High throughput genotyping technologies for pharmacogenomics

Fluorescent DNA Biosensor for Single-Base Mismatch Detection Assisted by Cationic Comb-Type Copolymer

Simple and rapid detection of DNA single base mismatch or point mutation is of great significance for the diagnosis, treatment, and detection of single nucleotide polymorphism (SNP) in genetic diseases. Homogeneous mutation assays with fast hybridization kinetics and amplified discrimination signals facilitate the automatic detection. Herein we report a quick and cost-effective assay for SNP analysis with a fluorescent single-labeled DNA probe. This convenient strategy is based on the efficient quenching effect and the preferential binding of graphene oxide (GO) to ssDNA over dsDNA. Further, a cationic comb-type copolymer (CCC), poly(l-lysine)-graft-dextran (PLL-g-Dex), significantly accelerates DNA hybridization and strand-exchange reaction, amplifying the effective distinction of the kinetic barrier between a perfect matched DNA and a mismatched DNA. Moreover, in vitro experiments indicate that RAW 264.7 cells cultured on PLL-g-Dex exhibits excellent survival and proliferation ability, which makes this mismatch detection strategy highly sensitive and practical.

Miniaturization applied to analysis of nucleic acids in heterogeneous tissues

Despite huge efforts in sample analysis, the measurement of marker nucleic acids within tissues remains largely nonquantitative. Gene analyses have benefited from sensitivity gains through in vitro gene amplification, including PCR. However, whilst these processes are intrinsically suited to highly reproducible, accurate and precise gene measurement, the term semiquantitative analysis is still commonly used, suggesting that other fundamental limitations preclude a generic quantitative basis to gene analysis. The most poorly defined aspect of gene analysis relates to the sample itself. The amount of cells and, particularly, cell subtype composition are rarely annotated before analysis; indeed, they are often extrapolated after analysis. To advance our understanding of pathogenesis, assay formats will benefit from resembling the dimensions of the cell, to assist in the analysis of cellular components of tissue complexes. This review is partly a perspective on how current miniaturization technologies, in association with molecular biology, microfluidics and surface chemistries, may evolve from the parts of a paradigm to enable the unambiguous quantitative analysis of complex biologic matter.

Rapid testing of clopidogrel resistance by genotyping of CYP2C19 and CYP2C9 polymorphisms using denaturing on-chip capillary electrophoresis

Antiplatelet therapy is a cornerstone of cardiovascular treatment in patients with coronary artery disease and after myocardial infarction. Clopidogrel has become a popular antiplatelet agent due to its fast action and low frequency of adverse effects. Kinetics of clopidogrel metabolism is driven by enzymatic activity of the Cytochrome P450 system. Genotyping of CYP2C19 and CYP2C9 polymorphisms allows to identify slow metabolizers showing resistance to clopidogrel therapy. Today, a number of PCR-based techniques for single nucleotide polymorphism genotyping directed at clopidogrel resistance polymorphisms are in use. Here, we describe a new alternative genotyping approach combining the separation power of denaturing capillary electrophoresis with the analysis speed and ease of use of Bioanalyzer chipCE platform. Using an upgraded heater control, we present an optimization for allele separation of CYP2C19 I331V, CYP2C9 R144C, and CYP2C9 I359L polymorphisms employing run temperatures of up to 55°C. We demonstrate rapid and accessible approach to reproducible clopidogrel resistance with feasibility and low cost.

Modified multiple primer extension method

A multiple primer extension (MPEX) was originally developed for the hybridization, extension, and amplification of a DNA template on a planar substrate by Kinoshita et al. in 2006. Herein we present a modified MPEX method refined by our group for single nucleotide polymorphism (SNP) detection. In this method, hybridization and extension reactions are performed on a plastic S-BIO PrimeSurface substrate, with a biocompatible polymer. Its surface chemistry offers extraordinarily stable thermal properties, as well as chemical properties advantageous for enzymatic reactions on the surface. To visualize allele-specific PCR products on the surface, biotin-dUTP was incorporated into newly synthesized complementary strands during the extension reaction. The products were ultimately detected by carrying out a colorimetric reaction with a substrate solution containing 5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium. We have further successfully combined this method with multiplex PCR. We demonstrate the advantages of this combined method by analyzing representative SNPs on different linkage disequilibrium blocks of the micro opioid receptor gene (OPRM1), which is a marker gene for pain threshold.

A novel SNP detection technique utilizing a multiple primer extension (MPEX) on a phospholipid polymer-coated surface

Conventional methods for detecting single nucleotide polymorphisms (SNPs), including direct DNA sequencing, pyrosequencing, and melting curve analysis, are to a great extent limited by their requirement for particular detection instruments. To overcome this limitation, we established a novel SNP detection technique utilizing multiple primer extension (MPEX) on a phospholipid polymer-coated surface. This technique is based on the development of a new plastic S-BIO PrimeSurface with a biocompatible polymer; its surface chemistry offers extraordinarily stable thermal properties, as well as chemical properties advantageous for enzymatic reactions on the surface. To visualize allele-specific PCR products on the surface, biotin-dUTP was incorporated into newly synthesized PCR products during the extension reaction. The products were ultimately detected by carrying out a colorimetric reaction with substrate solution containing 4-nitro-blue tetrazolium chloride (NBT) and 5-bromo-4-chloro-3-indolyl phosphate (BCIP). We demonstrated the significance of this novel SNP detection technique by analyzing representative SNPs on 4 LD blocks of the micro opioid receptor gene. We immobilized 20 allele-specific oligonucleotides on this substrate, and substantially reproduced the results previously obtained by other methods.

Quantitative PCR approach to SNP detection and linkage mapping in Caenorhabditis elegans

I report a method for single nucleotide polymorphism (SNP) detection and linkage mapping in Caenorhabditis elegans using automated oligonucleotide design and fluorescence-based quantitative PCR detection. Nine hundred twenty-three oligonucleotide pairs were designed to produce small products of <150 bp for efficient amplification in a PCR, with one oligonucleotide of each pair overlapping a SNP site at the 3'-most nucleotide. A subset of the pairs were tested, and efficient allelic discrimination was obtained for SNPs between N2, the canonical laboratory strain, and CB4856, a strain isolated from Hawaii commonly used for mapping studies. Linkage mapping is demonstrated using the unc-119 locus of C. elegans. This quantitative PCR method provides an inexpensive, uniform, and automatable detection alternative for genetic mapping strategies in C. elegans or other organisms.

Multiplexed SNP genotyping using nanobarcode particle technology

Single-nucleotide polymorphisms (SNP) are the most common form of sequence variation in the human genome. Large-scale studies demand high-throughput SNP genotyping platforms. Here we demonstrate the potential of encoded nanowires for use in a particles-based universal array for high-throughput SNP genotyping. The particles are encoded sub-micron metallic nanorods manufactured by electroplating inert metals such as gold and silver into templates and releasing the resulting striped nanoparticles. The power of this technology is that the particles are intrinsically encoded by virtue of the different reflectivity of adjacent metal stripes, enabling the generation of many thousands of unique encoded substrates. Using SNP found within the cytochrome P450 gene family, and a universal short oligonucleotide ligation strategy, we have demonstrated the simultaneous genotyping of 15 SNP; a format requiring discrimination of 30 encoded nanowires (one per allele). To demonstrate applicability to real-world applications, 160 genotypes were determined from multiplex PCR products from 20 genomic DNA samples.

A nano-circular single-stranded DNA as a novel tool for SNPs detection

Analysis of single nucleotides polymorphisms (SNPs) is very important for the elucidation of gene-based physiological differences. For high-throughput applications, detection systems need to be highly selective, highly sensitive, and simple. In this study, we investigated whether synchronous transcription and translation from nano-circular single-stranded DNA (ssDNA) might be useful for the detection of SNPs. A nano-circular probe ssDNA was designed to contain codons for a (His)6 peptide, and the sense mRNA transcribed from this ssDNA contains a Shine-Dalgarno sequence, a start AUG codon, 6 His codons (CAU), and a stop UAG codon. The entire circular ssDNA is 55 nt and contains T20 as a linker sequence and a binding site for the target SNP-containing DNAs. Our results that show SNPs can be detected by the cell-free synthesis of the (His)6 peptide from this ssDNA. Because this method allows sequence distinction, signal amplification, and easy detection in one system, it should improve the efficacy of high-throughput gene analysis.

Detection of DNA Sequence Variations in Homo- and Heterozygous Samples via Molecular Mass Measurements by Electrospray Ionization Time-of-Flight Mass Spectrometry

The potential of ion-pair reversed-phase high-performance liquid chromatography on-line hyphenated to electrospray ionization time-of-flight mass spectrometry for the characterization of polymerase chain reaction (PCR) amplified nucleic acids was evaluated. For that purpose, a "SNP toolbox" was constructed by cloning and PCR-mediated site-directed in vitro mutagenesis at nucleotide position (ntp) 16,519 of a sequence-verified fragment of the human mitochondrial genome (ntps 15,900-599). Confirmatory sequencing demonstrated that within the sequences of the clones one and the same base was mutated to all other bases. Using these clones or equimolar mixtures of these clones as PCR templates, 51-401-bp-long amplicons were generated, which were used to determine the upper size limits of PCR products for the unequivocal detection of sequence variations in homo- and heterozygous samples. Based on the high mass spectrometric performance of the applied time-of-flight mass spectrometer, the unequivocal genotyping of all kinds of single base exchanges in PCR amplicons from heterozygous samples with lengths up to 254 base pairs (bp) was demonstrated. Considering homozygous samples, the successful genotyping of single base substitutions in up to 401-bp-long PCR products was possible. Consequently, the described hyphenated technique represents one of the most powerful mass spectrometric genotyping assays available today.

A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome

A high-throughput genotyping system for scoring single nucleotide polymorphisms (SNPs) has been developed. With this system, >1000 SNPs can be analyzed in a single assay, with a sensitivity that allows the use of single haploid cells as starting material. In the multiplex polymorphic sequence amplification step, instead of attaching universal sequences to the amplicons, primers that are unlikely to have nonspecific and productive interactions are used. Genotypes of SNPs are then determined by using the widely accessible microarray technology and the simple single-base extension assay. Three SNP panels, each consisting of >1000 SNPs, were incorporated into this system. The system was used to analyze 24 human genomic DNA samples. With 5 ng of human genomic DNA, the average detection rate was 98.22% when single probes were used, and 96.71% could be detected by dual probes in different directions. When single sperm cells were used, 91.88% of the SNPs were detectable, which is comparable to the level that was reached when very few genetic markers were used. By using a dual-probe assay, the average genotyping accuracy was 99.96% for 5 ng of human genomic DNA and 99.95% for single sperm. This system may be used to significantly facilitate large-scale genetic analysis even if the amount of DNA template is very limited or even highly degraded as that obtained from paraffin-embedded cancer specimens, and to make many unpractical research projects highly realistic and affordable.

[Pharmacogenetics and pharmacogenomics of cancers]

Sequencing the human genome brings new tools for the individualisation of cancer chemotherapy, firstly thanks to the identification of polymorphisms of genes involved in anticancer drug metabolism or activity (Pharmacogenetics), and secondly thanks to the determination of tumour gene expression profiles and their relationship to chemosensitivity and chemoresistance (Pharmacogenomics). A few functional polymorphisms have been known for a long time (thiopurine methyltransferase, glutathion S-transferases), but several new ones have been identified recently, at the level of the genes encoding drug targets (thymidylate synthase), at the level of DNA repair enzymes (XPD) or at the level of transport proteins (MDR1). On the other hand, the research of correlations between gene expression profiles and chemosensitivity has been performed on the in vitro models of the National Cancer Institute and may allow crucial improvements in the identification of patients who would best take advantage of a specific chemotherapy. Clinical trials, first on a retrospective basis, then on a prospective one, are implemented to validate this approach.

Genotyping of Plasmodium falciparum pyrimethamine resistance by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry

Increasing resistance, recrudescences, and treatment failure have led to the replacement of chloroquine with the combination of pyrimethamine (PYR) and sulfadoxine (SDX) as the first-line antimalarial drugs for treatment of uncomplicated Plasmodium falciparum malaria in several areas where this disease is endemic. The development of resistance to PYR-SDX is favored by incomplete treatment courses or by subtherapeutic levels in plasma. PYR-SDX resistance has been associated with several single-nucleotide polymorphisms (SNPs) in the P. falciparum dihydrofolate reductase (pfdhfr) and the P. falciparum dihydropteroate synthetase (pfdhps) genes. We have established assays based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) that conveniently allow the identification of SNPs associated with PYR resistance. Variants occurring at codon positions 16, 51, 59, and 108 of the pfdhfr gene were analyzed by MALDI-TOF MS in synthetic oligonucleotides to determine the detection threshold. In addition, 63 blood samples from subjects with P. falciparum parasitemia of various degrees were analyzed. The results were compared to those obtained by DNA sequencing of the respective gene fragment. The results of MALDI-TOF MS and DNA sequencing were consistent in 40 samples. In 23 samples two or three pfdhfr variants were detected by MALDI-TOF assays, whereas DNA-sequencing revealed one variant only. Simultaneous detection of two different mutations by biplex assays was, in principle, feasible. As demonstrated by the example of PYR resistance, MALDI-TOF MS allows for rapid and automated high-throughput assessment of drug sensitivity in P. falciparum malaria.

Cationic comb-type copolymers for DNA analysis

Genetic diagnoses, such as single nucleotide polymorphism (SNP) typing, allow elucidation of gene-based physiological differences, such as susceptibility to diseases and response to drugs, among individuals. Many detection technologies, including allele-specific hybridization, allele-specific primer extension and oligonucleotide ligation, are being used to discriminate SNP alleles. These methods still have many unsolved practical issues. In general they require adequate and specific hybridizations of primer or probe DNAs with target DNAs. This frequently needs optimization of the probe/primer structures and operating conditions. In nature, highly homology-sensitive hybridization is assisted by a nucleic acid chaperone that reduces the energy barrier associated with breakage and reassociation of nucleic base pairs. Here we report a simple, quick, precise but enzyme-free method for SNP analysis. The method uses cationic comb-type copolymers (CCCs) producing high nucleic acid chaperone activities. A single-base mismatch in 20-mer DNA can be detected within a few minutes at ambient temperatures (25-37 degrees C). Even without careful optimization processes, the method has the sensitivity to detect the mismatches causing subtle changes (Delta T(m) equals approximately 1 degree C) in duplex thermal stability. CCCs may have various bioanalytical applications where precise hybridization of nucleic acids is needed.

Paired mutation in core promoter region of HBV in hepatocellular carcinoma by TDI-FP assay

AIM

To detect the A₁₇₆₂ T and G₁₇₆₄ A paired mutations in the core promoter region of the HBV DNA in the hepatocellular carcinoma, to investigate the relationship between them, and to establish a new method for genotyping of mutation patterns.

METHODS

The target DNA fragment of the HBV core promoter region which contains the paired mutations was amplified by polymerase chain reaction and the FP value of the R110- or TAMRA-labeled ddNTP was detected by TDI-FP assay to determine the nt₁₇₆₂ and nt₁₇₆₄ genotype.

RESULTS

Of 20 cases of hepatocellular carcinoma, 18 (90%) was positive for HBV infection. Through TDI-FP assay, there were 13 /20 for T₁₇₆₂ and A₁₇₆₄ paired mutations, 1/20 heterozygous for T₁₇₆₂-A₁₇₆₄/ A₁₇₆₂-G₁₇₆₄ 4/20 negative for the TDI-FP assay. By sequencing, the positive and heterozygous mutations completely accorded with the TDI-FP assay. In the negative results, 2/4 had 8-nucleotide deletion mutation, thus the mutation detection primer could not complement with the template and gave rise to the "false" negative results. The rate of T₁₇₆₂-A₁₇₆₄ positive mutation rate of HBV DNA in heaptocellular carcinoma was 85%, heterozygous 5%, and wild-type 10%.

CONCLUSION

The HBV infection is very high in the heaptocellular carcinoma. The great frequency of the paired mutations in the core promoter indicates that the paired mutations may be significantly related to the pathogenesis of hepatocellular carcinoma. The established TDI-FP is suitable for high throughput and automated genotyping assays due to its rapid and simple manipulation.