Use of GC clamps in DHPLC mutation scanning

The use of denaturing high performance liquid chromatography (DHPLC) for mutation scanning of hereditary cancer genes

Denaturing high performance liquid chromatography (DHPLC) facilitates automated mutation scanning of PCR products with the ability to detect nearly 100% of sequence variants including single nucleotide substitutions and small insertions or deletions. It has particular application for genetic screening in inherited conditions; both for the initial identification of a mutation in disease carriers followed by sequence analysis, and for screening "at-risk" individuals prior to the development of disease in families with a known mutation. Specifically, in familial cancer syndromes, DHPLC has been reported as a genetic screening tool for the risk of developing breast and ovarian cancer (BRCA1), von Hippel Lindau disease (VHL), Cowden syndrome (PTEN), and Multiple Endocrine Neoplasia types 1 and 2 (MEN1 and RET). This chapter focuses on the methodologies specific to the WAVE System for Mutation Detection 2100 (Transgenomic Inc., Omaha, NE, USA) and highlights the use of Navigator software (Transgenomic Inc.), including data analysis with scatter graphs.

Application of denaturing high-performance liquid chromatography in microbial ecology: fermentor sludge, compost, and soil community profiling

Genetic fingerprinting methods, such as denaturing gradient gel electrophoresis (DGGE), are used in microbial ecology for the analysis of mixed microbial communities but are associated with various problems. In the present study we used a new alternative method: denaturing high-performance liquid chromatography (dHPLC). This method was previously shown to work with samples from water and gut flora but had not yet been applied to complex environmental samples. In contrast to other publications dealing with dHPLC, we used a commonly available HPLC system. Samples from different origins (fermentor sludge, compost, and soil), all ecologically significant, were tested, and the 16S rRNA gene was amplified via PCR. After optimization of the HPLC elution conditions, amplicons of pure cultures and mixed microbial populations could be separated successfully. Systematic differentiation was carried out by a cloning approach, since fraction collection of the peaks did not result in satisfactory fragment separation. dHPLC was evaluated as a tool for microbial community analysis on a genetic level and demonstrated major improvements compared to gel-based fingerprinting methods, such as DGGE, that are commonly used in microbial ecology.

Enhanced detection of TP53 mutations using a GC-clamp in denaturing high performance liquid chromatography

Although denaturing gradient gel electrophoresis (DGGE) is a highly effective technique for screening for TP53 mutations, the use of denaturing high performance liquid chromatography (DHPLC) is a growing methodology. This report describes a comparison between DHPLC and DGGE in the detection of TP53 mutations in hematopoietic cell lines and lymphomas. In addition, the improved effectiveness of guanine cytosine (GC)-clamped DHPLC for TP53 screening is detailed. Thirty DNA samples with known TP53 mutations in the hotspot region of codons 5-8, previously identified by DGGE, were analyzed by DHPLC. We found 100% concordance in mutation detection by DHPLC with DGGE. Similar to the improved efficacy observed in DGGE, the addition of 40 nucleotide GC-clamps composed of guanine and cytosine bases at one end of the product enhanced the detection of a mutation pattern by DHPLC. DHPLC of GC-clamped products is a viable and faster alternative method for screening TP53 mutations.

Possible involvement of CCT5, RGS3, and YKT6 genes up-regulated in p53-mutated tumors in resistance to docetaxel in human breast cancers

BACKGROUND

Present study was aimed to investigate the relationship of p53 mutation status with response to docetaxel in breast cancers. In addition, attempts were made to identify the genes differentially expressed between p53-wild and p53-mutated breast tumors and to study their relationship with response to docetaxel.

METHODS

Mutational analysis of p53 was done in 50 breast tumor samples obtained from primary breast cancer patients (n = 33) and locally recurrent breast cancer patients (n = 17) before docetaxel therapy. Response to docetaxel was evaluated clinically. Gene expression profiling (n = 2,412) was conducted by adapter-tagged competitive-PCR in 186 tumor samples, which were also analyzed in their p53 mutational status in order to identify the differentially expressed genes according to p53 mutation status and their relationship with response to docetaxel.

RESULTS

Response rate of p53-mutated tumors (44%) was lower than that of p53-wild tumors (62%) though there was no statistical significance (P = 0.23). Of 2412 genes, mRNA expression of 13 genes was significantly different between p53-wild and p53-mutated tumors. Of these 13 genes, mRNA expression of CCT5, RGS3, and YKT6 was significantly up-regulated in p53-mutated tumors and associated with a low response rate to docetaxel. Treatment of MCF-7 cells with siRNA specific for CCT5, RGS3, or YKT6 resulted in a significant enhancement of docetaxel-induced apoptosis.

CONCLUSIONS

CCT5, RGS3, and YKT6 mRNA expressions, which are up-regulated in p53-mutated breast tumors, might be implicated in resistance to docetaxel and clinically useful in identifying the subset of breast cancer patients who may or may not benefit from docetaxel treatment.

Electrophoresis of DNA in human genetic diagnostics – state-of-the-art, alternatives and future prospects

Electrophoretic separation of nucleic acids according to their molecular weights has dominated the methods' spectrum in molecular genetics for nearly half a century. We review the current methodological basis and evaluate its impact with special reference to new developments in the microarray technology. Although electrophoresis may be made redundant for many applications in DNA diagnostics within a few years, a number of electrophoretic vestiges will remain irreplaceable in the foreseeable future.