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Background/Objectives: Allopurinol, a first-line drug for gout and hyperuricemia, carries a risk of severe cutaneous adverse reactions (SCARs). Studies have established a strong association between HLA-B*58:01 and this adverse reaction. Although pre-treatment genotyping is recommended, the reliability of HLA-B*58:01 genetic testing varies across laboratories. This study aims to assess the performance of HLA-B*58:01 genetic testing of clinical laboratories in Shanghai through an External Quality Assessment (EQA) program, evaluating accuracy and standardization. Methods: The EQA program was carried out twice a year in 2023 and 2024. Each EQA sample panel consisted of five distinct samples, including HLA-B*58:01 allele-positive and -negative cell cultures. Sample panels were distributed to clinical laboratories through the cold chain system and results were analyzed and scored. Results: EQA samples used in this study were optimized for evaluating current HLA-B*58:01 genotyping assays, and the EQA samples were proved to be homogeneous and stable through each EQA period. In 2023, 17 and 16 clinical laboratories participated in the two EQA schemes; in 2024, 34 and 33 laboratories participated. A total of 14/17 (82.4%), 16/16 (100%), 33/34 (97.1%), and 33/33 (100%) laboratories achieved “optimal” scores. Conclusions: EQA results indicate that most of clinical laboratories in Shanghai exhibit constantly satisfactory performance for HLA-B*58:01 genotyping. However, a few laboratories still need further improvement. Additionally, EQA has demonstrated to be an important method for monitoring clinical laboratories’ performance.

Long Yu and colleagues report a genome-wide association study for hepatitis B virus–related hepatocellular carcinoma (HBV-HCC). They report that genetic variants in STAT4 and HLA-DQ genes confer risk of HBV-HCC. To identify genetic susceptibility loci for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) in the Chinese population, we carried out a genome-wide association study (GWAS) in 2,514 chronic HBV carriers (1,161 HCC cases and 1,353 controls) followed by a 2-stage validation among 6 independent populations of chronic HBV carriers (4,319 cases and 4,966 controls). The joint analyses showed that HCC risk was significantly associated with two independent loci: rs7574865 at STAT4 , P meta = 2.48 × 10 −10 , odds ratio (OR) = 1.21; and rs9275319 at HLA-DQ, P meta = 2.72 × 10 −17 , OR = 1.49. The risk allele G at rs7574865 was significantly associated with lower mRNA levels of STAT4 in both the HCC tissues and nontumor tissues of 155 individuals with HBV-related HCC ( P trend = 0.0008 and 0.0002, respectively). We also found significantly lower mRNA expression of STAT4 in HCC tumor tissues compared with paired adjacent nontumor tissues ( P = 2.33 × 10 −14 ).

The aim of our study was to determine the impact of genetic polymorphisms in the caspase (CASP) genes on prognosis of hepatocellular carcinoma (HCC). We genotyped 7 potentially functional polymorphisms in CASP3, CASP7, CASP8, CASP9, CASP10 genes in 362 HCC patients of receiving surgical resection of HCC tumor. The associations of genotype and haplotype with overall survival (OS) and disease free survival (DFS) were analyzed by using the Cox proportional hazards model. We found that the CASP9 rs4645981 C allele was significantly associated with positive effect on DFS (P = 0.011 and 0.016 for CT+CC vs. TT in univariate and multivariate analysis, respectively), CT genotype was associated with a better OS of HCC than the TT genotype both in univariate and multivariate analysis (P = 0.048 and 0.041, respectively). Moreover, the CASP3 rs2705897 GT genotype showed marginally significant association with decreased OS and DFS, compared with the GG genotype. One haplotype TT/TG in CASP3 (constructed by rs12108497 T>C and rs2705897 T>G) was significantly associated with decreased OS and DFS, compared to the common haplotype TT/TT both in univariate analysis (P = 0.021 and 0.026, respectively) and multivariate analysis (P = 0.025 and 0.030, respectively). The haplotype GT/GT in CASP9 (constructed by rs4645978 A>G and rs4645981 C>T) was significantly associated with decreased DFS both in univariate and multivariate analysis (P = 0.012 and 0.010, respectively). In conclusion, the CASP9 rs4645981 polymorphism, CASP3 and CASP9 haplotypes may be useful prognosis markers for HCC patients with surgical resection of tumor.

Recent genome-wide associated studies (GWASs) have revealed several common loci associated with the risk of hepatitis B virus (HBV)- or hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC). We selected 15 single nucleotide polymorphisms (SNPs) identified through GWASs on HBV- or HCV-related HCC and genotyped them in two independent Chinese cohorts of chronic HBV carriers, including 712 LC cases and 2601 controls. The association of each SNP with the risk of HBV-related LC was assessed by meta-analysis of the two cohorts. Of the 12 SNPs reported in HBV-related HCC GWASs, five SNPs (rs7574865 in STAT4 , rs9267673 near C2 , rs2647073 and rs3997872 near HLA-DRB1 and rs9275319 near HLA-DQ ), were found to be significantly associated with the risk of HBV-related LC (rs7574865: P  = 1.79 × 10 −2 , OR = 1.17, 95% CI = 1.03–1.34; rs9267673: P  = 4.91 × 10 −4 , OR = 1.37, 95% CI = 1.15–1.63; rs2647073: P  = 3.53 × 10 −5 , OR = 1.63, 95% CI = 1.29–2.06; rs3997872: P  = 4.22 × 10 −4 , OR = 1.86, 95% CI = 1.32–2.62; rs9275319: P  = 1.30 × 10 −2 , OR = 1.32, 95% CI = 1.06–1.64). However, among the three SNPs associated with the risk of HCV-related HCC in previous GWASs, none of them showed significant association with the risk of HBV-related LC. Our results suggested that genetic variants associated with HBV-related hepatocarcinogenesis may already play an important role in the progression from CHB to LC.

Soybean [ Glycine max (L . ) Merr .] is a crop of great interest worldwide. Exploring molecular approaches to increase yield genetic gain has been one of the main challenges for soybean breeders and geneticists. Agronomic traits such as maturity, plant height, and seed weight have been found to contribute to yield. In this study, a total of 250 soybean accessions were genotyped with 10,259 high-quality SNPs postulated from genotyping by sequencing (GBS) and evaluated for grain yield, maturity, plant height, and seed weight over three years. A genome-wide association study (GWAS) was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model. Genomic selection (GS) was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that 20, 31, 37, and 23 SNPs were significantly associated with maturity, plant height, seed weight, and yield, respectively; Many SNPs were mapped to previously described maturity and plant height loci ( E2 , E4 , and Dt1 ) and a new plant height locus was mapped to chromosome 20. Candidate genes were found in the vicinity of the two SNPs with the highest significant levels associated with yield, maturity, plant height, seed weight, respectively. A 11.5-Mb region of chromosome 10 was associated with both yield and seed weight. Overall, the accuracy of GS was dependent on the trait, year, and population structure, and high accuracy indicates that these agronomic traits can be selected in molecular breeding through GS. The SNP markers identified in this study can be used to improve yield and agronomic traits through the marker-assisted selection and GS in breeding programs.

Background Cancer metastasis, the process by which tumor cells spread from the primary site to other organs, is one of the leading causes of death in cancer patients. However, due to its complexity and unpredictability, the study of cancer metastasis remains a significant challenge in medicine. In recent years, with the advancement of high-throughput sequencing technologies and single-cell transcriptomics, we could gain a deeper understanding of the molecular mechanisms and cellular heterogeneity underlying cancer metastasis. There is an accumulating volume of publicly available cancer metastasis research data. Nevertheless, these resources lack proper organization, hindering systematic analysis. Methods In this study, we developed an integrated resource named Panmim ( http://www.gdwk-bioinfo.com/pan_metastasis/home ) to investigate the immune microenvironment of metastatic tumors. The database currently encompasses 90 single-cell RNA-seq datasets from metastatic cancers of diverse origins, encapsulating 14 distinct metastatic sites and 36 primary cancer types. Panmim facilitates a cellular-level comparison of similarities and differences between primary and metastatic cancers, encompassing pathway analysis, alterations in cellular metabolic pathways, cellular distribution preferences, and various aspects of intercellular communication. Results Panmim presents the analysis results through an intuitive interactive graphical interface, enabling users to explore and understand the complex biological phenomena during cancer metastasis more conveniently. This resource will become a valuable tool for biologists and bioinformaticians to study the mechanisms of cancer metastasis, providing important data support and scientific basis for the optimization of cancer treatment strategies.

The sucrose and Alanine (Ala) content in edamame beans significantly impacts the sweetness flavor of edamame-derived products as an important attribute to consumers’ acceptance. Unlike grain-type soybeans, edamame beans are harvested as fresh beans at the R6 to R7 growth stages when beans are filled 80-90% of the pod capacity. The genetic basis of sucrose and Ala contents in fresh edamame beans may differ from those in dry seeds. To date, there is no report on the genetic basis of sucrose and Ala contents in the edamame beans. In this study, a genome-wide association study was conducted to identify single nucleotide polymorphisms (SNPs) related to sucrose and Ala levels in edamame beans using an association mapping panel of 189 edamame accessions genotyped with a SoySNP50K BeadChip. A total of 43 and 25 SNPs was associated with sucrose content and Ala content in the edamame beans, respectively. Four genes (Glyma.10g270800, Glyma.08g137500, Glyma.10g268500, and Glyma.18g193600) with known effects on the process of sucrose biosynthesis and 37 novel sucrose-related genes were characterized. Three genes (Gm17g070500, Glyma.14g201100 and Glyma.18g269600) with likely relevant effects in regulating Ala content and 22 novel Ala-related genes were identified. In addition, by summarizing the phenotypic data of edamame beans from three locations in two years, three PI accessions (PI 532469, PI 243551, and PI 407748) were selected as the high sucrose and high Ala parental lines for the perspective breeding of sweet edamame varieties. Thus, the beneficial alleles, candidate genes, and selected PI accessions identified in this study will be fundamental to develop edamame varieties with improved consumers’ acceptance, and eventually promote edamame production as a specialty crop in the United States.

Zao5241 is an elite soybean [Glycine max (L.) Merr.] line and backbone parent. In this study, we employed iTRAQ to analyze the proteomes and protein expression profiles of Zao5241 during leaf development. We identified 1,245 proteins in all experiments, of which only 45 had been previously annotated. Among overlapping proteins between three biological replicates, 598 proteins with 2 unique peptides identified were reliably quantified. The protein datasets were classified into 36 GO functional terms, and the photosynthesis term was most significantly enriched. A total of 113 proteins were defined as being differentially expressed during leaf development; 41 proteins were found to be differently expressed between two and four week old leaves, and 84 proteins were found to be differently expressed between two and six week old leaves, respectively. Cluster analysis of the data revealed dynamic proteomes. Proteins annotated as electron carrier activity were greatly enriched in the peak expression profiles, and photosynthesis proteins were negatively modulated along the whole time course. This dataset will serve as the foundation for a systems biology approach to understanding photosynthetic development.