Dramatic increase in signal by integration of polymerase chain reaction and hybridization on surface of DNA microarray

Direct Detection of Drug-Resistant Hepatitis B Virus in Serum Using a Dendron-Modified Microarray

Background/Aims

Direct sequencing is the gold standard for the detection of drug-resistance mutations in hepatitis B virus (HBV); however, this procedure is time-consuming, labor-intensive, and difficult to adapt to high-throughput screening. In this study, we aimed to develop a dendron-modified DNA microarray for the detection of genotypic resistance mutations and evaluate its efficiency.

Methods

The specificity, sensitivity, and selectivity of dendron-modified slides for the detection of representative drug-resistance mutations were evaluated and compared to those of conventional slides. The diagnostic accuracy was validated using sera obtained from 13 patients who developed viral breakthrough during lamivudine, adefovir, or entecavir therapy and compared with the accuracy of restriction fragment mass polymorphism and direct sequencing data.

Results

The dendron-modified slides significantly outperformed the conventional microarray slides and were able to detect HBV DNA at a very low level (1 copy/μL). Notably, HBV mutants could be detected in the chronic hepatitis B patient sera without virus purification. The validation of our data revealed that this technique is fully compatible with sequencing data of drug-resistant HBV.

Conclusions

We developed a novel diagnostic technique for the simultaneous detection of several drug-resistance mutations using a dendron-modified DNA microarray. This technique can be directly applied to sera from chronic hepatitis B patients who show resistance to several nucleos(t)ide analogues.

Genotyping of chimerical BCR-ABL1 RNA in chronic myeloid leukemia by integrated DNA chip

Chronic myelogenous leukemia (CML) and Philadelphia chromosome-positive (Ph(+)) acute lymphoblastic leukemia (ALL) are associated with fusion of the BCR and ABL1 genes by chromosome translocation. The chimerical BCR-ABL1 gene encodes different fusion proteins that vary in size, depending on the breakpoint in the BCR region. Different types of fusion genes in CML and Ph(+) ALL are thought to be related to the clinical course and outcome of each patient. Currently, the genotypes are determined by PCR, followed by gel electrophoresis or DNA sequencing (among other methodologies). Our major aim was to develop a diagnostic method for CML genotyping by means of an integrated process of DNA microarray. Here, we describe a method of integrated multiplex reverse transcription, asymmetric PCR, and hybridization, all in the same reaction mixture in a chamber assembled on the surface of capture oligonucleotide probes immobilized on a glass slide. The integrated system successfully identified the four predominant types of chimerical BCR-ABL1 RNA (b3a2, b2a2, e1a2, and c3a2), which together account for 98% of CML cases. The integrated multiplex system also had a high sensitivity of detection (as little as 200 molecules of target RNA molecules). The integrated process saves time and effort, and it also the advantage of minimizing the steps needed for automated detection of different types of chimerical CML RNA.

Dramatic increase in the signal and sensitivity of detection via self-assembly of branched DNA

In molecular testing using PCR, the target DNA is amplified via PCR and the sequence of interest is investigated via hybridization with short oligonucleotide capture probes that are either in a solution or immobilized on solid supports such as beads or glass slides. In this report, we report the discovery of assembly of DNA complex(es) between a capture probe and multiple strands of the PCR product. The DNA complex most likely has branched structure. The assembly of branched DNA was facilitated by the product of asymmetric PCR. The amount of branched DNA assembled was increased five fold when the asymmetric PCR product was denatured and hybridized with a capture probe all in the same PCR reaction mixture. The major branched DNA species appeared to contain three reverse strands (the strand complementary to the capture probe) and two forward strands. The DNA was sensitive to S1 nuclease suggesting that it had single-stranded gaps. Branched DNA also appeared to be assembled with the capture probes immobilized on the surface of solid support when the product of asymmetric PCR was hybridized. Assembly of the branched DNA was also increased when hybridization was performed in complete PCR reaction mixture suggesting the requirement of DNA synthesis. Integration of asymmetric PCR, heat denaturation and hybridization in the same PCR reaction mixture with the capture probes immobilized on the surface of solid support achieved dramatic increase in the signal and sensitivity of detection of DNA. Such a system should be advantageously applied for development of automated process for detection of DNA.