1.Multidimensional analysis of concurrent proximal bronchiolar adenoma and lung carcinoma
Lu-Yao LI ; Gong-Ming DONG ; Yun-Peng ZHANG ; Ting-Ting WANG ; Fu-Quan JIA ; Guan-Jun ZHANG
Journal of Pathology and Translational Medicine 2026;60(3):356-363
Bronchiolar adenoma (BA) is a rare type of lung tumor characterized by bilayered epithelial cells having a continuous basal layer and a luminal layer. It resembles mucinous adenocarcinoma (MA) on frozen section, with difficulty in distinguishing the basal layer. Immunohistochemistry is the best choice for verifying the diagnosis. This study aimed to comprehensively characterize three cases of BA-combined carcinoma using clinical, histopathological, and genetic features. BA and carcinoma sections were subjected to next-generation sequencing, respectively. It was hypothesized that while different mutation forms matched different regions, BA and lung adenocarcinoma shared the same gene mutation when they co-occurred in the same location. BA with extensive carcinoma is extremely rare and presents diagnostic challenges due to its overlap with conditions such as MA. Because of its distinctive morphological characteristics, BA may be regarded as a low-grade malignancy, particularly during a confusing evaluation. A multifaceted examination of clinical, radiological, immunohistochemical, and genetic data is necessary for an accurate diagnosis.
2.Serological and molecular genetic study of the Ael/AelB phenotype induced by the c. 575T>C variant in the ABO gene
Yanying DONG ; Qinqin ZUO ; Peixing XU ; Minggang ZHANG ; Xia JIANG ; Zixuan WANG ; Miao WANG ; Gengyuan LIU ; Yi DING ; Tianju WANG ; Junhui QUAN
Chinese Journal of Blood Transfusion 2026;39(7):922-927
Objective: To analyze the serological phenotypes and molecular genetic characteristics of a proband with ABO forward and reverse typing discrepancy and their family members, and to investigate the molecular genetic mechanism underlying the Ael/AelB phenotype caused by the c. 575T>C variant on an ABO
A1.02 background. Methods: Serological testing and adsorption-elution assays were performed for blood group identification of the proband and family members. PCR-SBT, cloning sequencing, and Nanopore third-generation sequencing were used to analyze ABO gene variants and haplotypes. Phyre2 and PyMOL were used to predict the effect of the p. Ile192Thr variant on the structure of glycosyltransferase A (GTA), and plasma GTA activity was evaluated using an in vitro transferase assay. Results: Among thirteen family members, four members showed a serological phenotype consistent with the Ael subtype and one with the AelB subtype. Cloning sequencing and third-generation sequencing confirmed that five family members carried the ABO
A1.02 (c. 575T>C) variant, which co-segregated with the weak A phenotype in the family. Structural modeling suggested that p. Ile192Thr may alter the local spatial conformation and hydrogen-bond interactions of GTA. Plasma GTA activity testing showed markedly reduced GTA activity in the tested individuals. Conclusion: The ABO
A1.02 (c. 575T>C) variant is associated with the Ael/AelB phenotype. The p. Ile192Thr substitution may weaken A antigen expression by altering GTA conformation and reducing enzymatic activity. This study provides additional evidence for the role of this variant in the Ael/AelB phenotype from the perspectives of familial inheritance, full-length haplotype analysis, and functional assessment, which is important for accurate ABO subtype identification and individualized transfusion strategies.
3.Clinical application of three-dimensional printing technology combined with customized bone plate in the treatment of acetabulum fracture.
Yan-Chao ZANG ; Quan-Yong ZHAO ; Li YANG ; Jin-Zeng ZUO ; Wei QI ; Wei-Dong LIANG ; Jie XING
China Journal of Orthopaedics and Traumatology 2025;38(2):203-207
OBJECTIVE:
To explore the application value and clinical effect of 3D printing combined with customized bone plate in the treatment of acetabular fracture.
METHODS:
From June 2020 to June 2022, 11 patients with acetabular fractures underwent preoperative planning using 3D printing technology and were treated with customized bone plates including 8 males and 3 females, aged 25 to 66 years old. The fractures were classified according to Letournel-Judet:4 posterior wall fractures, 2 T-type fractures, 2 transverse posterior wall fractures, 2 double column fractures, and 1 anterior column with posterior semi-transverse fractures. The operative time, intraoperative blood loss, intraoperative fluoroscopy times, postoperative drainage volume, postoperative fracture healing time, and hip function score were recorded and analyzed.
RESULTS:
The operation time of 11 patients was 80 to 150 min, intraoperative blood volume was 150 to 700 ml, fluoroscopy frequency was 2 to 6, postoperative drainage flow was 60 to 195 ml, and the fracture healing time was 2.5 to 6.0 months. Fracture reduction was evaluated according to Matta score:anatomical reduction in 3 cases and satisfactory reduction in 8 cases. Eleven patients were followed up for 7 to 18 months. The hip Merle d'Aubigne function scores were excellent in 6 cases, good in 3 cases, fair in 1 case and poor in 1 case. Incision fat liquefaction occurred in 1 case and obturator nerve traction in 1 case.
CONCLUSION
The application of 3D printing technology combined with customized bone plates in the treatment of acetabular fracture is effective. In addition, the printed model can provide the operator with the results of the three-dimensional shape of the fracture, which is convenient for surgical reduction and effectively improves the efficiency of surgery.
Humans
;
Female
;
Male
;
Middle Aged
;
Acetabulum/surgery*
;
Printing, Three-Dimensional
;
Adult
;
Aged
;
Bone Plates
;
Fractures, Bone/surgery*
;
Fracture Fixation, Internal/methods*
4.Comparison of therapeutic effects of tibial transverse transport microcirculation reconstruction and periosteal distraction in the treatment of early diabetic foot.
Bi-Hui SONG ; Kang-Quan SHOU ; Tong-Zhu BAO ; Hua-Rui YANG ; Ya-Dong TAN
China Journal of Orthopaedics and Traumatology 2025;38(9):910-916
OBJECTIVE:
To compare clinical efficacy of tibial transverse transport (TTT) microcirculation reconstruction and periosteal distraction in treating patients with early diabetic foot(DF).
METHODS:
From June 2021 to June 2024, 60 patients with DF were admitted and divided into bone transport group and stretch group according to different treatment methods. There were 30 patients in bone transport group, including 16 males and 14 females;aged from 48 to 65 years old with an average of (55.59±3.78) years old;the course of disease ranged from 2 to 9 months with an average of(5.95±1.32) months;TTT microcirculation reconstruction surgery was performed. There were 30 patients in distraction group, including 17 males and 13 females;aged from 47 to 67 years old with an average of (55.24±3.81) years old;the course of disease ranged from 2 to 10 months with an average of (5.68±1.54) months;periosteal distraction surgery was performed. The skin temperature of the affected feet, the time of getting out of bed and walking after operation, the time of full weight-bearing, the wound healing time and complications were compared between two groups;the pain was evaluated by visual analogue scale (VAS) before operation and one month after operation respectively;the changes of blood flow velocity of dorsal foot arteries, ankle brachial index(ABI), epidermal growth factor (EGF), and basic fibroblast growth factor (bFGF) before and after operation at 3 months were compared between two groups.
RESULTS:
All patients were followed up for 3 to 4 months with an average of (3.52±0.12) months. There were no statistically significant differences in comparison of foot skin temperature, postoperative walking time, full weight-bearing time and complications between two groups (P>0.05). The wound healing time of bone transport group (61.26±7.31) days was shorter than that of distraction group (70.17±7.15) days, and the difference was statistically significant (P<0.05). Postoperative VAS at 1 month of bone transport group (2.19±0.21) was lower than that of distraction group (2.55±0.20), and the difference was statistically significant (P<0.05). At 3 months after operation, the blood flow velocity of dorsal foot artery, ankle-brachial index, EGF and bFGF in bone transport group were(34.73±4.18) cm·s-1, (0.95±0.13), (716.61±71.13) pg·ml-1 and (175.69±31.28) pg·ml-1, respectively;which were higher than that of distraction group (31.86±3.23) cm·s-1, (0.84±0.11), (677.37±70.21) pg·ml-1, (149.26±30.13) pg·ml-1, and the differences were statistically significant (P<0.05). There was no recurrence of ulcers in situ or at other sites in both groups during follow-up.
CONCLUSION
Compared with periosteal distraction, TTT microcirculation reconstruction surgery has a definite effect in the treatment of early DF. It could effectively reduce pain level, improve blood flow indicators and vascular endothelial function of the foot, and has a relatively high safety.
Humans
;
Male
;
Female
;
Middle Aged
;
Aged
;
Tibia/blood supply*
;
Diabetic Foot/physiopathology*
;
Microcirculation
;
Periosteum/surgery*
;
Plastic Surgery Procedures/methods*
;
Osteogenesis, Distraction
5.Application of 3D-printed auxiliary guides in adolescent scoliosis surgery.
Dong HOU ; Jian-Tao WEN ; Chen ZHANG ; Jin HUANG ; Chang-Quan DAI ; Kai LI ; Han LENG ; Jing ZHANG ; Shao-Bo YANG ; Xiao-Juan CUI ; Juan WANG ; Xiao-Yun YUAN
China Journal of Orthopaedics and Traumatology 2025;38(11):1119-1125
OBJECTIVE:
To investigate the accuracy and safety of pedicle screw placement using 3D-printed auxiliary guides in scoliosis correction surgery for adolescents.
METHODS:
A retrospective analysis was conducted on the clinical data of 51 patients who underwent posterior scoliosis correction surgery from January 2020 to March 2023. Among them, there were 35 cases of adolescent idiopathic scoliosis and 16 cases of congenital scoliosis. The patients were divided into two groups based on the auxiliary tool used:the 3D-printed auxiliary guide screw placement group (3D printing group) and the free-hand screw placement group (free-hand group, without auxiliary tools). The 3D printing group included 32 patients (12 males and 20 females) with an average age of (12.59±2.60) years;the free-hand group included 19 patients (7 males and 12 females) with an average age of (14.58±3.53) years. The two groups were compared in terms of screw placement accuracy and safety, spinal correction rate, intraoperative blood loss, number of intraoperative fluoroscopies, operation time, hospital stay, and preoperative and last follow-up scores of the Scoliosis Research Society-22 (SRS-22) questionnaire.
RESULTS:
A total of 707 pedicle screws were placed in the two groups, with 441 screws in the 3D printing group and 266 screws in the free-hand group. All patients in both groups successfully completed the surgery. There was a statistically significant difference in operation time between the two groups (P<0.05). The screw placement accuracy rate of the 3D printing group was 95.46% (421/441), among which the Grade A placement rate was 89.34% (394/441);the screw placement accuracy rate of the free-hand group was 86.47% (230/266), with a Grade A placement rate of 73.31% (195/266). There were statistically significant differences in the accuracy of Grade A, B, and C screw placements between the two groups (P<0.05), while no statistically significant differences were observed in intraoperative blood loss, number of fluoroscopies, correction rate, or hospital stay (P>0.05). In the SRS-22 questionnaire scores, the scores of functional status and activity ability, self-image, mental status, and pain of patients in each group at the last follow-up were significantly improved compared with those before surgery (P<0.05), but there were no statistically significant differences in all scores between the two groups (P>0.05).
CONCLUSION
In scoliosis correction surgery, compared with traditional free-hand screw placement, the use of 3D-printed auxiliary guides for screw placement significantly improves the accuracy and safety of screw placement and shortens the operation time.
Humans
;
Male
;
Scoliosis/surgery*
;
Female
;
Adolescent
;
Printing, Three-Dimensional
;
Retrospective Studies
;
Pedicle Screws
;
Child
6.Characteristics of Gut Microbiota Changes and Their Relationship with Infectious Complications During Induction Chemotherapy in AML Patients.
Quan-Lei ZHANG ; Li-Li DONG ; Lin-Lin ZHANG ; Yu-Juan WU ; Meng LI ; Jian BO ; Li-Li WANG ; Yu JING ; Li-Ping DOU ; Dai-Hong LIU ; Zhen-Yang GU ; Chun-Ji GAO
Journal of Experimental Hematology 2025;33(3):738-744
OBJECTIVE:
To investigate the characteristics of gut microbiota changes in patients with acute myeloid leukemia (AML) undergoing induction chemotherapy and to explore the relationship between infectious complications and gut microbiota.
METHODS:
Fecal samples were collected from 37 newly diagnosed AML patients at four time points: before induction chemotherapy, during chemotherapy, during the neutropenic phase, and during the recovery phase. Metagenomic sequencing was used to analyze the dynamic changes in gut microbiota. Correlation analyses were conducted to assess the relationship between changes in gut microbiota and the occurrence of infectious complications.
RESULTS:
During chemotherapy, the gut microbiota α-diversity (Shannon index) of AML patients exhibited significant fluctuations. Specifically, the diversity decreased significantly during induction chemotherapy, further declined during the neutropenic phase (P < 0.05, compared to baseline), and gradually recovered during the recovery phase, though not fully returning to baseline levels.The abundances of beneficial bacteria, such as Firmicutes and Bacteroidetes, gradually decreased during chemotherapy, whereas the abundances of opportunistic pathogens, including Enterococcus, Klebsiella, and Escherichia coli, progressively increased.Analysis of the dynamic changes in gut microbiota of seven patients with bloodstream infections revealed that the bloodstream infection pathogens could be detected in the gut microbiota of the corresponding patients, with their abundance gradually increasing during the course of infection. This finding suggests that bloodstream infections may be associated with opportunistic pathogens originating from the gut microbiota.Compared to non-infected patients, the baseline samples of infected patients showed a significantly lower relative abundance of Bacteroidetes (P < 0.05). Regression analysis indicated that Bacteroidetes abundance is an independent predictive factor for infectious complications (P < 0.05, OR =13.143).
CONCLUSION
During induction chemotherapy in AML patients, gut microbiota α-diversity fluctuates significantly, and the abundance of opportunistic pathogens increase, which may be associated with bloodstream infections. Patients with lower baseline Bacteroidetes abundance are more prone to infections, and its abundance can serve as an independent predictor of infectious complications.
Humans
;
Gastrointestinal Microbiome
;
Leukemia, Myeloid, Acute/microbiology*
;
Induction Chemotherapy
;
Feces/microbiology*
;
Male
;
Female
;
Middle Aged
7.Plasma club cell secretory protein reflects early lung injury: comprehensive epidemiological evidence.
Jiajun WEI ; Jinyu WU ; Hongyue KONG ; Liuquan JIANG ; Yong WANG ; Ying GUO ; Quan FENG ; Jisheng NIE ; Yiwei SHI ; Xinri ZHANG ; Xiaomei KONG ; Xiao YU ; Gaisheng LIU ; Fan YANG ; Jun DONG ; Jin YANG
Environmental Health and Preventive Medicine 2025;30():26-26
BACKGROUND:
It is inaccurate to reflect the level of dust exposure through working years. Furthermore, identifying a predictive indicator for lung function decline is significant for coal miners. The study aimed to explored whether club cell secretory protein (CC16) levels can reflect early lung function changes.
METHODS:
The cumulative respiratory dust exposure (CDE) levels of 1,461 coal miners were retrospectively assessed by constructed a job-exposure matrix to replace working years. Important factors affecting lung function and CC16 were selected by establishing random forest models. Subsequently, the potential of CC16 to reflect lung injury was explored from multiple perspectives. First, restricted cubic spline (RCS) models were used to compare the trends of changes in lung function indicators and plasma CC16 levels after dust exposure. Then mediating analysis was performed to investigate the role of CC16 in the association between dust exposure and lung function decline. Finally, the association between baseline CC16 levels and follow-up lung function was explored.
RESULTS:
The median CDE were 35.13 mg/m3-years. RCS models revealed a rapid decline in forced vital capacity (FVC), forced expiratory volume in the first second (FEV1), and their percentages of predicted values when CDE exceeded 25 mg/m3-years. The dust exposure level (<5 mg/m3-years) causing significant changes in CC16 was much lower than the level (25 mg/m3-years) that caused changes in lung function indicators. CC16 mediated 11.1% to 26.0% of dust-related lung function decline. Additionally, workers with low baseline CC16 levels experienced greater reductions in lung function in the future.
CONCLUSIONS
CC16 levels are more sensitive than lung indicators in reflecting early lung function injury and plays mediating role in lung function decline induced by dust exposure. Low baseline CC16 levels predict poor future lung function.
Uteroglobin/blood*
;
Humans
;
Dust/analysis*
;
Occupational Exposure/analysis*
;
Male
;
Middle Aged
;
Adult
;
Retrospective Studies
;
Lung Injury/chemically induced*
;
Coal Mining
;
Biomarkers/blood*
;
China/epidemiology*
;
Air Pollutants, Occupational
;
Female
8.Glucocorticoid Discontinuation in Patients with Rheumatoid Arthritis under Background of Chinese Medicine: Challenges and Potentials Coexist.
Chuan-Hui YAO ; Chi ZHANG ; Meng-Ge SONG ; Cong-Min XIA ; Tian CHANG ; Xie-Li MA ; Wei-Xiang LIU ; Zi-Xia LIU ; Jia-Meng LIU ; Xiao-Po TANG ; Ying LIU ; Jian LIU ; Jiang-Yun PENG ; Dong-Yi HE ; Qing-Chun HUANG ; Ming-Li GAO ; Jian-Ping YU ; Wei LIU ; Jian-Yong ZHANG ; Yue-Lan ZHU ; Xiu-Juan HOU ; Hai-Dong WANG ; Yong-Fei FANG ; Yue WANG ; Yin SU ; Xin-Ping TIAN ; Ai-Ping LYU ; Xun GONG ; Quan JIANG
Chinese journal of integrative medicine 2025;31(7):581-589
OBJECTIVE:
To evaluate the dynamic changes of glucocorticoid (GC) dose and the feasibility of GC discontinuation in rheumatoid arthritis (RA) patients under the background of Chinese medicine (CM).
METHODS:
This multicenter retrospective cohort study included 1,196 RA patients enrolled in the China Rheumatoid Arthritis Registry of Patients with Chinese Medicine (CERTAIN) from September 1, 2019 to December 4, 2023, who initiated GC therapy. Participants were divided into the Western medicine (WM) and integrative medicine (IM, combination of CM and WM) groups based on medication regimen. Follow-up was performed at least every 3 months to assess dynamic changes in GC dose. Changes in GC dose were analyzed by generalized estimator equation, the probability of GC discontinuation was assessed using Kaplan-Meier curve, and predictors of GC discontinuation were analyzed by Cox regression. Patients with <12 months of follow-up were excluded for the sensitivity analysis.
RESULTS:
Among 1,196 patients (85.4% female; median age 56.4 years), 880 (73.6%) received IM. Over a median 12-month follow-up, 34.3% (410 cases) discontinued GC, with significantly higher rates in the IM group (40.8% vs. 16.1% in WM; P<0.05). GC dose declined progressively, with IM patients demonstrating faster reductions (median 3.75 mg vs. 5.00 mg in WM at 12 months; P<0.05). Multivariate Cox analysis identified age <60 years [P<0.001, hazard ratios (HR)=2.142, 95% confidence interval (CI): 1.523-3.012], IM therapy (P=0.001, HR=2.175, 95% CI: 1.369-3.456), baseline GC dose ⩽7.5 mg (P=0.003, HR=1.637, 95% CI: 1.177-2.275), and absence of non-steroidal anti-inflammatory drugs use (P=0.001, HR=2.546, 95% CI: 1.432-4.527) as significant predictors of GC discontinuation. Sensitivity analysis (545 cases) confirmed these findings.
CONCLUSIONS
RA patients receiving CM face difficulties in following guideline-recommended GC discontinuation protocols. IM can promote GC discontinuation and is a promising strategy to reduce GC dependency in RA management. (Trial registration: ClinicalTrials.gov, No. NCT05219214).
Adult
;
Aged
;
Female
;
Humans
;
Male
;
Middle Aged
;
Arthritis, Rheumatoid/drug therapy*
;
Glucocorticoids/therapeutic use*
;
Medicine, Chinese Traditional
;
Retrospective Studies
9.Correlation between serum levels of HAMP, SPP1, RGS2 and clinical pathological characteristics of gastric cancer patients and their predictive value for postoperative recurrence or metastasis
Guangxin LI ; Huijuan QUAN ; Zhijuan GAO ; Xiaojun WANG ; Liang LI ; Qian DONG ; Yongtao MIAO ; Dongsheng LIU
Journal of International Oncology 2025;52(8):502-507
Objective:To explore the correlation between serum hepcidin antimicrobial peptide (HAMP), secreted phosphoprotein 1 (SPP1), and regulator of G protein signaling 2 (RGS2) levels and the clinical pathological characteristics of gastric cancer patients, and their predictive value for postoperative recurrence or metastasis.Methods:A total of 92 gastric cancer patients treated at Handan First Hospital from March 2021 to March 2023 were selected as the gastric cancer group, and 92 healthy individuals who underwent physical examinations during the same period were selected as the control group. The serum levels of HAMP, SPP1 and RGS2 were compared between the two groups. According to the mean levels of HAMP, SPP1, and RGS2 in the serum of gastric cancer patients, they were divided into HAMP high level group and HAMP low level group, SPP1 high level group and SPP1 low level group, RGS2 high level group and RGS2 low level group. The clinicopathological characteristics of gastric cancer patients with different levels of HAMP, SPP1 and RGS2 were compared respectively. After a median follow-up of 18 months, gastric cancer patients were divided into a non-recurrence or metastasis group ( n=59) and a recurrence and metastasis group ( n=33) based on whether the tumor recurred or metastasized. The serum levels of HAMP, SPP1, and RGS2 were compared between the two groups of patients. The predictive value of HAMP, SPP1 and RGS2 for postoperative recurrence or metastasis in patients with gastric cancer was analyzed by using the receiver operator characteristic (ROC) curve. Results:Compared with the control group, the gastric cancer group had higher levels of serum HAMP [ (52.28±5.44) ng/ml vs. (31.22±4.18) ng/ml] and SPP1 [ (55.96±6.43) ng/ml vs. (36.99±5.25) ng/ml] ( t=29.44, P<0.001; t=21.92, P<0.001), and lower level of RGS2 [ (3.72±0.66) mg/L vs. (5.11±0.87) mg/L) ] ( t=12.21, P<0.001). There were statistically significant differences in maximum tumor diameter ( χ2=13.07, P<0.001; χ2=6.71, P=0.010; χ2=10.56, P=0.001), TNM staging ( χ2=7.42, P=0.006; χ2=6.36, P=0.012; χ2=5.39, P=0.020), lymph node metastasis ( χ2=23.41, P<0.001; χ2=6.52, P=0.011; χ2=13.11, P<0.001), and differentiation degree ( χ2=9.01, P=0.003; χ2=7.97, P=0.005; χ2=15.29, P<0.001) between the gastric cancer patients in the HAMP high level group ( n=44) and the HAMP low level group ( n=48), the SPP1 high level group ( n=43) and the SPP1 low level group ( n=49), and the RGS2 high level group ( n=50) and the RGS2 low level group ( n=42). Compared with the non-recurrence or metastatic group, the recurrence and metastatic group had higher levels of serum HAMP [ (59.26±5.66) ng/ml vs. (48.37±4.28) ng/ml] and SPP1 [ (62.85±6.36) ng/ml vs. (52.11±5.38) ng/ml] level ( t=10.40, P<0.001; t=8.60, P<0.001), and lower level of RGS2 [ (3.01±0.48) mg/L vs. (4.12±0.69) mg/L] ( t=8.19, P<0.001). ROC curve analysis showed that the area under the curve (AUC) values of serum HAMP, SPP1, and RGS2 levels alone for predicting postoperative recurrence or metastasis in gastric cancer patients were 0.777, 0.813, and 0.778, respectively. The AUC value of the combination of the three indicators for predicting postoperative recurrence or metastasis in gastric cancer patients was 0.871. The predictive efficacy of the combination of the three indicators for predicting postoperative recurrence or metastasis in gastric cancer patients was better than that alone ( Z=2.51, P=0.035; Z=2.61, P=0.032; Z=2.71, P=0.029) . Conclusions:The levels of HAMP and SPP1 in the serum of gastric cancer patients increase, while the level of RGS2 decreases, and the levels of the three are related to the maximum tumor diameter, TNM staging, lymph node metastasis and differentiation degree, and their combined detection has higher predictive value for postoperative recurrence or metastasis in gastric cancer patients.
10.Development of an Analytical Software for Forensic Proteomic SAP Typing
Feng HU ; Meng-Jiao WANG ; Jia-Lei WU ; Dong-Sheng DING ; Zhi-Yuan YANG ; An-Quan JI ; Lei FENG ; Jian YE
Progress in Biochemistry and Biophysics 2025;52(9):2406-2416
ObjectiveThe proteome of biological evidence contains rich genetic information, namely single amino acid polymorphisms (SAPs) in protein sequences. However, due to the lack of efficient and convenient analysis tools, the application of SAP in public security still faces many challenges. This paper aims to meet the application requirements of SAP analysis for forensic biological evidence’s proteome data. MethodsThe software is divided into three modules. First, based on a built-in database of common non-synonymous single nucleotide polymorphisms (nsSNPs) and SAPs in East Asian populations, the software integrates and annotates newly identified exonic nsSNPs as SAPs, thereby constructing a customized SAP protein sequence database. It then utilizes a pre-installed search engine—either pFind or MaxQuant—to perform analysis and output SAP typing results, identifying both reference and variant types, along with their corresponding imputed nsSNPs. Finally, SAPTyper compares the proteome-based typing results with the individual’s exome-derived nsSNP profile and outputs the comparison report. ResultsSAPTyper accepts proteomic DDA mass spectrometry raw data (DDA acquisition mode) and exome sequencing results of nsSNPs as input and outputs the report of SAPs result. The pFind and Maxquant search engines were used to test the proteome data of 2 hair shafts of2 individuals, and both obtained SAP results. It was found that the results of the Maxquant search engine were slightly less than those of pFind. This result shows that SAPTyper can achieve SAP fingding function. Moreover, the pFind search engine was used to test the proteome data of 3 hair shafts from 1 European person and 1 African person in the literature. Among the sites fully matched by the literature method, sites detected by SAPTyper are also included; for semi-matching sites, that is, nsSNPs are heterozygous, both literature method and SAPTyper method had the risk of missing detection for one type of the allele. Comparing the analysis results of SAPTyper with the SAP test results reported in the literature, it was found that some imputed nsSNP sites identified by the literature method but not detected by SAPTyper had a MAF of less than 0.1% in East Asian populations, and therefore they were not included in the common nsSNP database of East Asian populations constructed by this software. Since the database construction of this software is based on the genetic variation information of East Asian populations, it is currently unable to effectively identify representative unique common variation sites in European or African populations, but it can still identify SAP sites shared by these populations and East Asian populations. ConclusionAn automated SAP analysis algorithm was developed for East Asian populations, and the software named SAPTyper was developed. This software provides a convenient and efficient analysis tool for the research and application of forensic proteomic SAP and has important application prospects in individual identification and phenotypic inference based on SAP.

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