Detection of angiotensin-converting enzyme insertion/deletion polymorphisms using real-time polymerase chain reaction and melting curve analysis with SYBR Green I on a GeneAmp 5700

A label-free strategy for visual genotyping based on phosphate induced coloration reaction

Genetic variation plays a crucial role in disease occurrence and development. However, current genotyping strategies not only require a long turnaround time for DNA purification, but also depend on sophisticated apparatus and complex data interpretation, which seriously limits their application in point of care diagnostic test scenarios. In this study, by integrating phosphate induced coloration reaction and loop-mediated isothermal amplification, a rapid and portable strategy for straightforward genotyping has been established to cater to the demand of precision medicine. By employing phosphate ions produced during the amplification as a signal generator, not only can the genotyping result be interpreted with only naked eye from a low-cost label-free strip, but also the amplification efficiency is increased to facilitate genotyping with a robust biological specimen ignoring DNA polymerase inhibitors. Moreover, the introduction of alkaline lysis for DNA release allows whole blood to be identified accurately avoiding DNA purification. As a proof of concept, the insertion/deletion polymorphisms of the angiotensin-converting enzyme, a crucial factor associated with cardiovascular and cerebrovascular diseases, has been selected as a model to evaluate the performance of this method. Accurate results can be obtained from as low as 1 ng genomic DNA within 30 min. For clinical specimen detection, a concordance rate up to 100% has been found compared with PCR-based electrophoresis. Thus, this novel strategy may serve as a promising tool for straightforward genotyping to provide timely diagnostic information, especially in resource-poor medical institutions.

Phosphate induced coloration reaction facilitates visual genotyping and the target variant can be accurately identified within 30 min from blood directly.

Visual Detection of ACE I/D Polymorphism Using T-ARMS-PCR Combined with a Lateral Flow Assay and Its Clinical Application

Insertions/deletions (indels) variations have been recognized as a promising marker for the development of various diseases. However, methods used for the genotyping of indels in studies were tedious, complicated, and required sophisticated or expensive instruments, as well as complex data analysis, which makes it difficult to meet the demand of point of care testing. Herein, we presented a fast and accurate biosensor (T-ARMS-PCR-LFA) by the combination of tetra-primer amplification refractory mutation system polymerase chain reaction (T-ARMS-PCR) and GoldMag lateral flow assay (LFA) for visual genotyping of ACE I/D polymorphism. ACE I/D can be distinguished by employing four primers in one PCR reaction, and genotyping results were presented by the visual inspection of colors on the nitrocellulose membrane of LFA strips within 5 min. And 50 of the human genomic DNA samples were used for the detection of ACE I/D to further validate the accuracy of the T-ARMS-PCR-LFA system. As a demonstration, we showed that ACE I/D could be genotyped using a low amount of DNA sample (25 ng) with an accuracy of 100%, without complicated operation steps and data analysis, which is better than that of the conventional method (agarose gel electrophoresis analysis after common PCR). In conclusion, the biosensor is highly applicable for genotyping specific large indel variants in clinical practices, which enables rapid clinical decision-making, improves the management of disease diagnosis, and facilitates personalized medicine.

Development of Novel High-Resolution Melting-Based Assays for Genotyping Two Alu Insertion Polymorphisms (FXIIIB and PV92)

Insertion/Deletion polymorphisms (InDels) are a common type of genetic variation, with a growing role in population genetics and applied genomics. There is the need for the development of novel cost-effective assays for genotyping InDels of high importance. The main objective of this study was to develop high-resolution melting-based assays for genotyping two commonly studied Alu insertion polymorphisms: FXIIIB and PV92 (rs70942849 and rs3138523). Three primers (two forward and one reverse) were designed for each marker, and high-resolution melting (HRM) analyses in a qPCR platform were performed, using EvaGreen fluorescent dye. For each one of the two Alu insertion polymorphisms, HRM analyses identified distinguishable peaks for the three genotypes, allowing a robust genotyping. Results were validated using 96 DNA samples previously genotyped and the assays worked with different DNA concentrations. In this study, we developed novel cost-effective assays, using qPCR, for genotyping two Alu insertion polymorphisms (widely used as ancestry markers). Our results highlight the feasibility of using HRM analyses for genotyping InDel polymorphisms of medical and biotechnological importance.

High-resolution melting analysis for genotyping of the myotonic dystrophy type 1 associated Alu insertion/deletion polymorphism

Since its introduction, high-resolution melting (HRM) analysis has been used for genotyping of various types of sequence alterations. In this study, we report the use of HRM for genotyping of the 1-kb insertion/deletion polymorphism, involving a problematic region of five consecutive Alu elements, that is associated with myotonic dystrophy type 1. We combined a three-primer polymerase chain reaction (PCR) amplification approach with HRM using two primer sets. Analyses based on curve shapes are sensitive enough to differentiate between genotypes with both primer sets. In addition, the newly designed insertion-specific primer from the second primer set equalizes the allele-specific amplicon lengths, thereby reducing the possibility of preferential amplification of shorter fragments.

Identification of DNA copy number aberrations by array comparative genomic hybridization in patients with ruptured intracranial aneurysms

We aimed to use array comparative genomic hybridization (CGH) to identify chromosomal loci that contribute to the pathogenesis of ruptured intracranial aneurysms (IAs) in a Korean population and to confirm the results using real-time polymerase chain reaction (PCR). Twenty-three patients with ruptured IAs were enrolled in this study. Array CGH revealed copy number aberrations in 19 chromosomal regions. Chromosomal gains were identified at a high frequency in regions 1p12, 4q24, 5p15.31, 5p15.33, 6p12.2, 6q22.33, 7p21.1, 9q22.1, 10q24.32, 10q26.3, 12q13.13, 17p12, 18q12.3, 18q23, 19p13.3, 20q13.33, 21q11.2, and 21q22.3, whereas chromosomal losses were identified at 15q11.2 and 22q11.21. Real-time PCR confirmed the results of the array CGH studies of the COL6A2, GRIN3B, MUC17, and PRODH genes. This is the first study to identify candidate regions by array CGH in patients with IAs. The identification of genes that may predispose an individual to the development of IAs may lead to a better understanding of the mechanism of IA formation. Multicenter studies comparing cohorts of patients of different ethnicities are needed to better understand the mechanism of IA formation.

Identification of DNA copy-number aberrations by array-comparative genomic hybridization in patients with schizophrenia

Chromosomal abnormalities are implicated as important markers for the pathogenesis in patients with schizophrenia. In this study, with using bacterial artificial chromosome (BAC) array-based comparative genomic hybridization (CGH), we analyzed DNA copy-number changes among 30 patients with schizophrenia. The most frequent changes were partial gain of Xq23 (52%) and loss of 3q13.12 (32%). Other frequent gains were found in: 1p, 6q, 10p, 11p, 11q, 14p, and 15q regions, and frequent losses were found in: 2p, 9q, 10q, 14q, 20q, and 22q regions. The set of abnormal regions was confirmed by real-time PCR (9q12, 9q34.2, 11p15.4, 14q32.33, 15q15.1, 22q11.21, and Xq23). All real-time PCR results were consistent with the array-CGH results. Therefore, it is suggested that array-CGH and real-time PCR analysis could be used as powerful tools in screening for schizophrenia-related genes. Our results might be useful for further exploration of candidate genomic regions in the pathogenesis of schizophrenia.

Protection of Photoreceptor Cells from Phototoxicity by Transplanted Retinal Pigment Epithelial Cells Expressing Different Neurotrophic Factors

Transplantation of cells or tissues and the intravitreal injection of neurotrophic factors are two methods that have been used to treat retinal diseases. The purpose of this study was to examine the effects of combining both methods: the transplantation of retinal pigment epithelial (RPE) cells expressing different neurotrophic factors. The neutrophic factors were Axokine, brain derived-neurotrophic factor (BDNF), and basic fibroblast growth factor (bFGF). The enhanced green fluorescence protein (eGFP) gene was used as a reporter gene. These genes were transduced into RPE cells by lipofection, selected by antibiotics, and transplanted into the subretinal space of 108 rats. The rats were examined at 1 week and 3 months after the transplantation to determine whether the transduced cells were present, were expressing the protein, and were able to protect photoreceptors against phototoxicity. The survival of the transplanted cells was monitored by the presence of eGFP. The degree of protection was determined by the thickness of the outer nuclear layer. Our results showed that the degree of photoreceptor protection was different for the different types of neurotrophic factors at 1 week. After 3 months, the number of surviving transplanted cell was markedly reduced, and protection was observed only with the BDNF-transduced RPE cells. A significant degree of rescue was also observed by BDNF-transduced RPE cells in the nontransplanted area of the retina at both the early and late times. Lymphocytic infiltration was not detected in the vitreous, retina, and choroid at any time. We conclude that the transplantation of BDNF-transduced RPE cells can reduce the photoreceptor damage induced by phototoxicity in the transplanted area and weakly in the nontransplanted area.

Rapid detection of subtelomeric deletion/duplication by novel real-time quantitative PCR using SYBR-green dye

Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, miscarriages, and hematological malignancies. Automated detection of subtle deletions and duplications involving telomeres is essential for high-throughput screening procedures, but impractical when conventional cytogenetic methods are used. Novel real-time PCR quantitative genotyping of subtelomeric amplicons using SYBR-green dye allows high-resolution screening of single copy number gains and losses by their relative quantification against a diploid genome. To assess the applicability of the technique in the screening and diagnosis of subtelomeric imbalances, we describe here a blinded study in which DNA from 20 negative controls and 20 patients with known unbalanced cytogenetic abnormalities involving at least one or more telomeres were analyzed using a novel human subtelomere-specific primer set, producing altogether 86 amplicons, in the SYBR-green I-based real-time quantitative PCR screening approach. Screening of the DNA samples from 20 unrelated controls for copy number polymorphism do not detect any polymorphism in the set of amplicons, but single-copy-number gains and losses were accurately detected by quantitative PCR in all patients, except the copy number alterations of the subtelomeric p-arms of the acrocentric chromosomes in two cases. Furthermore, a detailed mapping of the deletion/translocation breakpoint was demonstrated in two cases by novel real-time PCR "primer-jumping." Because of the simplicity and flexibility of the SYBR-green I-based real-time detection, the primer-set can easily be extended, either to perform further detailed molecular characterization of breakpoints or to include amplicons for the detection and/or analysis of syndromes that are associated with genomic copy number alterations, e.g., deletion/duplication-syndromes and malignant cancers.

Comparative study of cathepsins D and S in rat IPE and RPE cells

To investigate differences between activities related to phagocytosis in iris pigment epithelial (IPE) and retinal pigment epithelial (RPE) cells, an aspartic protease, cathepsin D (cat D), and a cysteine protease, cathepsin S (cat S), of IPE and RPE were studied. IPE and RPE cells were isolated from Long Evans rat eyes. The origin of the isolated cells was determined by pigmentation and cytokeratin labelling. The mRNA expressions of cat D and cat S in cultured IPE or RPE cells were investigated by semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR). Enzyme activities of cat D and cat S in IPE or RPE cells were measured by using specific fluorogenic substrates, MOCAc-Gly-Lys-Pro-Ile-Leu-Phe-Phe-Arg-Leu-Lys-(Dnp)D-Arg-NH2 and Z-Val-Val-Arg-MCA, respectively. Western blot analysis of both proteins was also performed. The cultured cells, both of IPE and RPE cells were pigmented and showed positive labelling with an anti-cytokeratin monoclonal antibody. The cat D activity in RPE cells was 37 times that in IPE cells. The cat S activity in RPE cells was four times that in IPE cells. On the other hand, mRNA expression levels of cat D in RPE cells were at the same level with IPE cells, cat S mRNA expression in RPE cells were 10 times that in IPE cells. These results were also correlated with the Western blot analysis. In this study, we measured the characteristic expressions of cat D and S in IPE and RPE cells for the first time to compare their lysosomal activities. IPE cells have the lysosomal activities like RPE cells, however, the function of lysosomal activity in IPE cells is beneath RPE's. These results indicated that the ability of ROS digestion in IPE cells was not same as RPE cells.

[Development of simplified and rapid detection assay for genetic polymorphisms influencing drug response and its clinical applications]

Clinically important genetic polymorphisms influencing drug metabolism and drug response have typically been discovered on the basis of phenotypic differences among individuals from different populations. Routine genotyping before drug therapy may enable the identification of responders, nonresponders, or patients at increased risk of toxicity. Automated, high-throughput detecting methods for single-nucleotide polymorphisms (SNPs) are highly desirable in many clinical laboratories. The aim of this study is to develop a high-throughput genotyping method for detecting SNPs influencing drug response in the Japanese population. We have developed three real-time PCR assays for detecting SNPs in the human drug-metabolizing enzymes and drug targets. The assay for simultaneously detecting CYP2A6, CYP2B6, CYP2C9, CYP2C18, CYP2C19, CYP2D6, CYP2E1, CYP3A5, NAT2, TPMT, DPYD, UGT1A1, ALDH2, ADH2, MDR1, CETP, DCP-1, ADRB2, HTR2A, INPP1, SDF1, and mitochondrial DNA polymorphisms takes less than 1.5 h. With the clinical application of NAT2 genotyping, we found statistically significant difference between the incidence of adverse drug reactions (ADRs) and the NAT2 genotype. The incidence of the ADRs was significantly higher in the slow type than the in other two types, as 5 of the 6 patients were of the slowtype, and the other was the intermediatetype, while no patients of the rapidtype has developed any ADRs.

Real-time PCR for rapid genotyping of angiotensin-converting enzyme insertion/deletion polymorphism

OBJECTIVE

To develop a real-time PCR technique for detection of the insertion/deletion (I/D) polymorphism of angiotensin-converting enzyme (ACE) gene.

DESIGN AND METHODS

Three primers were designed for performing real-time PCR in the presence of SYBR Green I as flurochrome followed by melting curve analysis. Forty human genomic DNA that have been genotyped by two-rounds of conventional PCR were used for evaluation of this technique.

RESULTS

Melting curve analysis indicated the melting peak at 73.9 degrees C and 76.2 degrees C corresponding to the presence of I and D alleles, respectively. Comparable genotyping results were obtained by both conventional and real-time PCR. Besides, the mistyping of ID allele individuals by the first run of conventional PCR were accurately genotyped by single-tube real time PCR.

CONCLUSIONS

The real-time PCR method presented in this study provides a rapid and sensitive way for genotyping of ACE gene that may be suitable for large-scale clinical and epidemiologic study.