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PubMed2025

Newly identified single-nucleotide polymorphism associated with the transition from nonalcoholic fatty liver disease to liver fibrosis: results from a nested case-control study in the UK biobank.

BACKGROUND: Genetic factors may have a significant influence on the likelihood of liver fibrosis in individuals with nonalcoholic fatty liver disease (NAFLD). The present study was conducted to explore how single-nucleotide polymorphism (SNP) impacts the development of fibrosis in those suffering from NAFLD. MATERIALS AND METHODS: Utilizing the UK Biobank dataset, we conducted a nested case-control analysis among NAFLD participants, defining the case group as those with liver fibrosis and cirrhosis during follow-up. For our in vitro investigations, we employed the LX-2 human hepatic stellate cell line. Our procedures included cultivating these cells, employing SAMM50-rs2073080 plasmid techniques to enhance the expression of recently discovered SNPs, and conducting biochemical assays. To quantify gene expression, we used real-time PCR with fluorescence detection. RESULTS: The study analyzed data from 5467 participants (1094 cases and 4373 controls). Genome-wide association analysis identified nine significant loci, including the novel rs2073080 variant, strongly associated with NAFLD-associated hepatic fibrosis. In vitro TGF-β modeling revealed significant upregulation of α-SMA and COL1A1, confirming model effectiveness. Oxidative stress markers like elevated malondialdehyde (MDA) and reduced catalase (CAT) and superoxide dismutase (SOD) levels indicated liver damage in the TGF-β group. SAMM50-rs2073080 was upregulated in the NAFLD-associated fibrosis model. In vitro experiments on LX-2 cells showed that SAMM50-rs2073080 overexpression led to increased fibrosis, as indicated by higher cellular MDA levels and lower CAT and SOD levels, compared to the vector group. CONCLUSION: Our research highlights a significant association of SAMM50-rs2073080 with the progression of NAFLD to hepatic fibrosis, and the in vitro experiments further corroborated these findings.

Humans↗
PubMed2006

Analysis of single nucleotide polymorphism sites in exon 4 of the p53 gene using high-performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry.

Three groups of four oligonucleotides with special single nucleotide polymorphisms (SNP) sites in exon 4 of the p53 gene were analyzed with ion-pair reversed-phase high-performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry. The retention order of four oligonucleotides with SNPs was C < G < A < T, regardless of whether the polymorphisms were at the 3' end, the 5' end, or the middle of the oligonucleotides. The charge state of the molecular ion affects the MS/MS spectra of the oligonucleotides. SNPs at the 3' end can be easily identified from the fragmentation pattern of the 2- charge state, but not from the 3- charge state, especially from the w1 fragment. The single base may be taken as the symbol of the 5' end SNP site derived from [M3H]2, but not from the [M3H]2 charge state. The oligonucleotides with SNPs in the middle were also determined from the [M2H]2 precursor ion.

Chromatography, High Pressure Liquid↗
PubMed2005

[Single nucleotide polymorphism in the matrix metalloproteinases promoter is associated with susceptibility to endometriosis and adenomyosis].

OBJECTIVE: To investigate the association of the matrix metalloproteinases (MMP) 1, 3 promoter single nucleotide polymorphism (SNP) with the susceptibility to endometriosis (EM) and adenomyosis. METHODS: The SNP of the MMP-1 and MMP-3 gene promoter region was genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) among 100 endometriosis patients, 80 adenomyosis patients and 150 unrelated healthy women. RESULTS: (1) The frequency of 2G allelotype of MMP-1 in the EM and adenomyosis patients (79.0% and 79.4%, respectively) was significantly different from the control (67.0%) (P < 0.01). The frequencies of 1G/1G, 1G/2G and 2G/2G genotypes of EM and adenomyosis patients were significantly different from that in healthy controls (P < 0.05). Compared with 1G/1G genotype, both 2G/2G alone and in combination with 1G/2G genotype significantly increased the risk of developing EM (adjusted odds ratio was 3.65 and 3.25, 95% CI = 1.41-9.43 and 1.29-8.23, respectively), but only 2G/2G genotype significantly enhanced the risk of developing adenomyosis. (2) The frequencies of the 5A and 6A allelotype of MMP-3 among EM (14.0% and 86.0%, respectively) and adenomyosis patients (15.6% and 83.4%, respectively) were not significantly different from healthy controls (20.3% and 79.7%, respectively) (P > 0.05). The genotype distribution of 5A/5A, 5A/6A and 6A/6A in patients was not significantly different from controls (P > 0.05). Compared with the 6A/6A genotype, neither the 5A/5A alone nor in combination with the 5A/6A genotype significantly modified the risk of developing EM and adenomyosis. (3) The distribution of haplotype (1G/6A, 2G/6A, 1G/5A and 2G/5A) frequency of MMP-1 and MMP-3 SNP was significantly different between cases and controls. Compared with the 1G/6A haplotype, 2G/6A haplotype significantly enhanced the risk of developing EM, but not significantly enhanced the risk of developing adenomyosis. CONCLUSION: Individuals with the MMP-1 2G allelotype have significantly increased risk of developing EM and adenomyosis; MMP-3 promoter SNP is not associated with susceptibility to EM and adenomyosis, 2G/6A haplotype could be used as a stratified marker for EM.

Adult↗
PubMed2002

[Single nucleotide polymorphisms in CAPN10 gene of Chinese population and its correlation with type 2 diabetes mellitus in Han people of northern China].

OBJECTIVE: To investigate the distribution of the single nucleotide polymorphisms (SNPs) in CAPN10 gene in Chinese population and their relation with type 2 diabetes mellitus in Han people of Northern China. METHODS: CAPN10 gene was sequenced to detect SNPs in 27 samples of different nationalities in China. 5 SNPs were genotyped with single-base extension (SBE) method to perform case-control study in 156 normal Han people of Northern China and 173 type 2 diabetes and the 3 positive loci reported in the article were performed haplotype analysis. One positive locus was also analyzed with transmission-disequilibrium test (TDT) and sib transmission-disequilibrium test (STDT) in 68 type 2 diabetes pedigrees (377 cases). RESULTS: A total of 40 SNPs were identified in length of 8,936 bp, with an average of 1 in every 223 bp; The SNPs in CAPN10 gene did not distribute evenly and the SNPs in Chinese was different from that reported in American Mexicans. There was no significantly statistical difference in the allele frequency of the 5 SNPs between case and control (P > 0.05), and the haplotype frequencies in the two groups were not much different (P > 0.05). There was no positive results in TDT and STDT analysis (P > 0.05). CONCLUSIONS: The SNP distribution of CAPN10 gene varies with different nationalities. The studied SNPs in CAPN10 gene may not be the major susceptibility ones of type 2 diabetes mellitus in Han people of Northern China.

Alleles↗
PubMed2007

Genotyping of single-nucleotide polymorphisms by primer extension reaction in a dry-reagent dipstick format.

The primer extension (PEXT) reaction is the most widely used approach to genotyping of single-nucleotide polymorphisms (SNPs). Current methods for analysis of PEXT reaction products are based on electrophoresis, fluorescence resonance energy transfer, fluorescence polarization, pyrosequencing, mass spectrometry, microarrays, and spectrally encoded microspheres. We report the first dry-reagent dipstick method that enables rapid visual detection of PEXT products without instrumentation. The method is applied to the analysis of six SNPs in the mannose-binding lectin gene (MBL2). The genomic region that spans each SNP of interest is amplified by PCR. Two primer extension reactions are performed with allele-specific primers (for one or the other variant nucleotide), which contain an oligo(dA) segment at the 5'-end. Biotin-dUTP is incorporated in the extended strand. The product is applied to the strip followed by immersion in the appropriate buffer. As the DNA moves along the strip by capillary action, it hybridizes with oligo(dT)-functionalized gold nanoparticles, such that only extended products are captured by immobilized streptavidin at the test zone, generating a red line. A second red line is formed at the control zone of the strip by hybridization of the nanoparticles with immobilized oligo(dA). The dipstick test is complete within 10 min. We analyzed six SNPs of the mannose-binding lectin gene (MBL2) using genomic DNA from 27 patients, representing a total of 74 variant nucleotide positions. Patient genotypes showed 100% concordance with direct DNA sequencing data. The described PEXT-dipstick assay is rapid and highly accurate; it does not require specialized instrumentation or highly trained technical personnel. It is appropriate for a diagnostic laboratory where a few selected SNP markers are examined per patient with a low cost per assay.

DNA Primers↗
PubMed2004

A single-nucleotide polymorphism in the human beta-defensin 1 gene is associated with HIV-1 infection in Italian children.

In this study we show a significant correlation between a single-nucleotide polymorphism in the 5'-untranslated region of the DEFB1 gene, which probably regulates the gene expression of human beta defensin 1 (hBD-1) and the risk of HIV-1 infection in an Italian paediatric population (97 HIV-1 perinatally infected children), pointing to the importance of innate immunity in HIV-1 infection.

Child↗
PubMed2006

Efficient selection of tagging single-nucleotide polymorphisms in multiple populations.

Common genetic polymorphism may explain a portion of the heritable risk for common diseases, so considerable effort has been devoted to finding and typing common single-nucleotide polymorphisms (SNPs) in the human genome. Many SNPs show correlated genotypes, or linkage disequilibrium (LD), suggesting that only a subset of all SNPs (known as tagging SNPs, or tagSNPs) need to be genotyped for disease association studies. Based on the genetic differences that exist among human populations, most tagSNP sets are defined in a single population and applied only in populations that are closely related. To improve the efficiency of multi-population analyses, we have developed an algorithm called MultiPop-TagSelect that finds a near-minimal union of population-specific tagSNP sets across an arbitrary number of populations. We present this approach as an extension of LD-select, a tagSNP selection method that uses a greedy algorithm to group SNPs into bins based on their pairwise association patterns, although the MultiPop-TagSelect algorithm could be used with any SNP tagging approach that allows choices between nearly equivalent SNPs. We evaluate the algorithm by considering tagSNP selection in candidate-gene resequencing data and lower density whole-chromosome data. Our analysis reveals that an exhaustive search is often intractable, while the developed algorithm can quickly and reliably find near-optimal solutions even for difficult tagSNP selection problems. Using populations of African, Asian, and European ancestry, we also show that an optimal multi-population set of tagSNPs can be substantially smaller (up to 44%) than a typical set obtained through independent or sequential selection.

Algorithms↗
PubMed2006

Single nucleotide polymorphism discovery in the avian Tapasin gene.

Tapasin is a transmembrane glycoprotein located in the endoplasmic reticulum. Its function is to assist the assembly of major histocompatibility complex class I molecules. The chicken Tapasin gene includes 8 exons and is localized inside the major histocompatibility complex between the 2 class IIbeta genes. The aim of the current study was the estimation of single nucleotide polymorphism frequency within the avian Tapasin gene. The Tapasin gene sequence from exon 5 to exon 6 was amplified for the chicken, turkey, and pheasant, and sequences of different lengths were obtained. The sequence analysis based on PolyBayes identified 25 putative single nucleotide polymorphism sites when the 3 species were compared. The coding sequences were further translated and analyzed to identify amino acid substitutions. The results indicated that polymorphisms within this region of the gene was mainly observed in the heterozygous state. The level of conservation of the Tapasin gene sequence among species is likely to be related to the functional importance of the gene.

Amino Acid Sequence↗
PubMed2004

Whole genome amplification of DNA from laser capture-microdissected tissue for high-throughput single nucleotide polymorphism and short tandem repeat genotyping.

Genome-wide screening of genetic alterations between normal and cancer cells, as well as among subgroups of tumors, is important for establishing molecular mechanism and classification of cancer. Gene silencing through loss of heterozygosity is widely observed in cancer cells and detectable by analyzing allelic loss of single nucleotide polymorphism and/or short tandem repeat markers. To use minute quantities of DNA that are available through laser capture microdissection (LCM) of cancer cells, a whole genome amplification method that maintains locus and allele balance is essential. We have successfully used a ø29 polymerase-based isothermal whole genome amplification method to amplify LCM DNA using a proteinase K lysis procedure coupled with a pooling strategy. Through single nucleotide polymorphism and short tandem repeat genotype analysis we demonstrate that using pooled DNA from two or three separate amplification reactions significantly reduces any allele bias introduced during amplification. This strategy is especially effective when using small quantities of source DNA. Although a convenient alkaline lysis DNA extraction procedure provided satisfactory results from using 1500 to 3000 LCM cells, proteinase K digestion was superior for lower cell numbers. Accurate genotyping is achieved with as few as 100 cells when both proteinase K extraction and pooling are applied.

Female↗
PubMed2001

Single-nucleotide polymorphisms in the public domain: how useful are they?

There is a concerted effort by a number of public and private groups to identify a large set of human single-nucleotide polymorphisms (SNPs). As of March 2001, 2.84 million SNPs have been deposited in the public database, dbSNP, at the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/SNP/). The 2.84 million SNPs can be grouped into 1.65 million non-redundant SNPs. As part of the International SNP Map Working Group, we recently published a high-density SNP map of the human genome consisting of 1.42 million SNPs (ref. 3). In addition, numerous SNPs are maintained in proprietary databases. Our survey of more than 1,200 SNPs indicates that more than 80% of TSC and Washington University candidate SNPs are polymorphic and that approximately 50% of the candidate SNPs from these two sources are common SNPs (with minor allele frequency of > or =20%) in any given population.

DNA↗
PubMed2005

Functionally defective or altered CYP3A4 and CYP3A5 single nucleotide polymorphisms and their detection with genotyping tests.

Among the four cytochrome P450 (CYP)3A genes, CYP3A4 and CYP3A5 are the most abundantly expressed in the human liver. Eighty single nucleotide polymorphisms (SNPs) of CYP3A4/5 have been reported to the Human P450 Allele Nomenclature Committee. CYP3A4 alleles with minimal function compared with wild type include the CYP3A4*6 and CYP3A4*17. Alleles with moderately decreased or altered activity include: CYP3A4*2, *8, *11, *12, *13, *16, and *18. CYP3A5 alleles with minimal function include the splice variants CYP3A5*3, *5, *6 and CYP3A5* 10, as well as the null allele CYP3A5*7. Alleles with moderately decreased catalytic activity include CYP3A5*8 and CYP3A5*9. This report reviews the current progress in the functional characterization of CYP3A4 and CYP3A5 SNPs and provides genotyping tests for possible defective variants. A combination of genotyping tests for defective CYP3A4/CYP3A5 haplotypes will be necessary to understand the variations in the metabolism and clinical toxicity of a wide variety of clinical drugs, since these two CYP proteins have overlapping substrate specificities.

Cytochrome P-450 CYP3A↗
PubMed2004

[Distribution of -477C/T single nucleotide polymorphism in the promoter region of ABCA1 gene and its significance for plasma lipids levels in normal Chinese Han population].

OBJECTIVE: To investigate the distribution of -477C/T single nucleotide polymorphisms (SNP) in the promoter region of ATP binding cassette transporter (ABCA1) gene and its relation to plasma lipid levels in normal Chinese Han population. METHODS: The three genotypes of -477C/T polymorphisms in the promoter region of the ABCA1 gene were detected using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 113 normal Chinese Han subjects. RESULTS: -477C/T SNP was present in normal Chinese Han population, and 37.2% (42) of the examined subjects belonged to the genotype of CC, 46.9% (53) belonged to CT and 15.9% (18) to TT. The individuals with the TT genotype had a lower plasma high-density lipoprotein cholesterol (HDL-C) level than those with the CC genotype (P<0.05). No association was found between the genotypes and plasma levels of total cholesterol, triglyceride, low-density lipoprotein, very low-density lipoprotein and body mass index. CONCLUSION: The TT genotype significantly influences the plasma levels of HDL-C in normal Chinese Han individuals.

ATP Binding Cassette Transporter 1↗
PubMed2001

High-density single-nucleotide polymorphism (SNP) map in the 96-kb region containing the entire human DiGeorge syndrome critical region 2 (DGCR2) gene at 22q11.2.

We constructed a high-density single-nucleotide polymorphism (SNP) map in the 96-kb region containing the DiGeorge syndrome critical region 2 (DGCR2) gene at chromosome 22q11.2, a human counterpart of mouse seizure-related gene SEZ-12. A total of 102 SNPs were isolated from the region by systematic screening among 48 Japanese individuals: 9 SNPs in the 5' flanking region, 3 in the 5' untranslated region, 2 in the coding regions, 77 in introns, 7 in the 3' untranslated region, and 4 in the 3' flanking region. By a comparison of our data with SNPs deposited in the dbSNP database in the National Center for Biotechnology Information, 80 SNPs (78.4%) were considered to be novel. The ratio of transition to transversion was 3.08:1. In addition, eight other types of genetic variations (one GA dinucleotide polymorphism and seven insertion/deletion polymorphisms) were discovered. The high-resolution map that we constructed will be a useful resource for analyzing gene scans of complex diseases mapped to this local segment on chromosome 22.

3' Untranslated Regions↗
PubMed2006

Construction of a single nucleotide polymorphism linkage map for the silkworm, Bombyx mori, based on bacterial artificial chromosome end sequences.

We have developed a linkage map for the silkworm Bombyx mori based on single nucleotide polymorphisms (SNPs) between strains p50T and C108T initially found on regions corresponding to the end sequences of bacterial artificial chromosome (BAC) clones. Using 190 segregants from a backcross of a p50T female x an F1 (p50T x C108T) male, we analyzed segregation patterns of 534 SNPs between p50T and C108T, detected among 3840 PCR amplicons, each associated with a p50T BAC end sequence. This enabled us to construct a linkage map composed of 534 SNP markers spanning 1305 cM in total length distributed over the expected 28 linkage groups. Of the 534 BACs whose ends harbored the SNPs used to construct the linkage map, 89 were associated with 107 different ESTs. Since each of the SNP markers is directly linked to a specific genomic BAC clone and to whole-genome sequence data, and some of them are also linked to EST data, the SNP linkage map will be a powerful tool for investigating silkworm genome properties, mutation mapping, and map-based cloning of genes of industrial and agricultural interest.

Animals↗
PubMed2005

Comparison of the power between microsatellite and single-nucleotide polymorphism markers for linkage and linkage disequilibrium mapping of an electrophysiological phenotype.

We performed linkage and linkage disequilibrium (LD) mapping analyses to compare the power between microsatellite and single nucleotide polymorphism (SNP) markers. Chromosome-wide analyses were performed for a quantitative electrophysiological phenotype, ttth1, on chromosome 7. Multipoint analysis of microsatellite markers using the variance component (VC) method showed the highest LOD score of 4.20 at 162 cM, near D7S509 (163.7 cM). Two-point analysis of SNPs using the VC method yielded the highest LOD score of 3.98 in the Illumina SNP data and 3.45 in the Affymetrix SNP data around 152-153 cM. In family-based single SNP and SNP haplotype LD analysis, we identified seven SNPs associated with ttth1. We searched for any potential candidate genes in the location of the seven SNPs. The SNPs rs1476640 and rs768055 are located in the FLJ40852 gene (a hypothetical protein), and SNP rs1859646 is located in the TAS2R5 gene (a taste receptor). The other four SNPs are not located in any known or annotated genes. We found the high density SNP scan to be superior to microsatellites because it is effective in downstream fine mapping due to a better defined linkage region. Our study proves the utility of high density SNP in genome-wide mapping studies.

Aging↗
PubMed2006

A single-nucleotide polymorphism in the XPG gene, and tumour stage, grade, and clinical course in patients with nonmuscle-invasive neoplasms of the urinary bladder.

OBJECTIVE: To evaluate whether the single nucleotide polymorphism (SNP), Asp1104His (G3507C), in the XPG gene affects malignant phenotypes of nonmuscle-invasive urinary bladder neoplasms (NIBN), by investigating associations between the SNP and clinicopathological variables in patients with NIBN. PATIENTS AND METHODS: The 233 patients constituted newly diagnosed cases of primary NIBN in the Stockholm area. The Asp1104His polymorphism in the XPG gene was genotyped using a polymerase chain reaction-restriction fragment length polymorphism technique. RESULTS: The GC + CC genotypes were more frequent in stage pT1 tumours at initial diagnosis than pTa (odds ratio 1.9, 95% confidence interval 1.0-3.5, P = 0.048). The difference was larger in the young group (4.6, 1.9-11.8, P = 0.001). In the young group, the GC + CC genotypes were significantly more frequent in high-grade than in low-grade tumours (3.1, 1.5-6.8, P = 0.004) whereas in the older group the genotypes were less frequent in high-grade tumours (0.3, 0.1-0.7, P = 0.007). The XPG genotypes were not associated with tumour recurrence, stage progression or survival. CONCLUSION: These results suggest that the SNP in the XPG gene might be related to tumour invasiveness in NIBN.

Adult↗
PubMed2004

Distribution of a single nucleotide polymorphism on codon 211 of the androgen receptor gene and its correlation with human renal cell cancer in Japanese patients.

The human androgen receptor (AR) gene contains a single nucleotide polymorphism (SNP) on codon 211 and two polymorphic short tandem repeats of CAG and GGC in the N-terminal domain that may influence transcription efficiency of AR gene. We previously reported that the lengths of the CAG and GGC repeats are inversely and linearly related to AR activity and associated with several cancers. However, little is known about this SNP on codon 211 of the AR gene in human renal cell cancer. The cause of renal cell cancer is not well understood although several factors such as chemical carcinogens and hormones have been implicated. AR has been identified in human and animal renal cell cancer. We hypothesize that the SNP on codon 211 is associated with human renal cell cancer. To test this hypothesis, the genetic distribution of the SNP on codon 211 of AR gene was investigated in renal cell cancer patients (211 cases) and healthy controls (200 cases). The allelic and genotypic distributions were determined by PCR-RFLP and direct DNA sequencing techniques. The chi2 test for these data revealed that the distribution of this SNP was not different between renal cell cancer patients as compared to normal healthy controls. The findings suggest that the SNP on codon 211 in the AR gene may not have an important role in the carcinogenesis of human renal cell cancers.

Adult↗