Molecular diagnosis : a journal devoted to the understanding of human disease through the clinical application of molecular biology最新文献

Pharmacogenetics has assumed increasing importance with the developing concepts of personalized medicine. There is a need to determine the metabolic status of an individual when using drugs, the actions of which are influenced by drug-metabolizing enzymes. Cytochrome P450 (CYP) and its variants, particularly CYP2D6 and CYP2C19, play a role in the metabolism of approximately 25% of all prescription drugs. This review covers the role of the CYP system not only in the metabolism of drugs but also in the pathophysiology of disease. Various technologies for the assessment of CYP status are described, with the focus on AmpliChip CYP450 (Roche Molecular Diagnostics, Alameda, CA, USA), the first approved microarray molecular diagnostic test for the analysis of 29 polymorphisms and mutations of the CYP2D6 gene, and two polymorphisms of the CYP2C19 gene. It combines Roche's PCR technology with the GeneChip microarray system (Affymetrix, Santa Clara, CA, USA). Examples of numerous drugs that are metabolized by the CYP system are listed, and categories of antidepressants, antipsychotics, immunosuppressive and anticancer drugs are described to illustrate the role of testing for CYP polymorphisms in the therapeutic use of these drugs. CYP testing has applications in toxicology and absorption, distribution, metabolism and excretion (ADME) profiling as a guide to drug development. AmpliChip CYP450 may be used in conjunction with pharmacotherapy to guide decision making about selection of drugs and dosage. The test is not a solitary tool to determine optimum drug dosage, but is meant for use along with clinical evaluation and other methods for the selection of the treatment that is best suited for an individual patient. AmpliChip CYP450 is the first DNA microarray test to be cleared by the US FDA, and its clearance paves the way for similar microarray-based diagnostic tests to be developed in the future. This will facilitate the development of personalized medicine.

Objective: In order to evaluate the stability of Trypanosoma cruzi kinetoplast DNA (kDNA), the blood samples from seven patients with Chagas disease were stored in different buffers and at different temperatures.

Methods: Three different buffers were used: buffer A, 6 mol/L guanidine-HCl; buffer B, 6M guanidine-HCl and 0.2M EDTA pH 7.5; and buffer C, 6M guanidine-HCl, 0.2M EDTA pH 7.5 and 10 microM dl-alpha-tocopherol (Roche, Basal, Switzerland). Two temperatures were used: 4 degrees C and 25 degrees C. Vitamin E was added to the blood lysates as an antioxidant. T. cruzi kDNA was obtained by phenol extraction, and then PCR amplifications and Southern blot were carried out in each DNA sample up to 90 days of blood storage. The iron content of each sample was determined by atomic absorption spectrophotometry.

Results: Overall, there is an association between T. cruzi kDNA stability and the storage time of blood samples. No significant differences were detected in T. cruzi kDNA stability in the presence or absence of vitamin E or with citrate or EDTA as an anticoagulant. There was no statistical difference in the failure of PCR-based kDNA detection with these different storage buffers, temperatures or iron levels.

Conclusions: The blood lysates promote T. cruzi kDNA damage in a time-dependent manner that reduces the ability to detect the genomic DNA of an infectious agent by PCR. The high concentration of guanidine-HCl denatured proteins in these storage conditions probably denotes a non-enzymatic kDNA lysis.

Objective: The presence of exogenous DNA in commercially available polymerase chain reaction (PCR) reagent preparations is a serious problem when amplifying conserved regions of bacteria. The preferred and currently in-use method of decontamination using 8-methoxypsoralen (8-MOP) and UVA requires re-standardization of decontamination with increasing concentrations of 8-MOP and UVA irradiation timings, if the DNA load of reagents is high due to lot-to-lot differences. The objective of this study was to develop a decontamination method, which would (i) work at the minimum reported concentration of 8-MOP and UVA irridation timings; and (ii) take care of inter-batch DNA-load variability of reagents.

Materials and methods: The improved method described here was formulated after studying the exact molecular mechanism of action of 8-MOP with DNA. The successful working of the method was experimentally proven and validated with 6-7 new batches of PCR reagents. The sensitivity of eubacterial PCR, after using the new method of decontamination, to be used clinically was checked with both the spiked specimens and the actual clinical specimens.

Results and discussion: The new method was found to work at the same starting parameters of 8-MOP and UVA in such situations. The increased efficiency of this method was found to be due to the synergistic effect of both the selective treatment of Taq DNA polymerase and the split-irradiation approach.

Introduction: The presence of four virulence genes (racR, wlaN, cgtB, virB11) in 356 Campylobacter jejuni strains isolated from confirmed clinical cases was examined by PCR and sequence analysis. The investigated genes were chosen on the basis of their variation in prevalence.

Methods: The virulence genes were detected by PCR and the amplified products were submitted for sequence analysis.

Results: The gene with the highest prevalence was racR (87.08%). virB was present in only 1.69% of the C. jejuni strains, and wlaN and cgtB were detected in 16.01% and 24.44%, respectively. Five strains associated with Guillain-Barré syndrome and Miller-Fischer syndrome out of the total of 356 (1.40%) were positive for cgtB.

Conclusion: Our findings suggest that racR may encode factors necessary for bacterial pathogenicity in humans, while the roles of the other three genes remain ambiguous.

Introduction: The expansion of specific trinucleotide repeats results in certain genetic disorders.

Method: Real-time PCR analysis was used to rapidly discriminate between normal and expanded (CAG)(n) alleles in the androgen receptor gene.

Result: The difference in melting temperature (T(m)) between the most common normal and expanded alleles was approximately 1 degrees C.

Conclusion: Real-time PCR analysis seems to be a highly reliable and rapid method, which may facilitate the first molecular approach to human trinucleotide repeat disorders.

Background: Genetic polymorphisms and mutations of the genes involved in tumorigenesis may determine individual susceptibility for cancer. The p27/Kip1 protein belongs to the family of cyclin-dependent kinase-inhibitory proteins, which are negative regulators of cell-cycle progression. Reduced protein levels of p27/Kip1 have been reported in numerous human cancers including breast cancer.

Methods and results: p27 gene mutations and the codon 109 polymorphism were investigated in breast cancer patients by single strand conformation polymorphism analysis, PCR-restriction fragment length polymorphism analysis and DNA sequencing. Mutations were identified in 2 of 24 breast tumor samples. One G-->A transition resulting in a silent mutation and a single base deletion resulting in a nonsense mutation were detected in one patient. Another breast cancer sample harbored a T-->A transition at codon 159. An association between the codon 109 B allele and breast cancer was observed.

Conclusion: Our study indicates that mutational alterations in the p27 gene are rare in human breast cancer. The codon 109 B allele is associated with high-grade tumors.

Inherited thrombophilia, defined as an increased familial tendency to develop thrombosis, may be due to congenital deficiencies or abnormalities of antithrombin, protein C or protein S; to the presence of a point mutation in the factor V gene (G1691A, factor V Leiden) leading to a poor anticoagulant response to activated protein C; or to the presence of a mutation in the prothrombin gene (G20210A) leading to increased plasma levels of prothrombin. The laboratory investigation of inherited thrombophilia should be limited to patients with a history of venous thromboembolism and, if positive, to their family members even though they are still asymptomatic. There is no indication for indiscriminate screening of the general population or screening of asymptomatic women before prescribing oral contraceptives. Testing should be based on the phenotype for antithrombin, protein C and protein S; on the phenotype and genotype (factor V Leiden mutation) for activated protein C resistance; and on the genotype (G20210A mutation) for hyperprothrombinemia. Phenotypic testing should be performed no sooner than three months after acute thrombotic events and at least 2 weeks after discontinuation of oral anticoagulant treatment.

Introduction: Resistance to the thyroid hormone (RTH) is an inherited syndrome of reduced tissue responsiveness to hormonal action caused by mutations located in the ligand-binding domain and adjacent hinge region of the thyroid hormone receptor β (TRβ) gene.

Patient: The patient in this study, a 42-year-old Caucasian male, came to medical attention because he experienced atrial fibrillation. Clinical evaluation showed a small and diffuse goiter and biochemical tests revealed markedly elevated concentrations of total T(4), total T(3), and free T(4), normal thyroid-stimulating hormone (TSH) values and slightly increased I(131) thyroid uptake at 24 hours. The thyroperoxidase, thyroglobulin, and TSH receptor antibodies were positive. He was treated with cabergoline plus methimazole. This treatment was stopped because of the inconsistent response, monotherapy with tri-iodothyroacetic acid (TRIAC) was then prescribed after molecular diagnosis confirmed RTH syndrome.

Methods: The exons 9 and 10 of the TRβ gene, including splicing signals and the flanking intronic regions of each intron, were amplified with PCR. DNA sequences from each amplified fragment were performed with the Taq polymerase-based chain terminator method and using the specific TRβ forward and reverse primers.

Results: Direct sequence analysis of the exons 9 and 10 of the TRβ gene revealed an eight basepair deletion, 1297-1304delGCCTGCCA in exon 10. The mutation produces a frameshift at amino acid 433 and introduces a stop codon TGA at position 461, 85 nucleotides downstream from deletion. This alteration was not detected in either the father or mother of the patient, suggesting a de novo mutation that was confirmed by DNA fingerprint analysis.

Conclusions: In the present study we have identified a novel sporadic mutation corresponding to 1297-1304delGCCTGCCA deletion in the activating function 2 (AF-2) region of TRβ. To our knowledge, this is the first time that the presence of a partial deletion of eight nucleotides in the TRβ has been reported.

Introduction: Antimuscarinic drugs have frequently been used for the treatment for patients with an overactive bladder (OAB) and there have been many studies on the distribution of muscarinic receptor subtypes in the bladder. However, the distribution of muscarinic receptor subtypes in OAB patients has not been well investigated. In this study we investigated the distribution of muscarinic receptor subtypes with mRNA and protein expressions in patients with and without OAB, and investigated both the dome and trigone area.

Methods: Samples of bladder smooth muscle were obtained from 10 individuals, five patients with OAB and a non-OAB group consisting of five patients who received radical cystectomy.

Results: The M2 receptor was predominant, but there was no significant difference in the level of M2 expression between the groups in the dome area. M5 expression in the dome area was significantly higher in the OAB group than in the non-OAB group. In the trigone area, the level of M2 mRNA expression was the highest in the non-OAB group, and was significantly lower in the OAB group. The levels of M1 and M5 mRNA expression were also observed in samples obtained from the trigone area.

Conclusion: The multiformity of the muscarinic receptor subtypes in human bladder smooth muscle was confirmed, and our results suggest that the efficacy of a given pharmacologic therapy differs from patient to patient.