Diagnosis of sickle-cell disease with a universal heteroduplex generator

Rapid and simple detection of hot spot point mutations of epidermal growth factor receptor, BRAF, and NRAS in cancers using the loop-hybrid mobility shift assay

A simple and rapid method to detect the epidermal growth factor receptor hot spot mutation L858R in lung adenocarcinoma was developed based on principles similar to the universal heteroduplex generator technology. A single-stranded oligonucleotide with an internal deletion was used to generate heteroduplexes (loop-hybrids) bearing a loop in the complementary strand derived from the polymerase chain reaction product of the normal or mutant allele. By placing deletion in the oligonucleotide adjacent to the mutational site, difference in electrophoretic mobility between loop-hybrids with normal and mutated DNA was distinguishable in a native polyacrylamide gel. The method was also modified to detect in-frame deletion mutations of epidermal growth factor receptor in lung adenocarcinomas. In addition, the method was adapted to detect hot spot mutations in the B-type Raf kinase (BRAF) at V600 and in a Ras-oncogene (NRAS) at Q61, the mutations commonly found in thyroid carcinomas. Our mutation detection system, designated the loop-hybrid mobility shift assay was sensitive enough to detect mutant DNA comprising 7.5% of the total DNA. As a simple and straightforward mutation detection technique, loop-hybrid mobility shift assay may be useful for the molecular diagnosis of certain types of clinical cancers. Other applications are also discussed.

Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay

Drug-resistant viruses may be present as minority variants during early treatment failures or following discontinuation of failed antiretroviral regimens. A limitation of the traditional direct PCR population sequencing method is its inability to detect human immunodeficiency virus type 1 (HIV-1) variants present at frequencies lower than 20%. A drug resistance genotyping assay based on the isolation and DNA sequencing of minority HIV protease variants is presented here. A multiple-codon-specific heteroduplex generator probe was constructed to improve the separation of HIV protease genes varying in sequence at 12 codons associated with resistance to protease inhibitors. Using an RNA molecule as probe allowed the simple sequencing of protease variants isolated as RNA/DNA heteroduplexes with different electrophoretic mobilities. The protease gene RNA heteroduplex generator-tracking assay (RNA-HTA) was tested on plasma quasispecies from 21 HIV-1-infected persons in whom one or more protease resistance mutations emerged during therapy or following initiation of salvage regimens. In 11 of 21 cases, RNA-HTA testing of virus from the first episode of virologic failure identified protease resistance mutations not seen by population-based PCR sequencing. In 8 of these 11 cases, all of the low-frequency drug resistance mutations detected exclusively by RNA-HTA during the first episode became detectable by population-based PCR sequencing at the later time point. Distinct sets of protease mutations could be linked on different genomes in patients with high-frequency protease gene lineages. The enhanced detection of minority drug resistance variants using a sequencing-based assay may improve the efficacy of genotype-assisted salvage therapies.

Rapid detection of exon 1 NRAS gene mutations using universal heteroduplex generator technology

Specific NRAS oncogene missense mutations have been frequently found in some tumors and several hematological diseases, especially in those of myeloid origin. There is a wide range of PCR-based methods for screening and detection of NRAS exon 1 single-base substitutions. However, there are disadvantages and ambiguities associated with these techniques because all of them require either separate probes, separate PCR amplifications, or complicated post-PCR manipulations. This report describes a new approach for detection of NRAS gene mutations at codon 12 and 13 based on the DNA heteroduplex analysis method. The strategy relies upon differential electrophoretic behavior of induced heteroduplex molecules formed by cross-hybridization of two PCR-amplified species, the sample under analysis and the synthetic universal heteroduplex generator (UHG). The screening of a panel of all codon 12 and 13 NRAS mutant DNA variants indicated that this approach discriminates all 12 relevant mutations. The sensitivity of the method was estimated by a competitive assay where mutant alleles could be detected at a dilution level of 1 to 16 wild-type alleles. This UHG technology was tested on some clinical samples previously studied by PCR-ASO. This methodology is highly specific, sensitive, and achieves an appreciable reduction in workload and time because it requires one PCR amplification followed by polyacrylamide gel electrophoresis in standard conditions. We propose that this new approach may be applied as an alternative strategy for codon 12-13 NRAS mutations and it could be easily incorporated into the range of routine assays performed in oncology laboratories.

Sickle cell disease--pathophysiology, clinical and diagnostic implications

We review the current knowledge of the pathophysiology of sickle cell disease (SCD), the clinical complications and the state of the art in SCD diagnostics. Today, a flexible laboratory concept allows the fast and economic clarification of the patients' sickle cell hemoglobin (HbS) status, e.g. additional compound heterozygosities. In contrast to a well-investigated pathophysiology of the disease, factors influencing the severity of symptoms as well as some laboratory findings in SCD still lack a final explanation. In this review, we focus on red cell lysis resistance as an additional diagnostic tool in SCD. There is a need for further studies regarding lysis resistance in blood samples from patients with HbS.

Heteroduplex analysis in medical entomology: A rapid and sensitive sequence-based tool for population and phylogenetic studies

Classical studies on the insect vectors of parasitic diseases have relied on morphological, biochemical and cytological characters to classify vector species. These are often inadequate for a detailed dissection of the dynamics of the parasite-vector relationship. Molecular techniques have the potential to provide more reliable data on various aspects of vector biology, including population genetics, molecular phylogenetics, and molecular differentiation and classification of closely related species. However, most molecular techniques are expensive, cumbersome or difficult to apply to the analysis of a large number of samples. Here, Jianming Tang and Tom Unnasch discuss the practical advantages of heteroduplex analysis for the study of medically important vectors, using the black flies that serve as vectors for the filarial parasite Onchocerca volvulus as an example. This technique is simple, rapid, inexpensive and capable of detecting minor differences among DNA sequences.

Simultaneous genotyping for all three known structural mutations in the human mannose-binding lectin gene

We describe a rapid and simple method for genotyping the three known structural mutations within exon 1 of the mannan-binding lectin (MBL) gene. A PCR-amplifiable synthetic DNA (Universal Heteroduplex Generator) was annealed to genomic PCR product from exon 1 to generate unique DNA heteroduplexes for each mutation. Heteroduplexes were then resolved by non-denaturing polyacrylamide gel electrophoresis. The technique was initially validated with previously typed samples and then applied to previously untyped samples with the results confirmed by DNA sequencing.

Rapid detection of hemoglobin variants by mutagenically separated polymerase chain reaction (MS-PCR)

The detection of molecular defects of hemoglobin variants using mutagenically separated polymerase chain reaction (MS-PCR) was applied in this study. Using different lengths of allele-specific mutagenic primers, normal and mutant alleles of hemoglobin genes were amplified in the same reaction tube. Subsequent gel electrophoresis showed at least one of the two allelic products at the same loci or at least two of the several allelic products at different loci. We employed MS-PCR to test the following hemoglobin variants: Hb Constant Spring (Hb CS), Hb E, Hb G-Taichung, Hb J-Meinung, and Hb Kaohsiung. The results were the same as those obtained by amplified created reaction sites (ACRS) or direct sequencing. We conclude that the MS-PCR provides a rapid and simple alternative to other techniques for mutation detection in hemoglobin variants. Moreover, the principle can be extended to other genetic diseases.

Detection of beta-thalassaemia mutations using DNA heteroduplex generator molecules

In this report we describe a rapid polymerase chain reaction (PCR) based method for the detection of beta-thalassaemia (beta-thal) mutations. This method is based on the visualization of unique DNA heteroduplex banding patterns, following non-denaturing polyacrylamide gel electrophoresis, resulting from hybridization between mutant PCR products and synthetic DNA heteroduplex generator molecules. Using the Singaporean population, which consists of Chinese, Malay and Asian Indian ethnic groups, as a model, we have constructed and evaluated three DNA heteroduplex generator molecules for the detection of the common beta-thalassaemia mutations found in this population. The results show that these three molecules are capable of detecting approximately 95% of the mutations found in the Singaporean population. We propose that this technology may be applied as an alternative screening strategy for beta-thalassaemia mutations because it is technically simple, flexible, cost-effective, and requires only minimal laboratory resources.

Applications of heteroduplex analysis for mutation detection in disease genes

Double-stranded heteroduplex molecules that form between a mutant and wild-type DNA strand are often distinguished from homoduplex molecules upon gel electrophoresis. This method, heteroduplex analysis (HA), can be performed rapidly without radioisotopes or specialized equipment. Modifications and enhancements of the HA method have been developed that increase the sensitivity of detection of single-base pair alterations.