Microarray and microfluidic methodology for genotyping cytokine gene polymorphisms

Miniaturization of molecular biological techniques for gene assay

The rapid diagnosis of various diseases is a critical advantage of many emerging biomedical tools. Due to advances in preventive medicine, tools for the accurate analysis of genetic mutation and associated hereditary diseases have attracted significant interests in recent years. The entire diagnostic process usually involves two critical steps, namely, sample pre-treatment and genetic analysis. The sample pre-treatment processes such as extraction and purification of the target nucleic acids prior to genetic analysis are essential in molecular diagnostics. The genetic analysis process may require specialized apparatus for nucleic acid amplification, sequencing and detection. Traditionally, pre-treatment of clinical biological samples (e.g. the extraction of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)) and the analysis of genetic polymorphisms associated with genetic diseases are typically a lengthy and costly process. These labor-intensive and time-consuming processes usually result in a high-cost per diagnosis and hinder their practical applications. Besides, the accuracy of the diagnosis may be affected owing to potential contamination from manual processing. Alternatively, due to significant advances in micro-electro-mechanical-systems (MEMS) and microfluidic technology, there are numerous miniature systems employed in biomedical applications, especially for the rapid diagnosis of genetic diseases. A number of advantages including automation, compactness, disposability, portability, lower cost, shorter diagnosis time, lower sample and reagent consumption, and lower power consumption can be realized by using these microfluidic-based platforms. As a result, microfluidic-based systems are becoming promising platforms for genetic analysis, molecular biology and for the rapid detection of genetic diseases. In this review paper, microfluidic-based platforms capable of identifying genetic sequences and diagnosis of genetic mutations are surveyed and reviewed. Some critical issues with the use of microfluidic-based systems for diagnosis of genetic diseases are also highlighted.

Coffee, caffeine-related genes, and Parkinson's disease: a case-control study

An inverse association between coffee and Parkinson's disease (PD) has been reported. However, it remains uncertain why some but not all coffee drinkers are less susceptible to PD. We considered the possibility of a pharmacogenetic effect. In our study, we included 1,208 subjects (446 case-unaffected sibling pairs and 158 case-unrelated control pairs) recruited from an ongoing study of the molecular epidemiology of PD in the Upper Midwest (USA). We collected information on lifetime coffee drinking and we studied two genes: ADORA2A, which encodes the major receptor activity of caffeine in the brain (variants rs5751876 and rs3032740), and CYP1A2, which encodes the major rate-limiting step of caffeine metabolism (variants rs35694136 and rs762551). We did not observe significant associations of coffee drinking or of the genetic variants with PD susceptibility, either independently or jointly, in the sample overall and in most strata. Our study neither supports the hypothesis that coffee protects against PD nor provides evidence for a pharmacogenetic effect.

Interleukin-1beta and interleukin-1 receptor antagonist gene polymorphisms and gastric cancer: a meta-analysis

BACKGROUND

Polymorphisms of interleukin-1B (IL1B) and its receptor antagonist (IL1RN) genes have been inconsistently associated with gastric cancer risk. We examined these associations by performing meta-analyses.

MATERIALS AND METHODS

Twenty-five studies testing the association between IL1B and/or IL1RN gene polymorphisms and gastric cancer were examined: 14 studies of IL1B-511, 14 studies of IL1B-31, 8 studies of IL1B+3954, and 23 studies of IL1RN. Overall and ethnicity-specific summary odds ratios and corresponding 95% confidence intervals for gastric cancer associated with these polymorphisms were estimated using fixed- and random-effects models. Heterogeneity and publication bias were evaluated.

RESULTS

IL1B-511T and IL1RN*2 were associated with gastric cancer risk in Caucasians, but not in Asians. For IL1B-511T, the association in Caucasians was stronger when intestinal-subtype and noncardia gastric cancer cases were examined. A nonsignificant trend was observed between IL1B-31C and gastric cancer in Caucasians. No significant association of IL1B+3954T and gastric cancer risk was detected. Studies with better methodologic characteristics reported stronger effects. There was no evidence of publication bias.

CONCLUSION

IL1B-511T is associated with gastric cancer susceptibility in Caucasians. The meta-analyses suggest that the conflicting results among studies may be explained by variation in allele frequencies among the ethnic groups and variation in tumor types, as well as by the methodologic quality of the studies.

Estrogen bioactivation, genetic polymorphisms, and ovarian cancer

Recent experimental evidence has shown that catechol estrogens can be activated through metabolism to form depurinating DNA adducts and thereby initiate cancer. Limited data are available regarding this pathway in epithelial ovarian cancer. We conducted a case-control study of 503 incident epithelial ovarian cancer cases at the Mayo Clinic in Rochester, MN, and Jacksonville, FL, and a 48-county region in North Carolina. Six hundred nine cancer-free controls were frequency matched to the cases on age, race, and residence. After an interview to obtain data on risk factors, a sample of blood was collected for DNA isolation. Subjects were genotyped for seven common single nucleotide polymorphisms in four genes involved in catechol estrogen formation (CYP1A1 and CYP1B1) or conjugation (COMT and SULT1A1). Data were analyzed using logistic regression, stratified by race, and with adjustment for design factors and potential confounders. None of the individual genotypes were significantly associated with ovarian cancer risk. However, an oligogenic model that considered the joint effects of the four candidate genes provided evidence for an association between combinations of these genes and ovarian cancer status (P = 0.015). Although preliminary, this study provides some support for the hypothesis that low-penetrance susceptibility alleles may influence risk of epithelial ovarian cancer.

Molecular diagnostics by microelectronic microchips

Molecular diagnostics is being revolutionized by the development of highly advanced technologies for DNA and RNA testing. One of the most important challenges is the integration of microelectronics to microchip-based nucleic acid technologies. The specific characteristics of these microsystems make the miniaturization and automation of any step of a molecular diagnostic procedure possible. This review describes the application of microelectronics to all the processes involved in a genetic test, particularly to sample preparation, DNA amplification and sequence variation detection.

UCHL1 is associated with Parkinson's disease: A case-unaffected sibling and case-unrelated control study

To avoid the possible confounding effect of population stratification, we employed a discordant sibling study design and a liberalization of the sibling transmission disequilibrium test to confirm the association of the S18Y variant of the ubiquitin carboxi-terminal hydrolase L1 (UCHL1) gene with Parkinson's disease (PD). The study included 497 case-control pairs (427 case-unaffected sibling pairs and 70 case-unrelated control pairs). Analyses confirmed a significant inverse association of the UCHL1 S18Y polymorphism with PD overall (OR=0.18, 95% CI=0.05-0.64, p=0.002, recessive model) and in several strata.