An optimized microchip electrophoresis system for mutation detection by tandem SSCP and heteroduplex analysis for p53 gene exons 5-9

With the complete sequencing of the human genome, there is a growing need for rapid, highly sensitive genetic mutation detection methods suitable for clinical implementation. DNA-based diagnostics such as single-strand conformational polymorphism (SSCP) and heteroduplex analysis (HA) are commonly used in research laboratories to screen for mutations, but the slab gel electrophoresis (SGE) format is ill-suited for routine clinical use. The translation of these assays from SGE to microfluidic chips offers significant speed, cost, and sensitivity advantages; however, numerous parameters must be optimized to provide highly sensitive mutation detection. Here we present a methodical study of system parameters including polymer matrix, wall coating, analysis temperature, and electric field strengths on the effectiveness of mutation detection by tandem SSCP/HA for DNA samples from exons 5-9 of the p53 gene. The effects of polymer matrix concentration and average molar mass were studied for linear polyacrylamide (LPA) solutions. We determined that a matrix of 8% w/v 600 kDa LPA provides the most reliable SSCP/HA mutation detection on chips. The inclusion of a small amount of the dynamic wall-coating polymer poly-N-hydroxyethylacrylamide in the matrix substantially improves the resolution of SSCP conformers and extends the coating lifetime. We investigated electrophoresis temperatures between 17 and 35 degrees C and found that the lowest temperature accessible on our chip electrophoresis system gives the best condition for high sensitivity of the tandem SSCP/HA method, especially for the SSCP conformers. Finally, the use of electrical fields between 350 and 450 V/cm provided rapid separations (<10 min) with well-resolved DNA peaks for both SSCP and HA.     

Analytical validation of quality control materials for Huntington’s disease examination

The expansion of molecular diagnostics using nucleic acid technologies in clinical and public health practice has increased the need for appropriate reference materials and verified quality-control materials for quality assurance, test validation, proficiency testing and the development of new examination procedures. Good laboratory practice requires the use of reference materials to establish an examination procedure and assess the variability of the results. Reference materials are also required to assess the assay on a daily basis and to normalize results collected among different laboratories. Despite the growing volume, the rapidly increasing number of tests being offered, and the necessary routine use, certified reference materials are often not available. There is a wide range of human genetic bio-assays for which there are no available traceable certified reference materials. Several initiatives have been organized to provide well-characterized quality control specimens (e.g., cell lines) with known DNA mutations for use in diagnostics. Mutations are confirmed with bi-directional DNA sequence analysis, which is considered the reference examination procedure. In the field of personalized medicine, NIST has created and validated Standard Reference Material^® 2399 for fragile X examinations. Herein we describe our characterization of candidate reference materials for Huntington’s disease genetic examination. Bi-directional DNA sequencing confirmed the size of the CAG repeat contained on each allele from patient derived materials. Amplification and capillary electrophoresis of the CAG repeats had an uncertainty ranging from 2.06%CV to 7.83%CV.     

Blinded study determination of high sensitivity and specificity microchip electrophoresis-SSCP/HA to detect mutations in the p53 gene

Knowledge of the genetic changes that lead to disease has grown and continues to grow at a rapid pace. However, there is a need for clinical devices that can be used routinely to translate this knowledge into the treatment of patients. Use in a clinical setting requires high sensitivity and specificity (>97%) in order to prevent misdiagnoses. Single‐strand conformational polymorphism (SSCP) and heteroduplex analysis (HA) are two DNA‐based, complementary methods for mutation detection that are inexpensive and relatively easy to implement. However, both methods are most commonly detected by slab gel electrophoresis, which can be labor‐intensive, time‐consuming, and often the methods are unable to produce high sensitivity and specificity without the use of multiple analysis conditions. Here, we demonstrate the first blinded study using microchip electrophoresis (ME)‐SSCP/HA. We demonstrate the ability of ME‐SSCP/HA to detect with 98% sensitivity and specificity >100 samples from the p53 gene exons 5–9 in a blinded study in an analysis time of <10 min.     

Study of structural and electronic transport properties of Ce-doped LaMnO3

The structural and electronic transport properties of La_1−x Ce _x MnO₃ (x=0.0–1.0) have been studied. All the samples exhibit orthorhombic crystal symmetry and the unit cell volume decreases with Ce doping. They also make a metal-insulator transition (MIT) and transition temperature increases with increase in Ce concentration up to 50% doping. The system La_0.5Ce_0.5MnO₃ also exhibits MIT instead of charge-ordered state as observed in the hole doped systems of the same composition.     

Two connected inverse spectral transforms

We establish a transformation which connects the potentials of the one-dimensional Dirac and Klein-Gordon operators. This transformation links the solutions of the nonlinear evolution equations solvable by means of the two inverse spectral transforms which use the Dirac and Klein-Gordon direct and inverse spectral problems.