OBJECTIVE: To develop a user-friendly visualization application for the automatic annotation of Human Phenotype Ontology (HPO) terms based on large language models and retrieval-augmented generation (RAG) technology, and to validate its performance in an authoritative case dataset. METHODS: By integrating the domestic open-source large language model DeepSeek-V3 with RAG technology, an interactive web application was deployed on the Streamlit cloud platform. Using only the latest official HPO dataset as the data source, the lightweight sentence-embedding model BAAI/bge-small-en-v1.5 was employed to construct a FAISS vector index. During the online phase, a four-step closed-loop process is automatically completed: multilingual translation, phenotype phrase extraction, RAG candidate retrieval, term mapping, and official database validation. 121 English case reports publicly released by BMJ Case Reports and Oxford Medical Case Reports (with a gold-standard HPO set of 1 794 terms) were selected for application validation. Precision, recall, and F1 score were calculated and compared horizontally with traditional dictionary tools, standalone large language models, and the similar application "RAG-HPO". Finally, replace the model with the more advanced ChatGPT-5 and evaluate its performance on the newly extracted dataset. RESULTS: An HPO term automatic annotation visualization application named PhenoRAG, based on large language models and RAG technology, was successfully developed. Users can access it directly via a web link. Across the 112 cases, a total of 2 150 HPO terms were generated; 2,064 (96.0%) were fully validated by the official database, with a hallucination rate of 1.3% and an HPO ID-name mismatch rate of 2.7%. After deduplication, 1,906 terms remained for testing. The overall precision was 63.65%, recall was 67.34%, and F1 was 65.44%, significantly outperforming traditional annotation tools (F1: 0.45-0.49, P < 0.001). Although PhenoRAG's F1 was lower than that of RAG-HPO (F1 = 0.78, P < 0.001), which relies on a manually constructed synonym database of 54 000 entries plus the HPO dataset, it requires no additional dictionary maintenance and can be used without any background in computer programming. Moreover, after switching to the GPT-5 model, PhenoRAG exhibited no hallucination rate on the new dataset, and its F1 score significantly increased (P = 0.038). CONCLUSION Without constructing a synonym database, the PhenoRAG achieved high-accuracy automatic mapping from clinical text to standard HPO terms. It features a low usage threshold, free access, and a Chinese-language interface, and can directly serve rare disease diagnosis, genetic counseling, and research scenarios in China and worldwide, warranting further clinical promotion and multicenter validation.
Humans ; Phenotype ; Biological Ontologies ; Language ; Software ; Large Language Models

Objective:To evaluate the factors influencing test failure after resampling in non-invasive prenatal testing (NIPT) and to explore its impact on pregnancy outcomes.Methods:The information of pregnant women who failed to undergo NIPT for the first time and resampled for testing in Beijing Obstetrics and Gynecology Hospital, Capital Medical University from January 2018 to January 2022 were collected and retrospectively analyzed. According to the results of resampled NIPT, the pregnant women were divided into the failure group (170 cases) and the success group(485 cases), and the general clinical data and pregnancy outcomes of the two groups were compared.Results:(1) A total of 88 928 pregnant women underwent NIPT in Beijing Obstetrics and Gynecology Hospital during the study period, of which 1 299 (1.461%, 1 299/88 928) failed in the first NIPT. Among the 1 299 pregnant women who failed in the first NIPT, 720 were resampled for testing. Finally, 655 pregnant women who met the inclusion criteria and had complete clinical information and perinatal outcomes were collected. The success rate of resampling was 74.0% (485/655). Compared with the success group, the pregnant women in the failure group had a later gestational age at resampling, a higher pre-pregnancy body mass index (BMI) and a higher fetal fraction, and the differences were statistically significant (all P<0.001). (2) Among the 485 pregnant women in the success group, 130 cases (26.8%, 130/485) were detected with chromosome aneuploidy. Among the 170 pregnant women in the failure group, 8 cases had abnormal amniocentesis, 2 cases had abnormal maternal serum screening of aneuploidy in the second trimester, 3 cases had abnormal ultrasound anomaly removal, and 157 cases had no abnormality. (3) The incidence of fetal or neonatal malformation in the failure group was significantly higher than that in the success group [11.2% (19/170) vs 5.8% (28/485), P=0.019], but after adjusting for age and pre-pregnancy BMI, fetal or neonatal malformation was not associated with the success of resampling ( RR=0.675, 95% CI: 0.346-1.319; P=0.250). The incidences of gestational diabetes mellitus and hypertensive disorders in pregnancy in the failure group were significantly higher than those in the success group (all P<0.05), but after adjusting for age and pre-pregnancy BMI, only the incidence of gestational diabetes mellitus in the failure group was higher ( RR=0.630, 95% CI: 0.426-0.932; P=0.021). Conclusions:For pregnant women who failed the initial NIPT, the success of the resampling test is associated with pre-pregnancy BMI and the gestational week at the time of resampling. Those who failed the resampling test are more likely to develop gestational diabetes mellitus. When providing genetic counseling for pregnant women who failed the initial NIPT, it is important to consider the successful rate of resampling testing. The risk of chromosomal abnormalities should be comprehensively considered to develop further screening strategies.

BACKGROUND: The role of inflammation in the development of gestational diabetes mellitus (GDM) has recently become a focus of research. The systemic immune-inflammation index (SII) and systemic inflammation response index (SIRI), novel indices, reflect the body's chronic immune-inflammatory state. This study aimed to investigate the associations between the SII or SIRI and GDM. METHODS: A prospective birth cohort study was conducted at Beijing Obstetrics and Gynecology Hospital from February 2018 to December 2020, recruiting participants in their first trimester of pregnancy. Baseline SII and SIRI values were derived from routine clinical blood results, calculated as follows: SII = neutrophil (Neut) count × platelet (PLT) count/lymphocyte (Lymph) count, SIRI = Neut count × monocyte (Mono) count/Lymph count, with participants being grouped by quartiles of their SII or SIRI values. Participants were followed up for GDM with a 75-g, 2-h oral glucose tolerance test (OGTT) at 24-28 weeks of gestation using the glucose thresholds of the International Association of Diabetes and Pregnancy Study Groups (IADPSG). Logistic regression was used to analyze the odds ratios (ORs) (95% confidence intervals [CIs]) for the the associations between SII, SIRI, and the risk of GDM. RESULTS: Among the 28,124 women included in the study, the average age was 31.8 ± 3.8 years, and 15.76% (4432/28,124) developed GDM. Higher SII and SIRI quartiles were correlated with increased GDM rates, with rates ranging from 12.26% (862/7031) in the lowest quartile to 20.10% (1413/7031) in the highest quartile for the SII ( Ptrend <0.001) and 11.92-19.31% for the SIRI ( Ptrend <0.001). The ORs (95% CIs) of the second, third, and fourth SII quartiles were 1.09 (0.98-1.21), 1.21 (1.09-1.34), and 1.39 (1.26-1.54), respectively. The SIRI findings paralleled the SII outcomes. For the second through fourth quartiles, the ORs (95% CIs) were 1.24 (1.12-1.38), 1.41 (1.27-1.57), and 1.64 (1.48-1.82), respectively. These associations were maintained in subgroup and sensitivity analyses. CONCLUSION The SII and SIRI are potential independent risk factors contributing to the onset of GDM.
Humans ; Female ; Pregnancy ; Diabetes, Gestational/immunology* ; Prospective Studies ; Adult ; Inflammation/immunology* ; Glucose Tolerance Test ; Birth Cohort

Objective:To evaluate the factors influencing test failure after resampling in non-invasive prenatal testing (NIPT) and to explore its impact on pregnancy outcomes.Methods:The information of pregnant women who failed to undergo NIPT for the first time and resampled for testing in Beijing Obstetrics and Gynecology Hospital, Capital Medical University from January 2018 to January 2022 were collected and retrospectively analyzed. According to the results of resampled NIPT, the pregnant women were divided into the failure group (170 cases) and the success group(485 cases), and the general clinical data and pregnancy outcomes of the two groups were compared.Results:(1) A total of 88 928 pregnant women underwent NIPT in Beijing Obstetrics and Gynecology Hospital during the study period, of which 1 299 (1.461%, 1 299/88 928) failed in the first NIPT. Among the 1 299 pregnant women who failed in the first NIPT, 720 were resampled for testing. Finally, 655 pregnant women who met the inclusion criteria and had complete clinical information and perinatal outcomes were collected. The success rate of resampling was 74.0% (485/655). Compared with the success group, the pregnant women in the failure group had a later gestational age at resampling, a higher pre-pregnancy body mass index (BMI) and a higher fetal fraction, and the differences were statistically significant (all P<0.001). (2) Among the 485 pregnant women in the success group, 130 cases (26.8%, 130/485) were detected with chromosome aneuploidy. Among the 170 pregnant women in the failure group, 8 cases had abnormal amniocentesis, 2 cases had abnormal maternal serum screening of aneuploidy in the second trimester, 3 cases had abnormal ultrasound anomaly removal, and 157 cases had no abnormality. (3) The incidence of fetal or neonatal malformation in the failure group was significantly higher than that in the success group [11.2% (19/170) vs 5.8% (28/485), P=0.019], but after adjusting for age and pre-pregnancy BMI, fetal or neonatal malformation was not associated with the success of resampling ( RR=0.675, 95% CI: 0.346-1.319; P=0.250). The incidences of gestational diabetes mellitus and hypertensive disorders in pregnancy in the failure group were significantly higher than those in the success group (all P<0.05), but after adjusting for age and pre-pregnancy BMI, only the incidence of gestational diabetes mellitus in the failure group was higher ( RR=0.630, 95% CI: 0.426-0.932; P=0.021). Conclusions:For pregnant women who failed the initial NIPT, the success of the resampling test is associated with pre-pregnancy BMI and the gestational week at the time of resampling. Those who failed the resampling test are more likely to develop gestational diabetes mellitus. When providing genetic counseling for pregnant women who failed the initial NIPT, it is important to consider the successful rate of resampling testing. The risk of chromosomal abnormalities should be comprehensively considered to develop further screening strategies.

Objective To explore the content and psychometric properties of sarcopenia measurements for older adults. Methods Using the International Classification of Functioning,Disability and Health(ICF)linking and coding rules,a content analysis were conducted on the seven types of measurement tools for geriatric sarcopenia,including Strength,Assistance with walking,Rising from a chair,Climbing stairs,and Falls(SARC-F);Ishii Test;Mini Sar-copenia Risk Assessment-7(MSRA-7);6-minute walk test(6MWT);Barthel Index(BI);Short Physical Perfor-mance Battery(SPPB);and World Health Organization Disability Assessment Schedule 2.0(WHODAS 2.0),and psychometric property was explored. Results The seven measurement tools can be categorized into body functions and structures,activities and participation,and comprehensive categories.ICF coding for SARC-F involved muscle power functions(b730),walking(d450),changing basic body position(d410),etc.Ishii Test involved muscle power functions(b730)and weight maintenance functions(b530).MSRA-7 involved walking(d450),involuntary movement reaction functions(b755),muscle endurance functions(b740),etc.ICF coding for 6MWT involved walking(d450).SPPB involved changing basic body position(d410),control voluntary movement functions(b760),and walking(d450).BI in-volved eating(d550),drinking(d560),washing oneself(d510),caring for body parts(d520),etc.WHODAS 2.0 involved attention functions(b140),acquiring skills(d155),communication-receiving-verbal messages(d310),community life(d910),etc.SARC-F was low to medium in sensitivity,and medium to excellent in specificity.Ishii Test was medium to good in sensitivity,average to good in specificity,and good in diagnostic performance.MSRA-7 was medium to good in sensitivity,average in specificity,and average to medium in diagnostic perfor-mance,while MSRA-5 was average to good in sensitivity,average in specificity,and medium in diagnostic per-formance.6MWT was average to medium in sensitivity,and average in specificity.SPPB was average in sensitiv-ity,average to medium in specificity,and average to excellent in diagnostic performance.BI was good in reliabili-ty,and WHODAS 2.0 was excellent in reliability. Conclusion The measurement tools for sarcopenia can be categorized into body functions and structures,activities and participation,and comprehensive assessment tools combining the above.The psychometric properties of the sev-en measurement tools are low to excellent in sensitivity and average to excellent in specificity.

The new-generation non-invasive prenatal screening technology (NIPT2.0) is a new method successfully realized in recent years based on high-throughput sequencing to synchronously and accurately detect fetal chromosomal aneuploidies, microdeletion/microduplication syndromes and dominantly inherited monogenic disorders. NIPT2.0 can circumvent the shortcomings of previous non-invasive prenatal screening techniques (NIPT and NIPT Plus) including incapability to detect fetal monogenic disorders, insufficient accuracy of detection and low positive predictive values for certain chromosomal abnormalities (in particular trisomy 13, sex chromosomal abnormalities, and small-segment microdeletions and microduplication syndromes). How to apply NIPT2.0 reasonably and normatively to maximize its clinical value has become an issue which requires clarification. The Reproductive Health Branch of the Chinese Maternal and Child Health Care Association has organized experts to fully discuss and jointly drafted this consensus, which has put forwards suggestions over the clinical application strategy for NIPT2.0, including the scope of application, target disease, pre-test consultation, clinical application pathway, post-test genetic counseling and intervention, quality control and limitations, for the reference by peers, with a view to standardize its application and provide better clinical service.

Objective:To assess the effectiveness and feasibility of carrier detection for Spinal muscular atrophy (SMA) by using digital PCR assay.Methods:Peripheral blood samples were collected from 214 pregnant women who were routinely screened for SMA carriers, of which 204 were randomly selected samples and 10 were samples with known copy numbers of SMN1 exons 7 and 8. Samples with known copy numbers of SMN1 exons 7 and 8 were randomly mixed into the experiment to validate the performance of the digital PCR assay. The copy numbers of SMN1 exons 7 and 8 and SMN2 exons 7 and 8 in peripheral blood samples were detected by digital PCR assay. The results of SMN1 exons 7 and 8 were compared with those of the quantitative PCR method to assess the reliability and clinical performance of the digital PCR assay. Results:Among the 204 random samples, digital PCR has detected five samples with simultaneous heterozygous deletion of SMN1 exons 7 and 8, three samples with heterozygous deletion of SMN1 exon 8 only, and 196 samples with no deletion of SMN1 exons 7 and 8. Ten samples with known SMN1 exons 7 and 8 copy numbers were detected with the expected values. The digital PCR test results were fully consistent with that of the quantitative PCR. Conclusion:The results of digital PCR for the detection of copy number variation of SMN1 exons 7 and 8 were consistent with qPCR. Digital PCR assay was able to clearly distinguish the copy number of the target genes, therefore can be used for SMA carrier screening. Moreover, it can also detect copy number of SMN2 exons 7 and 8, which can provide more information for genetic counseling.

Objective:To make clear the duties of the clinical research coordinators (CRC) and evaluate any inadequacies in their management and training in the industry, ideas for ameliorating the construction of the CRC team and the promotion of clinical trial quality should be suggested.Methods:Drawing from the author′s experience in CRC management and a literature review, this paper assessed the current state of CRC work and management, and provides advice on how to improve CRC management.Results:In China, the CRC domain lacked a unified standard and access mechanism, leading to inconsistent levels of basic quality and business ability among CRC offerings within the sector.In order to maintain a steady CRC personnel team and promote the quality of clinical trials, it was essential to improve the training of CRC professionals, determine their career development paths, arrange different levels and fields of CRC training, adjust wages and appraisals, and take other suitable measures.Conclusions:It is proposed that the top medical organizations in China collaborate with sponsors and site management organizations to create a standardized and unified CRC occupational admission system and assessment criteria, in order to enhance the capacity and standard of CRC and addressing China′s increasing demand for clinical trials.

Objective:To provide evidence for medical institutions to explore the standardized management in Investigator Initiated Trials (IIT) through understanding the problems and providing suggestions of IIT management in the past 10 years.Methods:The publication year, region, content, existing problems, and suggestions were abstracted and analyzed by Bibliometric analysis.Results:58 studies were included in the analysis from 12 regions, and the top three regions were Shanghai, Beijing, and Guangdong Province. There were 10 items of IIT management, including management status, ethical management, process management, information management, contract management, approval management, human genetic resource management, researcher management, multi-center management, and methodology system management. The problems and suggestions of each item of IIT management were summarized respectively.Conclusions:The imperfect supervision system of IIT has brought great difficulties to the management department. Medical institutions should clarify management points and risk points from the item of IIT management and take targeted measures to actively promote high-quality IIT research.

Objective:The cluster analysis method was applied to evaluate the scientific research performance evaluation index system of departments in an obstetrics and gynecology hospital, and analyze the weaknesses of scientific research work of various departments, to provide a basis for the improvement of scientific research strength of departments.Methods:On the basis of the scientific research performance evaluation index system of departments in the obstetrics and gynecology hospital, the indicators and weights of the system were optimized through expert consultation, and the scientific research values from 2019 to 2021 were brought into the optimized scientific research performance evaluation index system to calculate the scientific research scores of each department, and then the cluster analysis method was applied to evaluate the index system.Results:Before and after the optimization of the scientific research performance evaluation index system of departments, the conformity with the discipline classification was 76.00% and 96.67% respectively ( P=0.039). In total of 30 departments were clustered into 4 categories: excellent (7), good (7), medium (4), and concerned (12). The average score of the total scientific research performance evaluation indicators of the 4 categories of departments was 15.022. The highest average score was for papers and monographs, and the lowest was for awards. Conclusions:This study applied the cluster analysis method to evaluate the scientific research performance evaluation index system of departments in the obstetrics and gynecology hospital and replaced quantitative indicators with quality indicators. It will optimize and improve the hospital hierarchical management methods, provide data support and classified guidance for the scientific research development of different categories of departments, and provide a reference basis for hospitals to formulate scientific research management policies such as achievement transformation, award, industry standard guidelines, etc.