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PubMed2005

Genotyping SNPs with the LightCycler.

Here, a single nucleotide polymorphism typing methodology is described based on polymerase chain reaction monitoring, in real time, of fluorescently labeled amplified products using the LightCycler. The main advantages of the system are the time required for the analysis (about 20 min), combined with the robustness, accuracy, and the sensitivity of the method.

Base Sequence↗
PubMed2005

Genetic studies to identify hepatic fibrosis genes and SNPs in human populations.

Increasing evidence suggests that non-sex-linked genetic factors play a role in determining both susceptibility to, and progression of, liver fibrosis. The elucidation of these factors will have many potential benefits in the management of patients with chronic liver disease. A variety of approaches can be used to look for genetic factors playing a role in liver fibrosis. In the future, genome-wide single nucleotide polymorphism (SNP) scanning of cases and controls may become feasible; however, to date, studies have relied on candidate-gene, case-control, allele-association methodology. This section will focus on the design and interpretation of case-control association studies in liver disease using non-alcoholic fatty liver disease (NAFLD) to illustrate the key issues and potential pitfalls of this approach.

Autoimmune Diseases↗
PubMed2000

Mining for SNPs: putting the common variants--common disease hypothesis to the test.

Classical molecular genetic strategies have succeeded in identifying mutations responsible for numerous rare diseases with Mendelian patterns of inheritance, but have been largely unsuccessful in unravelling the (genetic basis of complex medical conditions like cardiovascular disease' diabetes and mental illness. These common disorders are shaped by multiple genes that exert weak allelic effects in the setting of confounding environmental variables. Association study designs provide statistical povwer to reveal the modest contributions of weak alleles, and evidence is mounting that common genetic polymorphisms play a role in complex diseases. Cataloguing genetic variation in human populations is a prerequisite for further validation of the 'common variants-common disease' hypothesis, and polymorphism discovery has begun in earnest in the academic and private sector. We will review several strategies for high-throughput polymorphism discovery and discuss the implications of early results from polymorphism screens for future genetic studies.

Gene Frequency↗
PubMed2004

Genotyping of single nucleotide polymorphisms (SNPs) influencing drug response by competitive allele-specific short oligonucleotide hybridization (CASSOH) with immunochromatographic strip.

Using competitive allele-specific oligonucleotide hybridization with immunochromatographic strip (CASSOH), we have developed a simplified method for the detection of eight polymorphisms that are especially important in the identification of drug responders or non-responders and patients at increased risk of drug toxicity. The genotyping method is unambiguously determined by the presence or the absence of visible purple lines on the immunochromatographic strip, and results are obtained within 5 min after PCR. This method is rapid, highly sensitive, simplified, and should be suitable for point-of-care genotyping in clinical settings.

Alleles↗
PubMed1999

Snapping up SNPs.

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Databases, Factual↗
PubMed2005

Ultrafine mapping of SNPs from mouse strains C57BL/6J, DBA/2J, and C57BLKS/J for loci contributing to diabetes and atherosclerosis susceptibility.

The inbred mouse strain C57BLKS/J (BKS) carrying a mutation of the leptin receptor lepr(-/-) (BKS-db) is a classic mouse model of type 2 diabetes. While BKS was originally presumed to be a substrain of C57BL/6J (B6), it has become apparent that its genome contains introgressed regions from a DBA/2 (DBA)-like strain and perhaps other unidentified sources. It has been hypothesized that the strikingly enhanced diabetes susceptibility of BKS-db compared with B6-db is conferred by this introgressed DNA. Using high-density single nucleotide polymorphisms, we have mapped the DBA and other contaminating DNA regions present in BKS. Thus, approximately 70% of its genome appears to derive from B6, with approximately 20% from DBA and another 9% from an unidentified donor. Comparison with 56 diverse inbred strains suggests that this donor may be a less common inbred strain or an outbred or wild strain. Using expression data from a B6 x DBA cross, we identified differentially regulated genes between these two strains. Those cis-regulated genes located on DBA-like blocks in BKS constitute primary candidates for genes contributing to diabetes susceptibility in the BKS-db strain. To further prioritize these candidates, we identified those cis-acting expression quantitative trait loci whose expression significantly correlates with diabetes-related phenotypes.

Animals↗
PubMed2006

Innate immunity SNPs are associated with risk for severe sepsis after burn injury.

OBJECTIVE: To analyze allelic association with clinical outcome in a cohort of burn patients. PATIENTS: Two hundred twenty-eight individuals with burns > or =15% total body surface area without significant non-burn related trauma who survived >48 hours post-admission were enrolled. One hundred fifty-nine of these patients were analyzed previously. METHODS: Candidate polymorphisms within interleukin-1 beta (IL-1beta), interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-alpha), cellular differentiation marker 14 (CD14) and toll-like receptor 4 (TLR4) were evaluated by logistic regression analysis for association with increased risk for severe sepsis (sepsis plus organ dysfunction or shock). RESULTS: After adjustment for age, burn size, ethnicity, gender and inhalation injury, alleles at TNF-alpha (308G, p=0.013), TLR4 (+896G, p=0.027), IL-6 (174C, p=0.040) and CD14 (159C, p=0.047) were significantly associated with an increased risk for severe sepsis. CONCLUSIONS: Carriage of variant alleles at immune response genes were associated with increased risk for severe sepsis after burn injury.

Adult↗
PubMed2005

Chips and SNPs, bugs and thugs: a molecular sleuthing perspective.

Recent events both here and abroad have focused attention on the need for ensuring a safe and secure food supply. Although much has been written about the potential of particular select agents in bioterrorism, we must consider seriously the more mundane pathogens, especially those that have been implicated previously in foodborne outbreaks of human disease, as possible agents of bioterrorism. Given their evolutionary history, the enteric pathogens are more diverse than agents such as Bacillus anthracis, Francisella tularensis, or Yersinia pestis. This greater diversity, however, is a double-edged sword; although diversity affords the opportunity for unequivocal identification of an organism without the need for whole-genome sequencing, the same diversity can confound definitive forensic identification if boundaries are not well defined. Here, we discuss molecular approaches used for the identification of Salmonella enterica, Escherichia coli, and Shigella spp. and viral pathogens and discuss the utility of these approaches to the field of microbial molecular forensics.

Bacteria↗
PubMed2006

Single nucleotide polymorphisms (SNPs) at CDH1 promoter region in familial gastric cancer.

INTRODUCTION: Gastric cancer is the most frequent gastrointestinal malignancy in Mexico and the proportion of patients younger than 40 years is one of the highest reported in the world literature. Recently several families with familial diffuse gastric cancer have been identified at the National Institute of Medical Sciences and Nutrition. Germline mutations in the E-cadherin gene (CHD1) have been described that result in the development of diffuse hereditary gastric cancer in young patients. METHODS: The complete coding sequence at exons 1 to 16 and the promoter region of CDH1 was amplified by polymerase chain reaction in peripheral blood samples of two patients with early onset familial diffuse gastric cancer. RESULTS: No germline inactivating mutations of CHD1 were found on either patient. Single nucleotide polymorphisms -160 C->A were detected in the promoter region of CDH1 in both patients. CONCLUSIONS: The polymorphism -160 C->A theoretically confers an increased risk of developing diffuse gastric cancer. The relatives of these patients may an increased risk of gastric cancer among other tumors. There is presently not enough evidence to consider the -160 C->A polymorphism an etiologic factor of diffuse gastric cancer in these patients since the frequency and type of genetic alterations of CDH1 are largely unknown in the Mexican population. It will be necessary to conduct epidemiologic studies in the Mexican population to determine the influence that genetic alterations have on the genesis of diffuse gastric carcinoma.

Adult↗