1.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.
2.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.
3.Construction and Evaluation of "Constitution-disease-syndrome" Trinity Model for Rodents with Qi Deficiency
Yasheng DENG ; Jiang LIN ; Yujiang XI ; Qian ZHOU ; Yanping FAN ; Wenyue LI ; Yonghui LIU ; Zhaobing NI ; Qiu CHEN ; Xi MING
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(8):274-284
The theory of constitution in traditional Chinese medicine (TCM) has emerged as a new discipline in recent years. Constitution plays a vital role in the onset,progression,transformation,and prognosis of diseases. At present,some clinical scholars have adopted a novel diagnostic and treatment model of "constitution differentiation-disease identification-syndrome differentiation",in which constitution is regarded as a core element throughout the diagnostic and therapeutic process. Constitution is closely associated with etiology,onset,pathogenesis,syndrome differentiation,and treatment. Against this background,the construction of animal models based on constitution holds far-reaching significance for advancing clinical research. This paper focuses on the construction and evaluation of rodent models with Qi-deficiency constitution,aiming to explore how to further induce Qi-deficiency syndromes and related disease states on the basis of Qi-deficiency constitution models,thereby developing an integrated animal model that embodies the trinity of "constitution-disease-syndrome". The establishment of this model not only provides a solid experimental foundation for the development of new therapies and drugs in TCM targeting specific constitutions,diseases,and syndromes,but also greatly promotes the modernization and scientific advancement of TCM theory. By comprehensively applying multidisciplinary technologies and methods,the study evaluates the model's validity,reliability,and practicality,with the aim of opening new avenues for future research in TCM and promoting the development of the field.
4.Construction and Evaluation of "Constitution-disease-syndrome" Trinity Model for Rodents with Qi Deficiency
Yasheng DENG ; Jiang LIN ; Yujiang XI ; Qian ZHOU ; Yanping FAN ; Wenyue LI ; Yonghui LIU ; Zhaobing NI ; Qiu CHEN ; Xi MING
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(8):274-284
The theory of constitution in traditional Chinese medicine (TCM) has emerged as a new discipline in recent years. Constitution plays a vital role in the onset,progression,transformation,and prognosis of diseases. At present,some clinical scholars have adopted a novel diagnostic and treatment model of "constitution differentiation-disease identification-syndrome differentiation",in which constitution is regarded as a core element throughout the diagnostic and therapeutic process. Constitution is closely associated with etiology,onset,pathogenesis,syndrome differentiation,and treatment. Against this background,the construction of animal models based on constitution holds far-reaching significance for advancing clinical research. This paper focuses on the construction and evaluation of rodent models with Qi-deficiency constitution,aiming to explore how to further induce Qi-deficiency syndromes and related disease states on the basis of Qi-deficiency constitution models,thereby developing an integrated animal model that embodies the trinity of "constitution-disease-syndrome". The establishment of this model not only provides a solid experimental foundation for the development of new therapies and drugs in TCM targeting specific constitutions,diseases,and syndromes,but also greatly promotes the modernization and scientific advancement of TCM theory. By comprehensively applying multidisciplinary technologies and methods,the study evaluates the model's validity,reliability,and practicality,with the aim of opening new avenues for future research in TCM and promoting the development of the field.
5.Construction and validation of circadian rhythm genes-related prognostic risk model for lung adenocarcinoma
Yanqi CUI ; Hu ZHAO ; Yawei ZHANG ; Lin NI ; Duohuang LIAN ; Jingrong YANG ; Shixin YE ; Fengfeng XU ; Jincan ZHANG ; Zhiyong ZENG
Chinese Journal of Clinical Thoracic and Cardiovascular Surgery 2026;33(04):550-558
Objective To explore the relationship between circadian rhythm genes and the occurrence, development, prognosis, and tumor microenvironment (TME) of lung adenocarcinoma (LUAD). Methods The Cancer Genome Atlas data were used to evaluate the expression, copy number variation, and somatic mutation frequency of circadian gene sets in LUAD. Gene ontology, Kyoto encyclopedia of genes and genomes, and gene set enrichment analysis were used to explore the potential mechanisms by which circadian rhythm genes affected LUAD progression. Cox regression, least absolute shrinkage and selection operator regression, support vector machine recursive feature elimination, and random forest screened circadian genes and established prognostic models, and on this basis constructed nomogram to predict patients’ 1-, 3-, and 5-year survival rates. Kaplan-Meier survival curves, receiver operating characteristic (ROC) curves, and time-dependent ROC curves were drawn to evaluate the predictive ability of the model, and the external dataset of GEO further verified the prognostic value of the prediction model. In addition, we evaluated the association of the prognostic model with immune cells and immune checkpoint genes. Single cell RNA sequencing (scRNA-seq) analysis was used to explore the molecular characteristics between prognostically relevant circadian genes and different immune cell populations in TME. Results Differentially expressed circadian rhythm genes were mainly enriched in biological processes related to cGMP-PKG signaling pathway, lipid and atherosclerosis, and JAK-STAT signaling pathway. Seven circadian rhythm genes: LGR4, CDK1, KLF10, ARNTL2, RORA, NPAS2, PTGDS were screened out, and a RiskScore model was established. According to the median RiskScore, samples were divided into a high-risk group and a low-risk group. Compared with patients in the low-risk group, patients in the high-risk group showed a poorer prognosis (P<0.001). Immunological characterization analysis showed that there were differences in the infiltration of multiple immune cells between the low-risk group and high-risk group. Most immune checkpoint genes had higher expression levels in the high-risk group than those in the low-risk group, and RiskScore was positively correlated with the expression of CD276, TNFSF4, PDCD1LG2, CD274, and TNFRSF9, and negatively correlated with the expression of CD40LG and TNFSF15. The scRNA-seq analysis showed that RORA and KLF10 were mainly expressed in natural killer cells. Conclusion The prognostic model based on seven feature circadian rhythm genes has certain predictive value for predicting survival of LUAD patients. Dysregulated expression of circadian genes may regulate the occurrence, progression as well as prognosis of LUAD through affecting TME, which provides a possible direction for finding potential strategies for treating LUAD from the perspective of mechanism by which circadian disorder affects immune cells.
6.Prevention and Treatment of Asthma by Traditional Chinese Medicine Regulating PI3K/Akt Signaling Pathway: A Review
Yasheng DENG ; Yanping FAN ; Wenyue LI ; Yonghui LIU ; Zhaobing NI ; Jinjiang XU ; Haobin CHEN ; Qiuye WU ; Jiang LIN
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(17):262-275
Asthma is a chronic inflammatory respiratory disease involving multiple cells and cellular components, characterized by recurrent episodes of wheezing, shortness of breath, chest tightness, and coughing, significantly impacting patients' quality of life. The phosphatidylinositol 3-kinase/protein kinase B(PI3K/Akt) signaling pathway, as a crucial hub in intracellular signaling, is widely involved in the regulation of cell growth, proliferation, survival, metabolism, and a series of pathophysiological processes. Its regulatory role in the pathological progression of asthma is particularly significant, specifically in promoting airway inflammation, mediating epithelial mesenchymal transition, accelerating airway remodeling, regulating cell autophagy, inducing mucus hypersecretion, and influencing immune response balance. This study analyzed potential molecular targets of the PI3K/Akt pathway, including activators such as cysteine proteinase inhibitor 1(CST1), found in inflammatory zone 1(FIZZ1) and free fatty acid receptor 1(FFAR1), and inhibitors such as human β-defensin-3(hBD-3), disintegrins, metalloproteinase 33(ADAM33) and interleukin-27(IL-27), and initially revealed the potential molecular mechanisms of traditional Chinese medicine(TCM) in asthma intervention. Based on this, the authors systematically summarized the efficacy and specific mechanisms of TCM monomers, compounds, and external treatments for asthma by regulating the PI3K/Akt signaling pathway through literature review and analysis, aiming at establishing a robust foundation for the wide application and advanced development of TCM in asthma treatment, offering innovative insights for clinical research and drug development of asthma.
7.Prevention and Treatment of Asthma by Traditional Chinese Medicine Regulating PI3K/Akt Signaling Pathway: A Review
Yasheng DENG ; Yanping FAN ; Wenyue LI ; Yonghui LIU ; Zhaobing NI ; Jinjiang XU ; Haobin CHEN ; Qiuye WU ; Jiang LIN
Chinese Journal of Experimental Traditional Medical Formulae 2025;31(17):262-275
Asthma is a chronic inflammatory respiratory disease involving multiple cells and cellular components, characterized by recurrent episodes of wheezing, shortness of breath, chest tightness, and coughing, significantly impacting patients' quality of life. The phosphatidylinositol 3-kinase/protein kinase B(PI3K/Akt) signaling pathway, as a crucial hub in intracellular signaling, is widely involved in the regulation of cell growth, proliferation, survival, metabolism, and a series of pathophysiological processes. Its regulatory role in the pathological progression of asthma is particularly significant, specifically in promoting airway inflammation, mediating epithelial mesenchymal transition, accelerating airway remodeling, regulating cell autophagy, inducing mucus hypersecretion, and influencing immune response balance. This study analyzed potential molecular targets of the PI3K/Akt pathway, including activators such as cysteine proteinase inhibitor 1(CST1), found in inflammatory zone 1(FIZZ1) and free fatty acid receptor 1(FFAR1), and inhibitors such as human β-defensin-3(hBD-3), disintegrins, metalloproteinase 33(ADAM33) and interleukin-27(IL-27), and initially revealed the potential molecular mechanisms of traditional Chinese medicine(TCM) in asthma intervention. Based on this, the authors systematically summarized the efficacy and specific mechanisms of TCM monomers, compounds, and external treatments for asthma by regulating the PI3K/Akt signaling pathway through literature review and analysis, aiming at establishing a robust foundation for the wide application and advanced development of TCM in asthma treatment, offering innovative insights for clinical research and drug development of asthma.
8.Correlation between beverage dependence and sleep quality among college students
Chinese Journal of School Health 2025;46(8):1125-1129
Objective:
To explore the relationship between beverage dependence and sleep quality among college students, providing empirical evidence for improving their sleep quality.
Methods:
From December 2024 to January 2025, a convenience sampling method was used to conduct a questionnaire survey among 3 974 college students from four universities in Anhui Province. The Beverage Addiction Scale for College Students (BASCS) was used to assess beverage dependence, and the Self rating Scale of Sleep(SRSS) was used to evaluate sleep quality. A multivariate Logistic regression model was employed to analyze the relationship between beverage dependence and sleep quality, and a restricted cubic spline model was used to examine the dose response relationship between the two.
Results:
The positive rate of beverage dependence symptoms among college students was 7.6%, with positive rates of 9.6%, 13.8%, and 7.4% for the withdrawal symptoms, health effects, and dependence symptoms dimensions, respectively. The detection rate of sleep disorders was 23.6%. Multivariate Logistic regression analysis showed that after adjusting for covariates such as grade, gender, and body mass index, compared with the no beverage dependence group, students with positive beverage dependence symptoms had a higher risk of sleep disorders( OR =3.71, 95% CI =2.87-4.80, P <0.01). The OR (95% CI ) for sleep disorders among students with positive symptoms in the withdrawal symptoms, health effects, and dependence symptoms dimensions were 2.80(2.22-3.53), 2.38(1.95-2.91), and 2.45(1.89-3.18)(all P <0.01). Further analysis using a restricted cubic spline model revealed that the overall beverage dependence score and its three dimensional scores were approximately linearly related to the risk of sleep disorders among college students (all nonlinear P >0.05).
Conclusions
Beverage dependence is associated with sleep quality among college students. Schools should take multiple approaches, such as health education on beverage awareness, to improve students sleep quality.
9.Parents awareness and willingness regarding human papillomavirus and vaccination for male primary and secondary school students in Bao an District, Shenzhen
LU Fangfang, LIN Mingfeng, QIAN Miaofang, ZHANG Min, NI Xiuxian
Chinese Journal of School Health 2025;46(10):1432-1436
Objective:
To explore parents knowledge, vaccination attitude, and willingness influencing factors of human papillomavirus (HPV) and its vaccine for male primary and secondary school students, so as to provide a scientific basis for formulating targeted health education strategies and promoting the popularization of boys HPV vaccination.
Methods:
From March 3 to 14, 2025, a stratified cluster random sampling method was used to select 912 parents of boys in primary and secondary school in Bao an District, Shenzhen for a questionnaire survey. Data on their demographic characteristics, HPV related knowledge and its vaccine, vaccination attitude, and willingness were collected. Univariate analysis was performed by using the χ 2 test or t-test, and binary Logistic regression model was used to analyze related factors of HPV vaccine vaccination willingness.
Results:
The total awareness rate of parents knowledge related to HPV and its vaccine was 35.75%, among which the awareness rates of boys vaccine types ( 6.36% ), optimal age (21.16%), and optimal vaccination period (31.25%) were the lowest. The scores of parents knowledge and attitude related to HPV and its vaccine were (4.31±2.66) and (3.82±0.63). About 64.25% of parents expressed willingness to have boys vaccinated against HPV. The scores of knowledge and attitude related to HPV and its vaccine of parents with vaccination willingness (4.86±2.55, 4.02±0.58) were higher than those of parents without vaccination willingness (3.34±2.57, 3.46±0.55), and the differences were statistically significant ( t =8.59,13.96, both P <0.01). Logistic analysis showed that parents without raising daughters had a lower willingness to vaccinate boys against HPV ( OR=0.49, 95%CI =0.35-0.70); for each 1 increase in parents knowledge score related to HPV and its vaccine, the vaccination willingness increased by 9.0% ( OR=1.09, 95%CI =1.01-1.17); parents who were worried about boys infection risk ( OR=1.50, 95%CI =1.08-2.08) and parents who had their children vaccinated against HPV even if their classmates were not vaccinated ( OR=3.68, 95%CI =2.73-4.94) had higher willingness to vaccinate boys against HPV(all P <0.05).
Conclusions
Parents of boys in primary and secondary schools of Bao an District, Shenzhen have low scores of knowledge related to HPV and its vaccine.While parents show strong willingness to vaccinate boys against HPV, limited knowledge may hinder both the sustained growth of vaccination intentions and the actual implementation of vaccination practices.
10.Study on nonlinear spatiotemporal response characteristics of acupoint electrical signals to multi-mode acupuncture and moxibustion stimulation based on array multichannel data.
Shiyi QI ; Jinwen LIN ; Shihao WANG ; Jianguo CHEN ; Lili LIN ; Youcong NI ; Xin DU ; Dong LIN
Chinese Acupuncture & Moxibustion 2025;45(9):1209-1217
OBJECTIVE:
To elucidate the rules of temporal and spatial variations in distal skin potential at Hegu (LI4) under different stimulation modes by extracting nonlinear characteristic parameters from array multichannel data and adopting multivariate statistical analysis.
METHODS:
Seven healthy subjects were selected and the surface potential at the left Quchi (LI11) was collected using 14×9 array multichannel electrodes. Using Hegu (LI4) on the left as the stimulation point, four stimulation modes were applied, i.e. being quiescent, point pressing, moxibustion, and manual needling manipulation. Electrical signals were collected for 30 s in each mode, with a 5-min interval between operations, and a sampling frequency of 16 384 Hz. The data was denoised using ensemble empirical mode decomposition (EEMD), and sample entropy (SaEn) features were extracted. Statistical analysis was conducted on these data using factor analysis and multivariate analysis of variance.
RESULTS:
The SaEn values of most electrode channels were higher under point pressing, moxibustion and manual needling manipulation compared with those under quiescent condition. Under manual needling manipulation, the SaEn value of the electrode channel reached the peak in the first time interval (1-5 s) and it was declining thereafter. Factor analysis showed that the specificity of activation channels was concentrated at the left Quchi (LI11) (loading capacity ≥0.90). Analysis of variance indicated that the significant differences were presented in average sample entropy (SaEn()) values of activation channels among different stimulation modes at Hegu (LI4) (P<0.001), but there was no statistically significant interaction effect between groups and time intervals (P>0.05).
CONCLUSION
Through nonlinear characteristic parameter extraction and multivariate statistical analysis, we have uncovered the complex temporal and spatial dynamical rules of distal skin potential at Hegu (LI4) under various stimulation modes and successfully identified the specific activation characteristics at Quchi (LI11).
Humans
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Moxibustion
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Acupuncture Points
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Male
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Adult
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Female
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Young Adult
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Acupuncture Therapy/instrumentation*


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