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PubMed2002

Toward positional cloning with SNPs.

Efficient methods are available for positional cloning of major genes by linkage and linkage disequilibrium (LD). The application of these methods to complex diseases is more demanding, but advances in sequencing the human genome, SNP discovery, high-throughput genotyping techniques, LD maps, and haplotype annotation are revolutionizing positional cloning of oligogenes for common multifactorial disease.

Alleles↗
PubMed2003

SNPs and haplotypes: genetic markers for disease and drug response (review).

The genetic make-up of an individual not only determines disease susceptibility but also response to drug treatment. It is because of this reason tremendous progress has recently been made in cataloging human sequence variations with an intention such that a high-density map will provide necessary tools to develop genetic-based diagnostic and therapeutic options. The availability of the human DNA sequence, its variation between individuals and the functional understanding of genetic determinants between individuals may enable pharmaceutical companies to discover safer and effective drugs. This will provide physicians with better tools to select the most appropriate treatment for each patient and avoid drugs that cause adverse effects. When a personalized medication becomes a more realistic and beneficial treatment, every newborn child in the neonatal unit will probably be genotyped as a routine procedure for improved treatment. This newly developed toxicogenomic or pharmacogenomic field is rapidly advancing and may change the practice of medicine in the future, providing personalized medicine for each individual.

Animals↗
PubMed2005

[Genotype combination distribution of 5-site SNPs in 3 subtypes of beta adrenoceptor].

DNA was extracted from the peripheral venous blood of 338 subjects using BLOOD DNA MINI KIT. The 5 site SNP in 3 subtypes of Beta-AR were genotyped by PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) and allele-specific primer PCR techniques. The genotypes combination distribution of SNP at 5 sites in the 3 subtypes of Beta-AR were determined by clustering analysis technique. The natural combination distribution characteristics for SNP at 5 sites in the 3 subtypes of Beta-AR in 338 subjects were obtained. Sixty-seven combinations types were found. The preceding 5 combinations in the natural combination distribution of the SNP were: (1) The genotype combination of forty subjects was B1-AR S/S49+B1-AR R/R389+B2-AR R/G16+B2-AR Q/E27+B3-AR W/W64, its probability was 11.83%. (2) The genotype combination of thirty-three subjects was B1-AR S/S49+B1-AR R/R389+B2-AR R/G16+B2-AR Q/Q27+B3-AR W/W64, its probability was 9.76%. (3) The genotype combination of nineteen subjects was B1-AR S/S49+B1-AR R/G389+B2-AR R/G16+B2-AR Q/Q27+B3-AR W/W64, its probability was 5.62%. (4) The genotype combination of sixteen subjects was B1-AR S/S49+B1-AR R/G389+B2-AR R/G16+B2-AR Q/E27+B3-AR W/W64, its probability was 4.74%. (5) The genotype combination of thirteen subjects was B1-AR S/G49+B1-AR R/R389+B2-AR R/G16+B2-AR Q/E27+B3-AR W/W64, its probability was 3.85%. The obvious correlations exist among full sample and female or male subgroup, and between female and male subgroups.

Adult↗
PubMed2005

Mitochondrial DNA typing screens with control region and coding region SNPs.

Mitochondrial DNA (mtDNA) analysis has found an important niche in forensic DNA typing. It is used with highly degraded samples or low-copy number materials such as might be found from shed hair or bones exposed to severe environmental conditions. The primary advantage of mtDNA is that it is present in high copy number within cells and therefore more likely to be recovered from highly degraded specimens. A major disadvantage to traditional forensic mtDNA analysis is that it is time-consuming and labor-intensive to generate and review the 610 nucleotides of sequence information commonly targeted in hypervariable regions I and II (HVI and HVII) of the control region. In addition, common haplotypes exist in HVI/HVII mtDNA sequences that can reduce the ability to differentiate two unrelated samples. In this report we describe the utility of two newly available screening assays for rapid exclusion of non-matching samples. The LINEAR ARRAY mtDNA HVI/HVII Region-Sequencing Typing Kit (Roche Applied Science, Indianapolis, IN) was used to type 666 individuals from U.S. Caucasian, African American, and Hispanic groups. Processing of the LINEAR ARRAY probe panels "mito strips" was automated on a ProfiBlot workstation. Observable variation in 666 individuals is reported and frequencies of the mitotypes within and between populations are presented. Samples exhibiting the most common Caucasian mitotype were subdivided with a multiplexed amplification and detection assay using eleven single nucleotide polymorphisms in the mitochondrial genome. These types of screening assays should enable more rapid evaluation of forensic casework samples such that only samples not excluded would be subjected to further characterization through full HVI/HVII mtDNA sequence analysis.

Automation↗
PubMed2005

Age and hypertension related changes in genotypes of MTHFR 677C>T, 1298A>C and PON1 -108C>T SNPs in men with coronary artery disease (CAD).

The phenotypes of CAD related to arterial hypertension co-occurrence were analysed in 174 male patients and 117 control men for the associations with the polymorphisms of the MTHFR gene (677C>T and 1298A>C) and the PON1 gene (-108C>T) in relation to age at diagnosis (less or equal and more than 50 years). We noted the increased frequency of the three MTHFR genotypes: CC/AC, CT/AA and CC/CC in the CAD group (65.5%) in comparison to the control group (45.3%), corresponding to the 2.3-fold increased risk of CAD for men with these genotypes (95%CI (1.4-3.7); p=0.0005). The higher increase in risk of CAD was noted for the younger men (OR=3.6; 95%CI(1.6-8.3); p=0.002) and lower for the older (OR=1.8; 95%CI(1.0-3.4); p=0.03). In the normotensive men the greater impact on CAD risk had the homozygous genotypes; the 2.3-fold higher risk was associated with MTHFR CC/AC, CC/CC and TT/AA genotypes (95%CI(1.2-4.4); p=0.01). After adjustment for age, the association between CAD and MTHFR was significant only for the younger normotensive men (OR=2.8; 95%CI (1.0-8.0); p=0.04). Additionally, we found that the younger part of the control group was characterized by higher frequency of the low expression PON1 -108T allele and PON1 -108TT genotype (0.54 and 31.9% respectively) in comparison to the older men (0.41 and 17.1% respectively; p=0.03).

Adult↗
PubMed2005

SNPs and interaction analyses of myocilin, optineurin, and apolipoprotein E in primary open angle glaucoma patients.

PURPOSE: To evaluate the association of myocilin (MYOC), optineurin (OPTN), and apolipoprotein E (APOE) genes and their interactions in primary open angle glaucoma (POAG). METHODS: A cohort of 400 unrelated POAG patients (294 high tension glaucoma, HTG, and 106 normal tension glaucoma, NTG) and 281 unrelated control subjects were recruited. All coding exons and splicing junctions in MYOC and OPTN were screened for sequence alterations. Common polymorphisms in APOE were genotyped. Single genes were investigated by univariate and haplotype analysis, and gene-gene interactions by logistic regression and stratified analysis. Multiple comparisons were corrected by the Bonferroni method. Bioinformatics analysis was performed to assess the conservation of mutation sites across species and to predict putative motifs and secondary structures in mutated proteins. RESULTS: Disease-causing mutations in MYOC and OPTN were identified in 1.75% and 1% of POAG patients, respectively. Most of these mutations were highly conserved across species, many predicted to create new motifs or change protein secondary structures. No individual MYOC polymorphisms significantly contributed to HTG or NTG. A haplotype containing the minor allele of the MYOC IVS2+35A>G increased NTG risk (p=0.0001). Three OPTN polymorphisms, T34T, IVS5+38T>G, and IVS8-53T>C increased NTG risk (p<0.0008), while IVS5+38T>G increased HTG risk (p=0.0006). One haplotype that contains the minor alleles of 3 OPTN polymorphisms, T34T, IVS5+38T>G, and IVS7+24G>A, increased NTG risk (p=0.0002). APOE epsilon4 carriers had a decreased NTG risk (p=0.007). Possible gene-gene interactions were found between MYOC, OPTN, and APOE. CONCLUSIONS: Disease-causing mutations in MYOC and OPTN accounted for only a small proportion of Chinese POAG patients. Common polymorphisms in MYOC, OPTN, and APOE might interactively contribute to POAG, indicating a polygenic etiology.

Adolescent↗
PubMed2005

[SNPs associated with adverse effects].

In recent years, pharmacogenomics have received much attention from the increased expectations for so-called order-made medicine. It is experientially clear that inter-individual differences exist in the degree of efficacy and occurrence of adverse effects. These inter-individual differences are observed not only among anticancer chemotherapeutics but in almost all drugs. Several studies have revealed that genetic factors are involved in these inter-individual differences. To date, the relationships have been revealed between adverse effects of some anticancer drugs and polymorphisms of drug metabolizing genes. Such relationships include 5-FU and DPYD gene, methotorexate and MTHFR gene, irinotecan and UGT 1A1 gene and 6-MP and TPMT gene. By using information on these polymorphisms, it will be possible to predict the occurrence of adverse effects before using anticancer drugs. In particular, information on polymorphisms related to the possibly adverse effects of irinotecan is now given in its package leaflet. This means that order-made medicine is a step closer. In this review, we discuss the relationships between polymorphisms of genes and the adverse effects of anticancer drugs. Furthermore, we want to suggest the direction of further pharmacogenomic studies with an eye to the realization of order-made medicine.

Antineoplastic Agents↗
PubMedDate not supplied

[Detection of fluoroquinolone resistance SNPs in gyrA and parC genes of Neisseria gonorrhoeae using MALDI-TOF mass-spectrometry].

For many known mechanisms of the drug resistance in microorganisms are described genetic markers (specific changes in the genome of microorganism, in the majority of the cases representing single nucleotide polymorphism). The search for the new methods, which make possible to identify single nucleotide changes with the greater effectiveness and at smaller prime is actual for the solution of the problem of the identification of the resistant strains. In this work a new approach of the determination of single nucleotide polymorphisms is proposed. It is based on the reactions of mini-sequencing and/or sequencing with the subsequent Matrix-Assisted Laser Desorption/Ionisation Time Of Flight Mass-Spectrometry (MALDI-TOF MS) of the reaction products. The approach was tested on a clinical group of Neisseria gonorrhoeae strains to investigate specific single nucleotide polymorphisms in genes gyrA and parC (the genetic markers of the bacterium fluoroquinolone resistance). The results of the nucleotide polymorphism deter- mination was completely agreed with the data, obtained earlier with the use of a "gold standard" (sequencing with the classical gel-electrophoresis separation of the reaction products). There is specific interest in the method of sequencing of the short DNA sequences using MALDI-TOF MS. The new high-throughput approach of the single nucleotide polymorphisms determination in bacterial genes considerably increases the effectiveness of the methods of microorganism's identification, genotyping and determining the genetic markers of the drug resistance.

DNA Gyrase↗