Objective:To establish a prognostic prediction model for hepatocellular carcinoma (HCC) using bioinformatics approaches to guide personalized therapy.Methods:Based on bioinformatics, the differential analysis was carried out on the GSE19665 data set of The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) and Gene Expression Omnibus (GEO), and the same differentially expressed genes were obtained by means of Wayne diagram. Functional enrichment analyses using Gene Ontology, Kyoto Encyclopedia of Genes and Genome, and Gene Set Enrichment Analysis were conducted on co-expressed genes. Based on clinicopathological and transcriptomic profiles, TCGA-LIHC patients were stratified into training ( n=246) and internal validation ( n=116) cohorts, with external validation using Japanese liver cancer data ( n=231) from the International Cancer Genome Consortium. A LASSO-Cox regression-derived risk scoring model was established and visualized as a nomogram. The clinical utility of the risk score was evaluated through multiple analytical approaches.A nomogram incorporating the risk score was developed, and its predictive performance was validated using the concordance index (C-index) and calibration curves. The measurement data of normal distribution were expressed as mean±standard deviation( ± s), and the t-test was used for comparison between groups. The measurement data with non-normal distribution were expressed as M( Q1, Q3), and the Wilcoxon test was used for comparison between groups. The Kruskal-Wallis test was applied to evaluate the significance of the differences among multiple groups. The prognostic value of the risk score was estimated using Kaplan-Meier analysis and ROC curve. Multivariate Cox regression clarified the independent prognostic value of the risk score. Results:Differential analysis identified 457 commonly expressed differentially expressed genes (DEGs). Enrichment analysis revealed that these common DEGs were significantly enriched in pathways related to the cell cycle of tumor cells.The LASSO-Cox regression model selected eight candidate genes ( CENPA, NDC80, ANXA10, NEIL3, G6 PD, MCM10, SOCS2, MMP1). The predictive risk score generated using these eight genes demonstrated a strong association with the overall survival of HCC patients.The nomogram combining the predictive risk score with clinicopathological features exhibited high predictive performance in both the training and validation cohorts. Furthermore, the prognostic value of this risk score was successfully validated in the external validation cohort. Conclusion:This study successfully developed a new predictive model that accurately predicts the 1-year, 3-year and 5-year survival rates of patients with liver cancer. This can serve as a potential tool to help guide patients in personalized treatment.

Objective:To study the predictive role of tumor burden score (TBS) for tumor recurrence after radical resection in patients with hepatocellular carcinoma (HCC).Methods:Clinical data of 202 patients with HCC undergoing radical surgery at the 900th Hospital of Joint Logistics Support Force of the Chinese People's Liberation Army, between January 2015 and December 2017 were retrospectively analyzed, including 128 males and 74 females, aged (53.66±11.93) years old. The receiver operating characteristic (ROC) curve was used to assess the accuracy of TBS in predicting postoperative tumor recurrence. Univariate and multivariate logistic regression analyses were performed to identify independent risk factors influencing postoperative tumor recurrence. A nomogram was established and validated using calibration curves and the C-index. Kaplan-Meier survival analysis was utilized to compare survival differences between the two patient groups.Results:The area under the ROC curve for TBS in predicting postoperative tumor recurrence in HCC patients was 0.779 (95% CI: 0.717-0.842), with an optimal cutoff value of 6.2. Univariate analysis revealed that factors such as hepatitis B virus DNA level >500 IU/ml, larger maximum tumor dia-meter, and TBS>6.2 were significant risk factors for postoperative tumor recurrence (all P<0.05). Multivariate analysis further indicated that TBS>6.2 ( OR=3.60, 95% CI: 1.081-12.012, P=0.037) and maximum tumor diameter ( OR=1.240, 95% CI: 1.034-1.487, P=0.020) were independent risk factors for postoperative recurrence. Based on these risk factors, a nomogram model was established, achieving a C-index of 0.788. Kaplan-Meier survival analysis showed a better postoperative overall survival and recurrence-free survival of the low TBS group compared to those of the high TBS group (all P<0.05). Conclusion:TBS can serve as a predictive indicator for the recurrence after radical resection in patients with HCC. Both TBS and tumor size are independent risk factors for postoperative recurrence. The nomogram model can be used for predicting recurrence following radical resection in HCC patients.

Objective:To evaluate extrathecal vs. intrathecal approach of Glisson's pedicle in laparoscopic hepatectomy of hepatocellular carcinoma (HCC). Methods:Clinical data of 96 HCC patients receiving laparoscopic hepatectomy at the Department of Hepatobiliary Surgery, the 900 Hospital of the United Logistics Force from Jan 2019 to Jun 2022 were retrospectively analyzed. Thrity-six cases were treated with extrathecal approach of Glisson's pedicle and 60 cases were by intrathecal approach.All those 60 undergoing intrathecal approach cases were matched by 1∶1 propensity score matching, and the caliper value was 0.02. The duration of surgery, blocking-time of hepatoduodenal ligament, intraoperative blood loss, indexes of the liver function and the prothrombin time on the 1st day of the postoperative period, rate of the postoperative complications, postoperative hospital stay, postoperative survival and recurrence were compared between the two groups.Results:After propensity score matching, 32 cases in each group were identified. The operation time of the extrathecal group was shorter than that of the intrathecal group [(207.5±77.4) minutes vs. (248.6±74.7) minutes, P=0.03], the intraoperative bleeding volume was less than that of the intrathecal group [(150.0(100.0, 300.0) ml vs. 250.0(150.0, 587.5) ml, P=0.01], and the albumin level was higher on the 1st day after the surgery [(36.5±3.2) g/L vs. (34.3±3.2) g/L, P<0.01]. There was no statistically significant difference in postoperative liver function, coagulation, complications, hospitalization time, all over survival rate between the two groups (all P>0.05). Conclusion:Extrathecal approach for Glisson's pedicle is safe and feasible in laparoscopic hepatectomy for HCC, with simpler surgical procedure, less intraoperative trauma.

SARS-CoV-2 is a new RNA virus affecting humans and spreads extensively throughout the world since its first outbreak in December,2019.Whether the transmissibility and pathogenicity of SARS-CoV-2 in humans after zoonotic transfer are actively evolving,and driven by adaptation to the new host and environments is still under debate.Understanding the evolutionary mechanism underlying epidemiological and pathological characteristics of COVID-19 is essential for predicting the epidemic trend,and providing guidance for disease control and treatments.Interrogating novel strategies for identifying natural selection using within-species polymorphisms and 3,674,076 SARS-CoV-2 genome sequences of 169 countries as of December 30,2021,we demonstrate with popula-tion genetic evidence that during the course of SARS-CoV-2 pandemic in humans,1)SARS-CoV-2 genomes are overall conserved under purifying selection,especially for the 14 genes related to viral RNA replication,transcription,and assembly;2)ongoing positive selection is actively driving the evolution of 6 genes(e.g.,S,ORF3a,and N)that play critical roles in molecular processes involving pathogen-host interactions,including viral invasion into and egress from host cells,and viral inhi-bition and evasion of host immune response,possibly leading to high transmissibility and mild symptom in SARS-CoV-2 evolution.According to an established haplotype phylogenetic relation-ship of 138 viral clusters,a spatial and temporal landscape of 556 critical mutations is constructed based on their divergence among viral haplotype clusters or repeatedly increase in frequency within at least 2 clusters,of which multiple mutations potentially conferring alterations in viral transmis-sibility,pathogenicity,and virulence of SARS-CoV-2 are highlighted,warranting attention.

COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,2020.We identified a total of 347 mutated positions,31 of which were over-represented in Pakistan.Meanwhile,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or coevolution.Some of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying selections.The genomic epidemiology revealed five distinctive spreading clusters.The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF 1ab)of this cluster.Further-more,28 putative international introductions were identified,several of which are consistent with the epidemiological investigations.In all,this study has inferred the possible pathways of introduc-tions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control.

Objective:To investigate the predictive effect of neutrophil to lymphocyte ratio (NLR) for recurrence-free survival after liver transplantation in hepatocellular carcinoma (HCC) patients.Methods:The clinical data of 84 HCC patients who underwent liver transplantation in the 900th Hospital of the Joint Logistics Team, PLA, from January 2012 to December 2019 were included in this retrospective analysis. There were 73 males and 11 females, with an average age of 51 years. Univariate and multivariate Cox regression analyses were performed. The distinguishing ability of NLR for predicting recurrence-free survival in patients with HCC after liver transplantation was analyzed using the receiver operating characteristic (ROC) curvee. The two groups were generated according with the cut-off value, and the recurrence-free survival time to make the Kaplan-Meier survival curve.Results:The area under the ROC curve of NLR for predicting recurrence-free survival after liver transplantation in patients with HCC was 0.683, Yoden index was 0.319, and the optimal threshold was 3.2.Univariate analysis showed that maximum tumor diameter, number of tumors, Milan criteria, and NLR were associated with recurrence-free survival after liver transplantation in patients with HCC (all P<0.05). Multivariate analysis showed that maximum tumor diameter ( HR=2.412, 95% CI: 1.277-4.555), number of tumors ≥3 ( HR=5.595, 95% CI: 2.023-17.531) and NLR≥3.2 ( HR=2.891, 95% CI: 1.348-6.204) were independent risk factors for recurrence-free survival of HCC patients prediction after liver transplantation (all P<0.05). The 1-year recurrence-free survival rate was 78% in the NLR<3.2 group ( n=61), which was superior to 58% in the NLR≥3.2 group ( n=23), and the difference was statistically significant ( P<0.05). Conclusion:Tumor diameter, number of tumors and NLR are risk factors affecting the prognosis of liver transplantation in patients with HCC, and high serum NLR may indicate recurrence-free survival in patients with HCC after liver transplantation.

Objective:To find the chromosomal malfomations among microtia patients and the neighbouring genes of chromosomal aberrations or genes in the extra or deleted chromosome fragments would be screened to investigate the possible causative genes.Methods:According to the inclusion criteria, case group was selected from microtia patients referred to Plastic Surgery Hospital, Chinese Academy of Medical Science, between January 2012 and January 2014, and the control group was the normal people of similar age received plastic surgery in the same hospital in the same time who did not have any congenital genetic disease. Blood samples of two groups were collected, and genomic DNA was extracted, then copy number variation (CNV) analysis was performed in the two groups with gene chip technology and associated software for large fragment chromosomal malformations. The variations of chromosome copy number were recorded to further analyze the type and length of chromosome structure variation. The genes at the loci of break points were further screened referring to B allele frequency to interpret associated genes related to the occurrence of microtia. Fisher exact test were used for statistical analysis, and the difference was statistically significant ( P< 0.05). Results:942 patients with congenital microtia were included in the case group, 695 males and 247 females, aged (11.4±3.2) years; 1 802 normal controls, 1 290 males and 512 females, aged (11.6±4.9) years. Large chromosomal fragments variations were detected in 5 patients in chromosome in case group( P=0.003). The difference between the two groups was statistically significant( P=0.003). Three cases were found to carry an extra X chromosome. Among the 3 cases, one patient suffered from XXY karyotype and the other 2 patients X trisomy. Two cases were proved to be associated with chromosome structural variations. The malformations of the first case presented partial duplication of the long arm of chromosome 13 and 14. On searching for causative genes, OTX2, BMP4 and GSC were detected to be in the chromosome structural variations. The second case presented to be partial duplication of the long arm of chromosome 5. FGF pathway associated genes FGF18, FGFR4, FGF1 and BMP pathway associated genes FST, MSX2, SMAD5 were incorporated in the extra duplicated chromosome for possible gene dosage effect. Conclusions:The results indicated the possible association of chromosome abnormity and microtia and provide new insights in microtia-associated chromosome instability. Ten related genes were involved in the occurrence of microtia through various ways.

A novel RNA virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the ongoing outbreak of coronavirus disease 2019 (COVID-19). Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19. However, due to extensive sampling bias and existence of infection clusters during the epidemic spread, direct applications of existing approaches can lead to biased parameter estima-tions and data misinterpretation. In this study, we first present robust estimator for the time to the most recent common ancestor (TMRCA) and the mutation rate, and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2. The mutation rate is inferred to be 8.69 × 10-4 per site per year with a 95％ confidence interval (CI) of [8.61 × 10-4, 8.77 × 10-4], and the TMRCA of the samples inferred to be Nov 28, 2019 with a 95％ CI of [Oct 20, 2019, Dec 9, 2019]. The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market. We further demonstrate that genetic polymorphism patterns, including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters, are similar to those caused by evolutionary forces such as natural selection. Our results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism ofSARS-CoV-2. Software for implementing VirusMuT can be downloaded at https://bigd.big.ac.cn/biocode/tools/BT007081.

On January 22, 2020, China National Center for Bioinformation (CNCB) released the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access information resource for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 2019nCoVR features a comprehensive integra-tion of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline. Of particular note, 2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and their detailed statistics for each virus isolate, and congregates the quality score, functional annotation,and population frequency for each variant. Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019 (COVID-19), including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC. Furthermore, by linking with relevant databases in CNCB, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with NCBI. Collectively, SARS-CoV-2 is updated daily to collect the latest information on genome sequences, variants, hap-lotypes, and literature for a timely reflection, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.

Objective:To find the chromosomal malfomations among microtia patients and the neighbouring genes of chromosomal aberrations or genes in the extra or deleted chromosome fragments would be screened to investigate the possible causative genes.Methods:According to the inclusion criteria, case group was selected from microtia patients referred to Plastic Surgery Hospital, Chinese Academy of Medical Science, between January 2012 and January 2014, and the control group was the normal people of similar age received plastic surgery in the same hospital in the same time who did not have any congenital genetic disease. Blood samples of two groups were collected, and genomic DNA was extracted, then copy number variation (CNV) analysis was performed in the two groups with gene chip technology and associated software for large fragment chromosomal malformations. The variations of chromosome copy number were recorded to further analyze the type and length of chromosome structure variation. The genes at the loci of break points were further screened referring to B allele frequency to interpret associated genes related to the occurrence of microtia. Fisher exact test were used for statistical analysis, and the difference was statistically significant ( P< 0.05). Results:942 patients with congenital microtia were included in the case group, 695 males and 247 females, aged (11.4±3.2) years; 1 802 normal controls, 1 290 males and 512 females, aged (11.6±4.9) years. Large chromosomal fragments variations were detected in 5 patients in chromosome in case group( P=0.003). The difference between the two groups was statistically significant( P=0.003). Three cases were found to carry an extra X chromosome. Among the 3 cases, one patient suffered from XXY karyotype and the other 2 patients X trisomy. Two cases were proved to be associated with chromosome structural variations. The malformations of the first case presented partial duplication of the long arm of chromosome 13 and 14. On searching for causative genes, OTX2, BMP4 and GSC were detected to be in the chromosome structural variations. The second case presented to be partial duplication of the long arm of chromosome 5. FGF pathway associated genes FGF18, FGFR4, FGF1 and BMP pathway associated genes FST, MSX2, SMAD5 were incorporated in the extra duplicated chromosome for possible gene dosage effect. Conclusions:The results indicated the possible association of chromosome abnormity and microtia and provide new insights in microtia-associated chromosome instability. Ten related genes were involved in the occurrence of microtia through various ways.