Hematoxylin-eosin (HE) staining was applied to observe pathological morphological changes in the CA1 region of the hippocampus. Transmission electron microscopy was used to examine the ultrastructure of hippocampal neurons. Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) was used to detect neuronal apoptosis in the CA1 region. Immunohistochemistry was performed to determine the positive expression rate of neuronal nuclear antigen (NeuN). Immunofluorescence single staining was used to assess nuclear expression of NF-κB p65 in brain tissue. Western blot was used to detect the protein expression levels of inhibitor of κB kinase (IKK), NF-κB p65, NLRP3, Caspase-1, apoptosis-associated speck-like protein (ASC), and interleukin-1β (IL-1β). ResultsCompared with the blank group, the model group showed a significant reduction in platform-crossing frequency (P0.01), aggravated hippocampal injury, a significant increase in neuronal apoptosis (P0.05), decreased NeuN positivity in the CA1 region (P0.05), increased nuclear expression of NF-κB p65 (P0.05), and significantly elevated expression of p-IKK, p-NF-κB p65, NLRP3, cleaved Caspase-1, ASC, and cleaved IL-1β (P0.05). Compared with the model group, all drug-treated groups improved learning and spatial memory in VaD rats, alleviated hippocampal pathological injury and neuronal apoptosis, and protected neuronal ultrastructure. Yifei Xuanfei Jiangzhuo prescription at doses of 12.18 and 24.36 g·kg-1 reduced hippocampal expression levels of p-IKK, p-NF-κB p65, NLRP3, Caspase-1, ASC, and cleaved IL-1β in VaD rats (P0.05), showing dose-dependent inhibition of the NF-κB/NLRP3 signaling pathway. ConclusionYifei Xuanfei Jiangzhuo prescription may exert neuroprotective effects by regulating the NF-κB/NLRP3 signaling pathway, thereby reducing neuroinflammation and inhibiting hippocampal neuronal apoptosis.
3.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.
4.Review on identification and prevention-control strategies for public health risks in pharmacy intravenous admix-ture services
China Pharmacy 2026;37(2):268-272
Pharmacy intravenous admixture serves as a core link in the clinical medication supply chain. Its operational quality is directly related to drug safety and patient medication safety. This paper examines the challenges and measures for public health risk prevention and control in practical operational aspects of intravenous drug preparation, including prescription verification, drug compounding, drug management, and finished product distribution and traceability. Grounded in the “prevention-control-emergency response” full-chain management framework, it proposes systematic prevention and control strategies, including establishing a “public health-oriented” pharmacy intravenous admixture service management system, strengthening risk intervention measures throughout the entire process, improving risk monitoring and emergency response mechanisms, promoting technological empowerment, and refining pharmacist training and personnel qualification control mechanisms. These efforts aim to establish a comprehensive public health safety system that shifts from a “passive response” to an “active prevention and control” approach, thereby ensuring patient medication safety.
5.Expert consensus on neoadjuvant PD-1 inhibitors for locally advanced oral squamous cell carcinoma (2026)
LI Jinsong ; LIAO Guiqing ; LI Longjiang ; ZHANG Chenping ; SHANG Chenping ; ZHANG Jie ; ZHONG Laiping ; LIU Bing ; CHEN Gang ; WEI Jianhua ; JI Tong ; LI Chunjie ; LIN Lisong ; REN Guoxin ; LI Yi ; SHANG Wei ; HAN Bing ; JIANG Canhua ; ZHANG Sheng ; SONG Ming ; LIU Xuekui ; WANG Anxun ; LIU Shuguang ; CHEN Zhanhong ; WANG Youyuan ; LIN Zhaoyu ; LI Haigang ; DUAN Xiaohui ; YE Ling ; ZHENG Jun ; WANG Jun ; LV Xiaozhi ; ZHU Lijun ; CAO Haotian
Journal of Prevention and Treatment for Stomatological Diseases 2026;34(2):105-118
Oral squamous cell carcinoma (OSCC) is a common head and neck malignancy. Approximately 50% to 60% of patients with OSCC are diagnosed at a locally advanced stage (clinical staging III-IVa). Even with comprehensive and sequential treatment primarily based on surgery, the 5-year overall survival rate remains below 50%, and patients often suffer from postoperative functional impairments such as difficulties with speaking and swallowing. Programmed death receptor-1 (PD-1) inhibitors are increasingly used in the neoadjuvant treatment of locally advanced OSCC and have shown encouraging efficacy. However, clinical practice still faces key challenges, including the definition of indications, optimization of combination regimens, and standards for efficacy evaluation. Based on the latest research advances worldwide and the clinical experience of the expert group, this expert consensus systematically evaluates the application of PD-1 inhibitors in the neoadjuvant treatment of locally advanced OSCC, covering combination strategies, treatment cycles and surgical timing, efficacy assessment, use of biomarkers, management of special populations and immune related adverse events, principles for immunotherapy rechallenge, and function preservation strategies. After multiple rounds of panel discussion and through anonymous voting using the Delphi method, the following consensus statements have been formulated: 1) Neoadjuvant therapy with PD-1 inhibitors can be used preoperatively in patients with locally advanced OSCC. The preferred regimen is a PD-1 inhibitor combined with platinum based chemotherapy, administered for 2-3 cycles. 2) During the efficacy evaluation of neoadjuvant therapy, radiographic assessment should follow the dual criteria of Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1 and immune RECIST (iRECIST). After surgery, systematic pathological evaluation of both the primary lesion and regional lymph nodes is required. For combination chemotherapy regimens, PD-L1 expression and combined positive score need not be used as mandatory inclusion or exclusion criteria. 3) For special populations such as the elderly (≥ 70 years), individuals with stable HIV viral load, and carriers of chronic HBV/HCV, PD-1 inhibitors may be used cautiously under the guidance of a multidisciplinary team (MDT), with close monitoring for adverse events. 4) For patients with a poor response to neoadjuvant therapy, continuation of the original treatment regimen is not recommended; the subsequent treatment plan should be adjusted promptly after MDT assessment. Organ transplant recipients and patients with active autoimmune diseases are not recommended to receive neoadjuvant PD-1 inhibitor therapy due to the high risk of immune related activation. Rechallenge is generally not advised for patients who have experienced high risk immune related adverse events such as immune mediated myocarditis, neurotoxicity, or pneumonitis. 5) For patients with a good pathological response, individualized de escalation surgery and function preservation strategies can be explored. This consensus aims to promote the standardized, safe, and precise application of neoadjuvant PD-1 inhibitor strategies in the management of locally advanced OSCC patients.
6.Epidemiological characteristics analysis of tuberculosis among college students in Yangzhou during 2020-2024
Chinese Journal of School Health 2026;47(1):109-112
Objective:
To analyze the epidemiological characteristics of pulmonary tuberculosis (PTB) among college students in Yangzhou from 2020 to 2024, so as to provide a scientific basis for developing prevention and control strategies.
Methods:
An epidemiological investigation was conducted among 162 college students with PTB, and 7 134 of their contacts were screened. Data were obtained from the tuberculosis information management system and on campus screening records. Using descriptive epidemiological methods, trends in incidence, seasonal distribution, and bacteriological characteristics were analyzed.
Results:
From 2020 to 2024, the annual average incidence of pulmonary tuberculosis among college students in Yangzhou was 29.42 per 100 000, showing an overall fluctuating downward trend ( χ 2=12.36, P <0.01). Cases were mainly concentrated in summer and autumn, with the highest proportion in autumn (41.36%, 67/162), followed by summer (23.46%, 38/162). The proportion of etiologically positive cases increased from 37.21% in 2020 to 71.43% in 2024; among positive cases, the proportion of latent tuberculosis infection (LTBI) decreased from 66.67% (10/15) to 26.67% (4/15). The etiological positive rate was higher in females than in males ( χ 2= 11.76 , P <0.01). Comparison of screening methods showed that among index cases, the LTBI detection rate of the recombinant Mycobacterium tuberculosis fusion protein skin test (C-TST) was higher than that of the tuberculin skin test (TST), but the difference was not statistically significant ( χ 2=0.65, P =0.42); among close contacts, the detection rate of TST was higher than that of C-TST (15.1%,10.1%; χ 2=5.23, P <0.05).
Conclusion
From 2020 to 2024, the annual average incidence of pulmonary tuberculosis among college students in Yangzhou showed an overall fluctuating downward trend, with differences in TB infection screening methods and gender.
7.Association of microRNA gene polymorphisms with risk, clinicopathological characteristics and therapeutical efficacy among Chinese patients with Crohn's disease.
Yanlun ZHANG ; Xiaoxiao SHAO ; Daopo LIN ; Yuan XU ; Guolong MA ; Yi JIANG
Chinese Journal of Medical Genetics 2026;43(2):111-122
OBJECTIVE:
To assess the association of microribonucleic acid (miRNA) gene polymorphisms with the risk and clinicopathological characteristics of Crohn's disease (CD) and the influence of miRNA gene variants on the response to ustekinumab (UST) treatment among CD patients.
METHODS:
From January 2018 to February 2025, 312 patients diagnosed with CD and 527 gender- and age-matched normal controls were selected as the study subjects at the Department of Gastroenterology of the Second Affiliated Hospital of Wenzhou Medical University. Genotypes of miR-155 (rs767649), miR-21 (rs13137), miR-124 (rs531564) and miR-146a (rs57095329, rs2431697) were determined with multiplex polymerase chain reaction-ligase detection reaction (PCR-LDR) technique. The patients were divided into different subgroups according to the Montreal Classification Criteria for CD. Harvey-Bradshaw index (HBI) and simplified endoscopic score for CD were respectively applied to assess the clinical and endoscopic disease activity of CD. Unconditional logistic regression model was employed to analyze the distribution of miRNA gene polymorphisms between the two groups, as well as their influence on the clinicopathological characteristics of CD patients. Among them, 185 CD patients received first-line UST treatment, with the first sufficient dose of UST (6 mg/kg) administered intravenously. Based on the changes in HBI at week 8, the response of patients to UST treatment was evaluated. Unconditional logistic regression model was employed to analyze the distribution of miRNA gene polymorphisms between clinically responsive group (the decline of HBI ≥ 3 scores compared to week 0) and non-responsive group. All of the P values were adjusted by Bonferroni correction. This study has been approved by the Medical Ethics Committee of the Second Affiliated Hospital of Wenzhou Medical University (Ethics No.: 2025-K-12-01).
RESULTS:
No significant difference was found in the distribution of miRNA gene polymorphisms between the two groups (all P > 0.05). The variant genotype (TC+CC) of rs2431697 was more common among patients with terminal ileal-type and ileocolic-type CD than those with the colonic-type CD (OR = 4.98, 95%CI: 1.49~16.68, P = 0.009, adjusted P = 0.045). However, the opposite conclusion was drawn for the homozygous variant genotype (TT) of rs13137 and variant genotype (GC+CC) of rs531564 (OR = 0.37, 95%CI: 0.18~0.76, P = 0.007, adjusted P = 0.035; OR = 0.36, 95%CI: 0.18~0.73, P = 0.004, adjusted P = 0.020). Compared to patients with non-stricturing and penetrating CD, the variant genotype (AG+GG) and variant allele (G) of rs57095329 were more common in those with stricturing and penetrating CD (OR = 4.06, 95%CI: 2.46~6.71, P < 0.001, adjusted P < 0.005; OR = 3.12, 95%CI: 2.06~4.73, P < 0.001, adjusted P < 0.005). However, the frequencies of variant genotype (AT+TT) and variant allele (T) of rs13137 were lower among patients with stricturing and penetrating CD than in those without (OR = 0.25, 95%CI: 0.15~0.41, P < 0.001, adjusted P < 0.005; OR = 0.45, 95%CI: 0.33~0.63, P < 0.001, adjusted P < 0.005). Additionally, the variant genotype (AG+GG) and variant allele (G) of rs57095329 were more common among those with moderately to severely endoscopic activity than those with mildly endoscopic activity (OR = 2.01, 95%CI: 1.19~3.42, P = 0.009, adjusted P = 0.045; OR = 2.04, 95%CI: 1.28~3.25, P = 0.003, adjusted P = 0.015). In total 117 cases had shown clinical response by week 8, while 68 cases showed no response. Compared with t he clinically non-responsive group, the variant genotype (TC+CC) and variant allele (C) of rs2431697 were more common in the clinically responsive group (OR = 3.86, 95%CI: 1.80~8.32, P = 0.001, adjusted P = 0.005; OR = 2.60, 95%CI: 1.34~5.06, P = 0.005, adjusted P = 0.025). However, the variant genotype (TA+AA) of rs767649 was less frequent in the clinically responsive group than the non-responsive group (OR = 0.40, 95%CI: 0.21~0.74, P = 0.004, adjusted P = 0.020). The same conclusion was drawn for the variant genotype (AT+TT) and variant allele (T) of rs13137 when the clinically responsive group was compared with the non-responsive group (OR = 0.30, 95%CI: 0.14~0.63, P = 0.002, adjusted P = 0.010; OR = 0.54, 95%CI: 0.35~0.82, P = 0.005, adjusted P = 0.025).
CONCLUSION
Genetic polymorphisms of miRNAs are not associated with the risk of developing CD. The miR-146a (rs57095329) variant may increase the endoscopic activity of CD and the risk for stenosis or penetration. However, the miR-146a (rs2431697) variant may increase the risk of ileal involvement. The miR-21 (rs13137) variant may reduce the risk of ileal involvement and the risk of stenosis or penetration. The miR-124 (rs531564) variant may reduce the risk of ileal involvement. Among patients receiving UST treatment, the miR-146a (rs2431697) variant may increase the clinical response by week 8. However, both the miR-155 (rs767649) and miR-21 (rs13137) variants may decrease the clinical response by week 8.
Humans
;
MicroRNAs/genetics*
;
Crohn Disease/pathology*
;
Male
;
Female
;
Adult
;
Polymorphism, Single Nucleotide
;
Middle Aged
;
Asian People/genetics*
;
Genetic Predisposition to Disease
;
Genotype
;
Young Adult
;
Case-Control Studies
;
Adolescent
;
East Asian People
8.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.
9.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.
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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