Genetic mutation analysis by CE with LIF detection using inverse-flow derivatization of DNA fragments

ABO genotyping by capillary electrophoresis

Single-strand conformation polymorphism by capillary electrophoresis (SSCP-CE) has been developed to detect single nucleotide mutations. This method is used to identify the ABO alleles A(1), A(1v), B, O(1), O(1v), and O(2) in this chapter. Four amplicons (112, 121, 123, and 160 bp) labeled with fluorescence are separately amplified by polymerase chain reaction from exons 6 and 7 of ABO gene. These four fragments are combined into a single tube for SSCP-CE analysis using native gel to identify their single nucleotide polymorphism. This method can fast screen ABO genotypes from unknown samples and will be valuable in clinical transfusion or forensic applications.

Capillary electrophoretic genotyping of epidermal growth factor receptor for pharmacogenomic assay of lung cancer therapy

In this research, a universal multiplex PCR method combining capillary gel electrophoresis was established for simultaneous analysis of mutations in exons 18-21 of EGFR kinase domain gene. After rinsing of the gel solution (1 × TBE buffer containing 2% HEC and 1.5% HPC), the diluted PCR sample was electrokinetically injected and separated at 35°C. Several parameters were investigated for method optimization, including the kinds of polymer, capillary temperature and separation voltage. Under optimal conditions, time taken for analyzing mutations of EGFR kinase domain gene in lung cancer patients was short (within 15 min). A total of 50 lung cancer patients' tumor tissues were analyzed, and two frequent mutations associated with therapeutic efficiency of lung cancer were identified, including deletion of exon 19 (8/50) and L858R point mutation in exon 21 (12/50). This method is feasible for application in pharmacogenomic assay of lung cancer therapy. By applying this simple and effective method for genotyping of lung cancer patients, the information of pharmacogenomics was supplied for lung cancer therapy and to assist diagnosis to prolong patients' lives.

ABO genotyping by single strand conformation polymorphism--using CE

This study describes a novel method of ABO genotyping using amplicons generated by PCR-SSCP and separated by CE. We describe four amplicons with sizes of 112, 121, 123 and 160 bp based on SSCP analysis. These amplicons are amplified from exons 6 and 7 and include polymorphic sites of cDNA 261, 297, 467, 526, 646, 657, 681, 703, 1061 and 1096 generated from the ABO gene. The positions of the SSCP alleles, when rescaled using SSCP pattern as the mobility values based on an internal standard ranged, ranged from 146 to 210. The mobility variations of alleles with 1-4 SNPs within the same amplicons were from 1.88 to 12.01. These wide mobility differences allow for unambiguous allele determination. The use of different fluorescent dyes allows for the identification of two fragments with overlapping size ranges. The validity of the test was confirmed based on the SD of the mobility values from the eleven fragments of allelic ladder and it never exceeded 0.37. The mean values of the mobility variation between the samples and the ladders for the four amplicons ranged only from 0.05 to 0.39. This method was shown to successfully identify alleles A(1), A(1v), B, O(1), O(1v) and O(2) in tested samples. Since the largest amplicons are only 160 bp, this method is ideal for the fast screening ABO genotypes from trace, or seriously, degraded samples and may be valuable in clinical transfusion or forensic applications.

A new strategy to screen MMR genes in Lynch Syndrome: HA-CAE, MLPA and RT-PCR

AIMS

Hereditary non-polyposis colon cancer (HNPCC) is an autosomal dominant disorder that is genetically heterogeneous because of underlying mutations in mismatch repair (MMR) genes, primarily MLH1, MSH2 and MSH6. One challenge to correctly diagnose HNPCC is that the large size of the causative genes makes identification of mutations both labour intensive and expensive.

METHODS

Our heteroduplex analysis by capillary array electrophoresis (HA-CAE) method, previously developed to increase the throughput and allow other multi-exon genes to be scanned, has been adapted for MMR genes. The altered peak patterns were then sequenced. Furthermore, the mutational scanning was completed using the Multiplex Ligation-Dependent Probe Amplification (MLPA) test in all negative HA-CAE cases, and these results were confirmed by RT-PCR.

RESULTS

We studied 216 individuals belonging to 100 unrelated families that met the Amsterdam I/II criteria for HNPCC. We detected 40 different variants that are classified as follows: 8 (20%) deleterious mutation, 8 (20%) unknown pathogenic significance variants and 24 (60%) coding and intronic sequence variants. Pathogenic mutations were detected in 12% of the families and about 42% of these had a deletion variant. Unknown pathogenic significance variants (UVs) affected 13% of the families. We also found 12.5% of novel polymorphisms in the rest of the variants. CONCLUDING: In short, using a combined method that includes HA-CAE, MLPA and RT-PCR, it is possible to detect the entire mutational spectrum of MMR genes. Twenty percent of the mutations found in the three genes have not been reported before. Relatives at risk will be offered predictive molecular analysis with potential exclusion of non-carriers of mutations.

Single nucleotide polymorphism detection in the hMSH2 gene using conformation-sensitive CE

CE allows for highly reproducible analysis of DNA fragments which can be used to detect DNA mutations including SNPs. We have utilized a simple and direct CE analysis method for SNP analysis called conformation-sensitive CE (CSCE), based on the principle of single nucleotide different to produce conformational changes in the mildly denaturing solvent system. This method was applied to analysis of a mutation in the promoter region of the hMSH2 gene. This gene belongs to the human DNA mismatch repair system, which is responsible for recognizing and repairing mispaired nucleotides, and mutations in the hMSH2 gene are known to cause hereditary nonpolyposis colorectal cancer (HNPCC). PCR fragments generated from the promoter region of the hMSH2 gene, displaying either a C/C homozygote, C/T heterozygote, or T/T homozygote genotype, did not require further pretreatment before electrokinetic injection. The CE separation, using a 1xTris-borate-EDTA (TBE) buffer containing 3% w/v hydroxylethyl cellulose (HEC) and 6 M urea, was performed under reverse polarity with a separation temperature of 15 degrees C. The genotypes of 204 healthy volunteers and 13 colorectal cancer patients were determined using CSCE, and the results confirmed by DNA sequencing. While the CSCE separations were shown to be highly reproducible and sensitive for screening large populations, no correlation was observed between cancer patients and this hMSH2 gene polymorphism.

Characterization of EvaGreen and the implication of its physicochemical properties for qPCR applications

Background

EvaGreen (EG) is a newly developed DNA-binding dye that has recently been used in quantitative real-time PCR (qPCR), post-PCR DNA melt curve analysis and several other applications. However, very little is known about the physicochemical properties of the dye and their relevance to the applications, particularly to qPCR and post PCR DNA melt curve analysis. In this paper, we characterized EG along with a widely used qPCR dye, SYBR Green I (SG), for their DNA-binding properties and stability, and compared their performance in qPCR under a variety of conditions.

Results

This study systematically compared the DNA binding profiles of the two dyes under different conditions and had these findings: a) EG had a lower binding affinity for both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) than SG; b) EG showed no apparent preference for either GC- or AT-rich sequence while SG had a slight preference for AT-rich sequence; c) both dyes showed substantially lower affinity toward ssDNA than toward dsDNA and even lower affinity toward shorter ssDNA fragments except that this trend was more pronounced for EG. Our results also demonstrated that EG was stable both under PCR condition and during routine storage and handling. In the comparative qPCR study, both EG and SG exhibited PCR interference when used at high dye concentration, as evident from delayed Ct and/or nonspecific product formation. The problem worsened when the chain extension time was shortened or when the amplicon size was relatively long (>500 bp). However, qPCR using EG tolerated a significantly higher dye concentration, thus permitting a more robust PCR signal as well as a sharper and stronger DNA melt peak. These differences in qPCR performance between the two dyes are believed to be attributable to their differences in DNA binding profiles.

Conclusion

These findings suggest that an ideal qPCR dye should possess several DNA-binding characteristics, including a "just right" affinity for dsDNA and low or no affinity for ssDNA and short DNA fragments. The favorable DNA-binding profile of EG, coupled with its good stability and instrument-compatibility, should make EG a promising dye for qPCR and related applications.