Genetic variation of FUT3 gene in the Han population from Northern China.

BACKGROUND AND OBJECTIVES: The FUT3 gene encodes α(1,3/1,4)-fucosyltransferase, which is a crucial enzyme in the synthesis of Lewis antigens. FUT3 gene variants show race-specific differences. In this study, we conducted a systematic sequence analysis of the FUT3 coding sequence. The objective was to explore genetic variations of the FUT3 gene within the Han population of Northern China. MATERIALS AND METHODS: A cohort of 313 blood donors was recruited for the study. The coding sequence of the FUT3 gene was amplified using polymerase chain reaction, followed by sequencing and haplotype construction. RESULTS: Twelve single nucleotide variations (SNVs) were identified within the coding sequence of the FUT3 gene. Notably, the c.59 T > G site exhibited the highest mutation frequency of 43.13%, followed by the c.508G > A and c.1067 T > A sites with mutation frequencies of 27.48% and 16.93%, respectively. Le was the most common haplotype, accounting for 67.57% of the cases, and Le/Le was the most common diplotype, accounting for 46.33% of the cases. The study also highlighted a significant difference in mutation frequencies of FUT3 gene between the Han Chinese of Northern China and the Dai of Xishuangbanna, China, but not the Han Chinese in Beijing in the North and the Southern Han Chinese, emphasising that Han Chinese in Northern China are genetically most distant from Europeans and closest to East Asians. CONCLUSIONS: Our study characterises FUT3 gene variations in Han Chinese from Northern China, and provides basic genetic data for genetics, forensic medicine, and genotyping of Lewis blood groups.

Accuracy of RHC/c genotyping in Chinese Han population.

BACKGROUND AND OBJECTIVES: The RHCE gene plays an important role in the complex and polymorphic Rh blood group system. RHCE genotyping holds significant clinical and transfusion-related implications. The objective of this study was to evaluate the accuracy of RHC/c genotyping in the Chinese Han population. MATERIALS AND METHODS: Blood samples were obtained from 653 Chinese Han blood donors. The serological RhD and RhCcEe types were determined using monoclonal antibodies. Subsequently, multiplex real-time polymerase chain reaction (PCR) analysis was performed for RHC and RHc genotyping. Additionally, exon 2 of RHCE and exon 1 of RHD were sequenced. RESULTS: The analysis in this study found 443 RhD-positive donors and 210 RhD-negative donors. Among the 653 total donors, discrepancies between the RHC genotyping results and the serological results were found in 37 individuals. Specifically, 6 false-positive RhC results in RhD-positive donors and 28 false-positive RhC results in RhD-negative donors were identified based on c.48C in RHCE exon 1. Additionally, 3 false-negative RhC results were observed in the RhD-positive donors due to a 109 bp insertion in RHCE intron 2. RHc typing demonstrated complete consistency between the real-time PCR and the serological results. CONCLUSION: In the Chinese Han population, RHC genotyping was reliable when consistent results were achieved by both c.48C-based and 109 bp insertion-based genotyping. Moreover, RHc genotyping based on c.203A and c.307C polymorphic loci demonstrated dependable performance.

RHC genotyping in Chinese Han population.

BACKGROUND: The Rh blood group system is characterized by its complexity and polymorphism, encompassing 56 different antigens. Accurately predicting the presence of the C antigen using genotyping methods has been challenging. The objective of this study was to evaluate the accuracy of various genotyping methods for predicting the Rh C and to identify a suitable method for the Chinese Han population. METHODS: In total, 317 donors, consisting 223 D+ (including 20 with the Del phenotype) and 94 D- were randomly selected. For RHC genotyping, 48C and 109bp insertion were detected on the Real-time PCR platform and -292 substitution was analyzed via restriction fragment length polymorphism (RFLP). Moreover, the promoter region of the RHCE gene was sequenced to search for other nucleotide substitutions between RHC and RHc. Agreement between prediction methods was evaluated using the Kappa statistic, and comparisons between methods were conducted via the χ2 test. RESULTS: The analysis revealed that the 48C allele, 109bp insertion, a specific pattern observed in RFLP results, and wild-type alleles of seven single nucleotide polymorphisms (SNPs) were in strong agreement with the Rh C, with Kappa coefficients exceeding 0.8. However, there were instances of false positives or false negatives (0.6% false negative rate for 109bp insertion and 5.4-8.2% false positive rates for other methods). The 109bp insertion method exhibited the highest accuracy in predicting the Rh C, at 99.4%, compared to other methods (P values≤0.001). Although no statistical differences were found among other methods for predicting Rh C (P values>0.05), the accuracies in descending order were 48C (94.6%) > rs586178 (92.7%) > rs4649082, rs2375313, rs2281179, rs2072933, rs2072932, and RFLP (92.4%) > rs2072931 (91.8%). CONCLUSIONS: None of the methods examined can independently and accurately predict the Rh C. However, the 109bp insertion test demonstrated the highest accuracy for predicting the Rh C in the Chinese Han population. Utilizing the 109bp insertion test in combination with other methods may enhance the accuracy of Rh C prediction.

Novel missense mutation c.797T>C (p.Met266Thr) gives rise to the rare B(A) phenotype in a Chinese family.

BACKGROUND AND OBJECTIVES: B(A) phenotype is usually formed by nucleotide mutations in the ABO*B.01 allele, with their products exhibiting glycosyltransferases (GTs) A and B overlapping functionality. We herein report a B(A) allele found in a Chinese family. MATERIALS AND METHODS: The entire ABO genes of the probands, including flanking regulatory regions, were sequenced through PacBio third-generation long-read single-molecule real-time sequencing. 3D molecular models of the wild-type and mutant GTB were generated using the DynaMut web server. The effect of the mutation on the enzyme function was predicted by PROVEAN and PolyPhen2. The predictions of stability changes were performed using DynaMut and SNPeffect. RESULTS: Based on serological and sequencing features, we concluded the two probands as possible cases of the B(A) phenotype. Crystallization analysis showed that Thr266 substitution does not disrupt the hydrogen bonds. However, some changes in interatomic contacts, such as loss of ionic interactions and hydrophobic contacts, and addition of weak hydrogen bonds, may have affected protein stability to some extent. This mutation was predicted to have a benign effect on enzyme function and slightly reduce protein stability. CONCLUSION: The probands had the same novel B(A) allele with a c.797T>C (p.Met266Thr) mutation on the ABO*B.01 backbone.

A novel allele of FUT2 gene containing a deletion of nine bases (c.461_469delGGACCTTCT) in a Chinese Han blood donor.

BACKGROUND AND OBJECTIVES: The FUT2 gene is responsible for the synthesis of the H antigen in body secretions. It is highly polymorphic and population specific. We investigated the FUT2 gene polymorphism in Chinese blood donors and found a novel deletion mutation in one non-secretor individual. This study aimed to identify mutation(s) responsible for a non-secretor phenotype. MATERIALS AND METHODS: The Lewis blood group of a Chinese Han blood donor was typed using the standard serological technique and the FUT2 gene of the sample was analysed by Sanger sequencing. Clone sequencing was performed for determining the haplotype of the FUT2 gene. Bioinformatics tools were used for predicting the effect of the deletion on the FUT2 gene. RESULTS: A novel nine-base deletion (c.461_469delGGACCTTCT) in the FUT2 gene was identified in a Chinese Han blood donor. Two haplotypes Se390,418 and se204,249,461_469del,772,993 were determined by clone sequencing. According to the prediction of bioinformatics tools, the mutation at c.461_469delGGACCTTCT might not influence the activity of the Se enzyme. CONCLUSION: We identified a new FUT2 mutation, the deletion of nine bases (c.461_469delGGACCTTCT), in a Chinese Han blood donor. This deletion was reported for the first time.

Polymorphisms in the promoter regions of RHD and RHCE genes in the Chinese Han population.

BACKGROUND AND OBJECTIVES: The Rh blood group system is the most polymorphic human blood group system. Previous studies have investigated variants in the RHD and RHCE promoter. The relevance of these variants to the Chinese Han population is further clarified in this study. MATERIALS AND METHODS: In total, 317 donors (223 Rh D-positive [D+], including 20 Del and 94 Rh D-negative [D-]) were randomly selected. The promoter regions and exon 1 of RHD and RHCE were amplified through polymerase chain reaction (PCR) whose products were directly sequenced using forward and reverse primers. RESULTS: Expected PCR products of the RHD promoter and exon 1 were amplified in 223 D+ individuals, including 20 Del individuals, and were absent in 81 of 94 D- individuals. Expected PCR products of RHCE were observed in all donors. Two single nucleotide variants (SNVs) were observed in the RHD promoter region. Moreover, 11 SNVs were observed in the promoter and exon 1 of RHCE. rs4649082, rs2375313, rs2281179, rs2072933, rs2072932, rs2072931 and rs586178 with strong linkage disequilibria were significantly different between the D+ and D- groups. [A;C] was the most common haplotype in the RHD promoter (NC_000001.11:g.[-1033A>G;-831C>T]). [G;T;T;A;T;A;C;G;A;C;G] was the most predominant haplotype in both total and D- groups. In D+ individuals, [A;C;T;G;C;G;C;G;C;C;C] was the most frequent haplotype in the RHCE promoter (NC_000001.11:g.[-1080A>G;-958C>T;-390T>C;-378G>A;-369C>T;-296G>A;-144C>G;-132G>A;-122C>A;28C>T;48C>G]). CONCLUSION: We speculate that the SNVs/haplotypes found in this article cannot significantly affect gene expression. The present study findings should help elucidate the molecular basis of the polymorphic expression of RHD and RHCE promoter regions.

Non-invasive prenatal paternity testing by analysis of Y-chromosome mini-STR haplotype using next-generation sequencing.

OBJECTIVES: To assess the efficacy of Y-chromosome mini-STR-based next-generation sequencing (NGS) for non-invasive prenatal paternity testing (NIPPT). METHODS: DNA was extracted from the plasma of 24 pregnant women, and cell-free fetal DNA (cffDNA) haplotyping was performed at 12 Y-chromosome mini-STR loci using the Illumina NextSeq 500 system. The cffDNA haplotype was validated by the paternal haplotype. Subsequentlly, the paternity testing parameters were attributed to each case quantitatively. RESULTS: The biological relationship between the alleged fathers and infants in all 24 family cases were confirmed by capillary electrophoresis (CE). The Y-chromosome mini-STR haplotypes of all 14 male cffDNA were obtained by NGS without any missing loci. The alleles of cffDNA and paternal genomic DNA were matched in 13 cases, and a mismatched allele was detected at the DYS393 locus in one case and considered as mutation. No allele was detected in the 10 female cffDNA. The combined paternity index (CPI) and probability of paternity calculation was based on 6 loci Y-haplotype distributions of a local population. The probability of paternity was 98.2699-99.8828% for the cases without mutation, and 14.8719% for the case harboring mutation. CONCLUSIONS: Our proof-of-concept study demonstrated that Y-chromosome mini-STR can be used for NGS-based NIPPT with high accuracy in real cases, and is a promising tool for familial searching, paternity exclusion and sex selection in forensic and medical applications.

Association between the Genetic Polymorphisms of CCL2, CCL5, CCL8, CCR2, and CCR5 with Chronic Hepatitis C Virus Infection in the Chinese Han Population.

Hepatitis C virus (HCV) infection is a global public health burden. Chronic HCV infection leads to the development of fibrosis, cirrhosis, liver cancer, and liver failure over time. A total of 250 patients with chronic HCV infection and 299 healthy blood donors were recruited. Sixteen candidate single nucleotide polymorphisms (SNPs) in chemokine (C-C motif) ligand 2 (CCL2), CCL5, CCL8, C-C chemokine receptor 2 (CCR2), and CCR5 were genotyped in all participants. The rs1024610 AA genotype was significantly associated with decreased susceptibility to chronic HCV infection. Aspartate aminotransferase (AST) levels, AST/platelet ratio index, and the fibrosis 4 score were significantly lower in the CCL2 rs1024610 T allele and haplotype ATGC carriers. Moreover, expression levels of collagen IV (C-IV) and laminin (LN) were significantly higher in patients with the CCL5 rs2280788 C allele compared to the non-carriers. Similarly, the expression levels of C-IV, LN, and hyaluronic acid were significantly higher in patients with the CCL5 haplotype, TGCT. No significant differences were identified between the SNPs/haplotypes and plasma levels of CCL2, CCL5, CCL8, CCR2, and CCR5 in the healthy controls, and the rs1024610 allele alteration had no effect on CCL2 promoter activity. This is the first study to report an association between CCL2 rs1024610 and the risk of chronic HCV infection in the Chinese Han population. rs1024610 and ATGC haplotype in CCL2 were reasonable candidate markers of liver abnormalities. rs2280788 and TGCT haplotype in CCL5 are likely to play a significant role in liver fibrosis during chronic HCV infection.

Association of the 3' untranslated region polymorphisms of HLA-G with susceptibility to chronic hepatitis C virus infection in the Chinese population.

Hepatitis C virus (HCV) infection is a global health problem. Several previous studies have addressed the role of host single-nucleotide polymorphisms (SNPs) in HCV infection. SNPs in the regulatory region of the human leukocyte antigen G (HLA-G) gene play an important role in several diseases. The objective of this study is to determine the association of HLA-G 3'untranslated region (UTR) polymorphisms with the susceptibility to chronic hepatitis C infection in the Chinese population. HLA-G 3' UTR polymorphisms, which include 14-bp Ins/Del (rs371194629), +3003T/C (rs1707), +3010C/G (rs1710), +3027 A/C (rs17179101), +3035C/T (rs17179108), +3142 G/C (rs1063320), +3187 A/G (rs9380142) and + 3196C/G (rs1610696), were analyzed in 246 patients with chronic hepatitis C infection and 294 healthy individuals. The alleles, genotypes, and haplotypes were compared between chronic hepatitis C-infected subjects and controls using chi-square tests and logistic regression models. After a correction of multiple comparisons by the false discovery rate (FDR), the allele frequency of + 3196C, genotype frequencies of + 3187 AA and + 3196CC and frequency of the UTR-3 haplotype were significantly higher in the patients than in the control group (P < 0.05), whereas the frequencies of UTR-1 and UTR-2 haplotypes were significantly lower in the patients than in the control group (P < 0.05). After a correction of multiple comparisons by FDR, UTR-2 and UTR-3 maintained significant associations with chronic hepatitis C. This study indicates that HLA-G 3'UTR polymorphisms are associated with the susceptibility to chronic hepatitis C infection in the Chinese population. HLA-G 3'UTR may play an important role in risk modulation toward HCV infection.

Genotyping of RHD c.1227G>A allele by melting curve analysis.

BACKGROUND: DEL is the weakest known D-positive phenotype and is detectable only by adsorption and elution tests. RHD c.1227G>A is an important marker for DEL phenotype in East Asians. The aim of this study was to develop a method for RHD c.1227G>A genotyping by single-tube PCR with melting curve analysis. METHODS: Two GC-rich tails of different lengths were attached to the 5'-end of allele-specific primers for RHD 1227G and 1227A alleles, such that RHD c.1227G>A could be distinguished by the melting temperature. A total of 145 D-negative Chinese Han blood donors were genotyped for RHD c.1227G>A by melting curve analysis, conventional polymerase chain reaction with sequence-specific primers (PCR-SSP), and sequencing. RESULTS: In 143 subjects (143/145, 98.6%), PCR-SSP and melting curve analysis produced consistent results with RHD exon 9 sequencings. Two samples were genotyped as RHD 1227G/A by PCR-SSP, but as RHD 1227A/A or A/- by melting curve analysis. These two samples were confirmed to be RHD 1227A/A or A/-. Based on RHD exon 9 sequencing, the accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of the melting curve analysis for detecting both RHD 1227A and 1227G were all 100%. In contrast, the accuracy, specificity and positive predictive value of PCR-SSP for RHD 1227G detection were 98.62%, 98.21% and 94.29%, respectively, which were lower than those observed with the melting curve analysis. CONCLUSION: Melting curve analysis for RHD c.1227G>A genotyping is a simple, rapid, and reliable method, superior to conventional PCR-SSP.

Association of human platelet antigens polymorphisms with the levels of serum fibrosis marks in chronic hepatitis C patients.

BACKGROUND: Host genetic polymorphisms influence the fibrosis progression of chronic hepatitis C (CHC) patients. Previous studies have shown the association of human platelet antigens (HPAs) polymorphisms with CHC. However, little is known regarding the association of HPAs polymorphisms with the fibrosis progression of CHC. The aim of this study was to determine the association of HPA -2, -3, -5 and -15 polymorphisms with the levels of serum fibrosis marks in CHC patients. METHODS: The HPA -2, -3, -5 and -15 were genotyped by 5'-nuclease assay in 211 CHC patients, while the serum concentration of hyaluronic acid (HA), collagen IV (CIV), amino-terminal pro-peptide of type III procollagen (PIIINP), and laminin (LN) from the same samples were measured by time resolved fluorescence immunoassay. RESULTS: The level of serum LN was significantly lower in CHC patients with HPA-15aa genotype compared to those with HPA-15ab/bb (P = 0.032) but did not differ among HPA-2, -3 and -5 genotypes. There were no difference in HA, CIV and PIIINP levels among HPA-2, -3,-5 and -15 genotypes. CONCLUSIONS: This study demonstrates that HPA-15 aa polymorphism is associated lower serum LN in CHC, which suggests that HPA -15 aa may be involved in the fibrosis progression of CHC.

Associations between human leukocyte antigen C locus polymorphism and psoriatic arthritis in populations of European and Middle Eastern descent: a meta-analysis.

BACKGROUND: Gene-disease association between human leukocyte antigen (HLA)-C locus polymorphism and psoriatic arthritis (PsA) remains controversial. OBJECTIVE: Evaluate the relationship between HLA-C locus polymorphism and PsA in populations of European and Middle Eastern descent. SEARCH METHODS: PubMed, PMC, Elsevier and Google Scholar databases from 1980 to January 2020. The search was limited to articles in English. SELECTION CRITERIA: Case-control studies (with unrelated participants) that had allele/genotype data on the association between HLA-C locus polymorphism and PsA susceptibility. DATA COLLECTION AND ANALYSIS: Two investigators searched independently in searching the literature. Disagreements were resolved by discussion and consultation with a third researcher. The Q-Genie tool was used to assess the quality of articles. RESULTS: Twenty-five studies met the inclusion criteria. At the allelic level, three alleles were associated with an increased risk of PsA and five were associated with a reduced risk. At the phenotypic level, four alleles were associated with increased risk of PsA and three were associated with a reduced risk. At both the allelic and phenotypic levels, the results revealed that HLA-C*04 played a protective role in PsA (The pooled odds ratio [OR] is 0.66 for allelic level and 0.63 for phenotypic level), while HLA-C*02, *06 and *12 increased the risk of suffering from PsA (The pooled ORs of C*02, *06 and *12 are 2.21, 2.63 and 1.49 for allelic level, and 1.79, 2.96 and 2.25 for phenotypic level, respectively). CONCLUSION: The pooled results showed a significant association between PsA and the HLA-C gene in populations of European and Middle Eastern descent. At both the allelic and phenotypic levels, the HLA-C*02, *06 and *12 may contribute to susceptibility to PsA, while HLA-C*04 may confer a protective role against PsA. REGISTRATION: Not registered. CONFLICT OF INTEREST: None.

Platelet indices significantly correlate with liver fibrosis in HCV-infected patients.

AIM: A total of 241 patients with chronic HCV infection were recruited to investigate the association between liver fibrosis and PLT counts, as well as with MPV, PDW and P-LCR indices. METHODS: The determination of PLT indices was carried out using a Sysmex XT-1800i automated hematology analyzer. Serological tests for HA, LN, C-IV and PIIINP were performed in 210 patients. The liver stiffness was measured in 69 patients by transient elastography (FibroScan). RESULTS: The analysis showed that the four serum fibrosis markers were negatively correlated with PLT counts, but positively correlated with the MPV, PDW and P-LCR values. Moreover, a similar pattern was found after analyzing the FibroScan measurements, which were negatively correlated with PLT counts, but positively correlated with MPV, PDW and P-LCR values. We subdivided the HCV-infected patients into mild and advanced fibrosis groups. The PLT counts were significantly decreased and the MPV, PDW and P-LCR values were significantly increased in the advanced fibrosis group when compared with the mild fibrosis group. CONCLUSIONS: Our results demonstrate that not only the PLT counts but also the MPV, PDW and P-LCR indices significantly correlate with liver fibrosis in HCV-infected patients. Therefore, these indices may be useful laboratory measures for evaluating liver fibrosis progression.

The prognostic significance of long noncoding RNAs in bladder cancer: A meta-analysis.

INTRODUCTION: Bladder cancer (BC) is one of the most common urologic malignancies and it is urgently needed to identify novel potential prognostic biomarkers for predicting prognosis and progression of patients with BC in clinical practice. Previous research has revealed that long noncoding RNAs (lncRNAs) played critical roles in BC, and may serve as novel potential prognostic biomarkers in patients with BC. Therefore, we conducted this meta-analysis to clarify the prognostic potential of lncRNAs in BC patients. METHODS: A comprehensive search was performed in PubMed, Web of Science, and China National Knowledge Infrastructure (CNKI). According to the predefined exclusion and inclusion criteria, a total of 9 recently published articles comprising 13 lncRNAs and 666 BC patients were included into this meta-analysis. We analyzed the hazard ratios (HRs) and 95% confidence intervals (CIs) to determine the relationship between lncRNAs expression and survival outcomes. We also analyzed the odds ratio (ORs) and 95% confidence intervals (CIs) to assess the association between lncRNAs expression and clinicopathological characteristics, including histological grade, gender, multifocality, tumor size, and tumor stage. RESULTS: Our results revealed that high lncRNAs expression was associated with shorter overall survival in Asian BC patients (pooled HR = 2.32, 95% CI: 1.35-4.00, P = 0.002, random-effect). High lncRNAs expression levels were significantly associated with histological grade (G2-G3 vs. G1: OR = 3.857, 95%CI: 1.293-11.502, P = 0.015, random-effect). CONCLUSIONS: In summary, this meta-analysis has demonstrated that lncRNAs could be used as potential prognostic markers for BC and high lncRNAs expression could predict poor prognosis among Asian BC patients.

Association of human platelet antigen polymorphisms with platelet count and mean platelet volume.

OBJECTIVES: Although recent genome-wide association studies have identified a number of single nucleotide polymorphisms associated with platelet count and mean platelet volume (MPV), it is unclear whether polymorphisms in the human platelet antigens (HPA) genes are associated with platelet count and MPV. The aim of this study was to determine the association of the HPA-2, -3, -5 and -15 polymorphisms with platelet count and MPV. METHODS: The HPA were genotyped by 5'-nuclease assay in 139 healthy Chinese Han individuals, while platelet count and MPV from the same samples were measured using an hematology cell analyzer. RESULTS: The platelet count was significantly lower in the individuals with the HPA-2aa genotype compared to those with HPA-2ab (P = 0.020), and significantly higher in individuals with HPA-5aa and HPA-15aa genotypes compared to those with HPA-5ab (P = 0.045) and HPA-15ab/bb (P = 0.032), respectively. On the other hand, platelet count of individuals with the HPA-3aa and HPA-3ab/bb genotypes did not differ significantly (P = 0.084). The MPV was significantly lower in individuals with HPA-5aa genotype compared to those with HPA-5ab (P = 0.001) but did not differ among the HPA-2, -3 and -15 genotypes. Furthermore, HPA-2, -5 and -15 polymorphisms were identified as independent factors for the platelet count and HPA-5 polymorphism was shown as an independent factor for MPV. CONCLUSIONS: This study demonstrates that HPA-2, -5 and -15 polymorphisms are associated with the platelet count while HPA-5 polymorphism is associated with MPV. This finding will further our understanding of the association of HPA polymorphisms with platelet-related diseases.