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PubMed2001

[Single nucleotide polymorphisms(SNPs)and SNP databases].

Along the rapid development of human genome sequencing project, the variation data of human DNA sequence has become more and more useful not only for studying the origin, evolution and the mechanisms of maintenance of genetic variability in human populations, but also for detection of genetic association in complex disease such as diabetes, obesity, hypertension, Alzheimer's disease, etc. In recent two years, the databases such as dbSNP, CGAP, HGBASE, JST and Go!Poly etc. to collect and exploit data of genomic polymorphisms mainly single nucleotide polymorphisms (SNPs) have been respectively established in the United States, European countries, Japan and China. This overview summarized the development and applications of those SNP databases and also discussed some issues regarding the potential improvement of accuracy of SNP data collected. China has one fifth population in the world. Therefore, development of the SNP database for Chinese populations is of importance in developing complete SNP databases of human genome and may also stimulate the further development of biomedical research and production in China.

Databases, Nucleic Acid↗
PubMed2003

A single nucleotide polymorphism in the E-cadherin gene promoter-160 is not associated with risk of Korean gastric cancer.

Recently, the -160 C/A polymorphism, located within the regulatory region of Ecadherin promoter, has been shown to influence E-cadherin transcription by altering transcription factor binding. We examined the effect of this polymorphism on risk of gastric cancer and on histological classification of intestinal- and diffuse-type gastric cancer in 146 normal healthy individuals and 292 Korean gastric cancer patients. Genomic DNA samples were examined by polymerase chain reaction (PCR)-single strand conformational polymorphism (SSCP)-sequencing and confirmed by restriction fragment length polymorphism (RFLP). Unexpectedly, there was no significant difference in the genotype frequencies of the polymorphism between normal control and gastric cancer patients (x(2) test, p=0.433). The estimated odd ratio of C/C to A/A genotype in gastric cancer cases was 1.07 (95% confidence interval, 0.396-2.870). We also found no evidence for differences in risk for the intestinal- and diffuse-type gastric cancer. These results suggest that the -160 C/A polymorphism of the E-cadherin has no direct effect on the risk of Korean gastric cancer development and on its histological classification.

Alleles↗
PubMed2000

A single nucleotide polymorphism of dopamine transporter gene is associated with Parkinson's disease.

We identified two polymorphisms out of all coding regions of the dopamine transporter gene. One existed in exon 9 (1215A/G) and another in exon 15 (1898T/C). The 1215G was significantly less frequent among patients with Parkinson's disease than the controls. Although the polymorphism caused no amino acid substitution, we concluded that it was associated with decreasing the susceptibility to Parkinson's disease through mechanisms other than the protein function of dopamine transporter.

Aged↗
PubMed2006

Single nucleotide polymorphisms in the chicken Lmbr1 gene are associated with chicken polydactyly.

Polydactyly is a common malformation of vertebrate limbs. Preaxial polydactyly (PPD) has been mapped in human, mouse and chicken to the syntenic region of human 7q36. Lmbr1 was thought as the critical candidate gene for human and mouse PPD. To understand the molecular mechanism underlying chicken polydactyly, we have cloned the open reading frame (ORF) of chicken Lmbr1, which contains 1467 nucleotides. Within this ORF, we found one short and one long splice forms. The short splice form has a complete deletion of exon 4. Six cSNPs were found in the chicken ORF, and two of these cSNPs, G797A and G1255A, lead to amino acid substitutions. However, G797A substitution had no significant association with polydactyly and the G1255A substitution had very low frequency in the population. The T1254C polymorphism in exon 13 was found to be strongly associated with polydactyly. Radiation hybrid mapping of a DNA fragment containing intron 13 of the chicken Lmbr1 assigned the gene to chromosome 2 between MCW071 (a marker within the EN2 gene) and ADL0270, a syntenic region to human 7q36.

Alleles↗
PubMed2004

Development of a rapid genotyping method for single nucleotide polymorphisms and its application in cancer studies.

Single nucleotide polymorphisms (SNPs) in cancer-related genes can act as low risk genetic factors for the development of this disease. SNPs have also been shown to influence the efficacy and toxicity of various cytotoxic agents used in the treatment of cancer. Progress in these important areas of cancer research relies upon rapid, inexpensive and accurate means of SNP genotyping. In the present study we describe a fluorescent PCR-based method that utilizes single strand conformation polymorphism (SSCP) analysis to distinguish between different alleles. A real-time DNA fragment analysis platform and ultra-thin, re-useable gels allow short run times and hence a relatively high throughput to be achieved. A standardised procedure for the identification of optimal running conditions for each SNP is presented. We used this fluorescent-SSCP method to genotype SNPs in the MTHFR, p21, cyclin D1, MMP-2, vitamin D receptor, TNF-alpha and IL-6 genes. Multiplex PCR of two SNPs allows up to 500 genotypes per day to be evaluated with 100% accuracy. The low start-up and running costs make this method particularly well suited for SNP genotyping studies that involve up to 1,000 DNA samples.

Base Sequence↗
PubMed2004

[Correlation analysis between single nucleotide polymorphism of the leptin receptor intron 8 and fatness traits in chickens].

Leptin receptor plays an important role in leptin functioning signal transduction and it may have direct effects on the deposition of adipose tissues and the body weight, the leptin receptor (OBR) gene, therefore, can be considered as a candidate gene in the study of fat deposition of the chicken. The function of OBR gene has been intensively studied in mammals, but study of OBR gene in the chicken is still rare. In this paper, the NEAU divergent selection broiler lines for abdominal fat were used. Body weight and fatness traits were measured in the sixth generation broiler population of the two lines at 7 week of age. Two pairs of primers for intron 8 of OBR gene were designed according to the database of chicken genomic sequence (Accession No. AF222783). The SNP was detected by DNA sequencing, and PCR-SSCP method was then developed to screen the population. The correlation analysis between the polymorphisms of the intron 8 of OBR gene and growth and fatness traits in the population was carried out using the appropriate statistical model. Two SNPs were found in the population. Those were T500C and G659A. The least square analysis showed that BB genotype birds had significant higher (P < 0.05) abdominal fat weight and percentage of abdominal fat than AA and AB genotype birds, and AA genotype birds had significant lower (P < 0.05) weights of livers than AB and BB genotype birds at the same time. From these results we can putatively drew the conclusion that OBR gene may be a major gene to affect the fatness traits or linked to the major gene, and the two polymorphisms found in OBR gene intron 8 region could be used to select the chicken for low abdominal fat in molecular marker-assisted selection programs.

Adipose Tissue↗
PubMed2001

A single nucleotide polymorphism in the 3'untranslated region of the CDKN2A gene is common in sporadic primary melanomas but mutations in the CDKN2B, CDKN2C, CDK4 and p53 genes are rare.

In this report we present the results of mutational analysis of the CDKN2B, CDKN2C, CDK4, p53 genes and 5'UTR of the CDKN2A gene in a set of 44 sporadic primary melanomas, which had been earlier analysed for mutations in the CDKN2A (p16/p14(ARF)) gene. No tumour-associated mutations were detected except in 1 melanoma where we found a CC>T* deletion-mutation in the codon 151-152 (exon 5) of the p53 gene. On the basis of our preliminary results, we did extended genotyping of the 500 C>G and 540 C>T polymorphisms in the 3'UTR of the CDKN2A gene in 229 melanoma cases and 235 controls. The T-allele frequency (for 540 C>T polymorphism) in melanomas was significantly higher than in controls (0.14 vs. 0.08; chi(2) = 5.95, p = 0.01; OR = 1.71, 95%CI = 1.11-2.66). The heterozygote frequency for this polymorphism was 0.26 (59/229) in melanomas compared to 0.13 (30/235) in healthy controls (chi(2) = 11.4; p = 0.0007; OR = 2.34, 95% CI = 1.40-3.92). The frequency of the 500 C>G polymorphism in the 3'UTR in the CDKN2A gene was not significantly higher in melanomas compared to healthy controls. The 500 C>G polymorphism, however, was in linkage disequilibrium with approximately 50 kb apart the C>A intronic polymorphism in the CDKN2B gene (determined in 44 melanomas and 90 controls; Fisher exact test, p<0.0001). Finally, the sequence analysis of genomic DNA isolated from T cell lymphocytes of healthy individuals exhibited that the codon reported as last of exon 2 of the CDKN2C gene is rather the first codon of exon 3.

3' Untranslated Regions↗
PubMed2004

A new method for detecting single nucleotide polymorphism using GFP-display.

The single nucleotide polymorphism (SNP) of aldehyde dehydrogenase-2 (ALDH2) codon 487, GAA (Glu) or AAA (Lys), was examined using green fluorescent protein (GFP)-display, an electrophoretic detection method for single amino acid changes. Although no shift in migration between the GFP-ALDH (Glu487) and GFP-ALDH (Lys487) fusion proteins was observed on SDS/urea gel, the two migrated to different positions when tagged with Asp. The SNP analysis was performed with GFP-ALDH-Asp3, and GFP-ALDH-Asp3 constructed from donors having the codon GAA/GAA, GAA/AAA or AAA/AAA was detected as different patterns as expected. GFP-display is potentially a unique method in SNP analysis, which does not require any special equipment or chemicals.

Aldehyde Dehydrogenase↗
PubMed2006

Miniaturized platforms for the detection of single-nucleotide polymorphisms.

Conventional methods for detecting single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in human beings, are mostly limited by their analysis time and throughputs. In contrast, advances in microfabrication technology have led to the development of miniaturized platforms that can potentially provide rapid high-throughput analysis at small sample volumes. This review highlights some of the recent developments in the miniaturization of SNP detection platforms, including microarray-based, bead-based microfluidic and microelectrophoresis-based platforms. Particular attention is paid to their ease of fabrication, analysis time, and level of throughput.

Electrophoresis↗
PubMed2006

[Advances in high-density whole genome-wide single nucleotide polymorphism array in cancer research].

A single nucleotide polymorphism (SNP) is the most common type of genetic variation, and millions of SNPs have been documented so far. Because of dense distribution of SNPs across the genome, SNPs are viewed as ideal markers for research use in the post-genomic era. The application of the high-density whole genome-wide SNP array not only leads to more rapid, economical, and high throughput genotyping but also makes the investigation of the genetic variety or change in global patterns possible. The SNP array will be widely used in various research fields, such as large-scale genome-wide linkage and association studies to discover susceptibility genes in cancer, and loss of heterozygosity analysis to discover tumor suppressor genes and tumor molecular markers, and so on.

Genetic Predisposition to Disease↗
PubMed1999

Single nucleotide polymorphisms in the equine transferrin gene.

Single nucleotide polymorphisms (SNPs) in exons 13, 15 and 16 of equine transferrin for common, rare and mutant variants were investigated. Compared with previous work a further 13 SNPs have been identified, allowing for the two previously identified clades to be subdivided into 11 groups. A combination of one or more of eight SNPs can be used to classify the equine variants into these 11 groups, since most are co-inherited. Putative sites of glycosylation in exons 13 and 16 showed no polymorphism, suggesting that presence or absence of sugar moieties does not lead to electrophoretic variation between the variants. Using the 26 SNPs currently identified in transferrin it is still not possible to differentiate variants F1 from F2, or D from H2, which represent 75% of the variants occurring in Thoroughbred equine population. This suggests that further SNPs exist in equine transferrin. The significance of the high level of variation in exon 15 is discussed.

Animals↗
PubMed2001

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms.

We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout the human genome, providing an average density on available sequence of one SNP every 1.9 kilobases. These SNPs were primarily discovered by two projects: The SNP Consortium and the analysis of clone overlaps by the International Human Genome Sequencing Consortium. The map integrates all publicly available SNPs with described genes and other genomic features. We estimate that 60,000 SNPs fall within exon (coding and untranslated regions), and 85% of exons are within 5 kb of the nearest SNP. Nucleotide diversity varies greatly across the genome, in a manner broadly consistent with a standard population genetic model of human history. This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.

Chromosome Mapping↗
PubMed2003

Mining single-nucleotide polymorphisms from hexaploid wheat ESTs.

Single-nucleotide polymorphisms (SNPs) represent a new form of functional marker, particularly when they are derived from expressed sequence tags (ESTs). A bioinformatics strategy was developed to discover SNPs within a large wheat EST database and to demonstrate the utility of SNPs in genetic mapping and genetic diversity applications. A collection of > 90000 wheat ESTs was assembled into contiguous sequences (contigs), and 45 random contigs were then visually inspected to identify primer pairs capable of amplifying specific alleles. We estimate that homoeologue sequence variants occurred 1 in 24 bp and the frequency of SNPs between wheat genotypes was 1 SNP/540 bp (theta = 0.0069). Furthermore, we estimate that one diagnostic SNP test can be developed from every contig with 10-60 EST members. Thus, EST databases are an abundant source of SNP markers. Polymorphism information content for SNPs ranged from 0.04 to 0.50 and ESTs could be mapped into a framework of microsatellite markers using segregating populations. The results showed that SNPs in wheat can be discovered in ESTs, validated, and be applied to conventional genetic studies.

Base Sequence↗
PubMed2002

A nanobiotechnology roadmap for high-throughput single nucleotide polymorphism analysis.

Genetic analysis based on single nucleotide polymorphisms (SNPs) has the potential to enable identification of genes associated with disease susceptibility, to facilitate improved understanding and diagnosis of those diseases, and should ultimately contribute to the provision of new therapies. To achieve this end, new technology platforms are required that can increase genotyping throughput, while simultaneously reducing costs by as much as two orders of magnitude. Development of a variety of genotyping platforms with the potential to resolve this dilemma is already well advanced through research in the field of nanobiotechnology. Novel approaches to DNA extraction and amplification have reduced the times required for these processes to seconds. Microfluidic devices enable polymorphism detection through very rapid fragment separation using capillary electrophoresis and high-performance liquid chromatography, together with mixing and transport of reagents and biomolecules in integrated systems. The potential for application of established microelectronic fabrication processes to genetic analyses systems has been demonstrated (e.g. photolithography-based in situ synthesis of oligonucleotides on microarrays). Innovative application of state-of-the-art photonics and integrated circuitry are leading to improved detection capabilities. The diversity of genotyping applications envisaged in the future, ranging from the very high-throughput requirements for drug discovery through to rapid and cheap near-patient genotype analysis, suggests that several SNP genotyping platforms will be necessary to optimally address the different niches.

Genetic Predisposition to Disease↗