Microdevice DNA forensics by the simple tandem repeat method

A valveless microfluidic device for integrated solid phase extraction and polymerase chain reaction for short tandem repeat (STR) analysis

A valveless microdevice has been developed for the integration of solid phase extraction (SPE) and polymerase chain reaction (PCR) on a single chip for the short tandem repeat (STR) analysis of DNA from a biological sample. The device consists of two domains--a SPE domain filled with silica beads as a solid phase and a PCR domain with an ~500 nL reaction chamber. DNA from buccal swabs was purified and amplified using the integrated device and a full STR profile (16 loci) resulted. The 16 loci Identifiler® multiplex amplification was performed using a non-contact infrared (IR)-mediated PCR system built in-house, after syringe-driven SPE, providing an ~80-fold and 2.2-fold reduction in sample and reagent volumes consumed, respectively, as well as an ~5-fold reduction in the overall analysis time in comparison to conventional analysis. Results indicate that the SPE-PCR system can be used for many applications requiring genetic analysis, and the future addition of microchip electrophoresis (ME) to the system would allow for the complete processing of biological samples for forensic STR analysis on a single microdevice.

Microarray-based STR genotyping using RecA-mediated ligation

We describe a novel assay capable of accurately determining the length of short tandem repeat (STR) alleles. STR genotyping is achieved utilizing RecA-mediated ligation (RML), which combines the high fidelity of RecA-mediated homology searching with allele-specific ligation. RecA catalyzes the pairing of synthetic oligonucleotides with one strand of a double-stranded DNA target, in this case a PCR amplicon. Ligation occurs only when two adjacent oligonucleotides are base paired to the STR region without any overlap or gap. RecA activity is required to overcome the inherent difficulty of annealing repeated sequences in register. This assay is capable of determining STR genotypes of human samples, is easily adapted to high throughput or automated systems and can have widespread utility in diagnostic and forensic applications.

Vertical hydrodynamic focusing in glass microchannels

Vertical hydrodynamic focusing in microfluidic devices is investigated through simulation and through direct experimental verification using a confocal microscope and a novel form of stroboscopic imaging. Optimization for microfluidic cytometry of biological cells is examined. By combining multiple crossing junctions, it is possible to confine cells to a single analytic layer of interest. Subtractive flows are investigated as a means to move the analysis layer vertically in the channel and to correct the flatness of this layer. The simulation software (ADINA and Coventor) is shown to accurately capture the complex dependencies of the layer interfaces, which vary strongly with channel geometry and relative flow rates.

AOTF-based multicolor fluorescence detection for short tandem repeat (STR) analysis in an electrophoretic microdevice

An acousto-optic tunable filter (AOTF) has been used to perform multicolor fluorescence detection for four and five-color short tandem repeat (STR) analysis on glass microchips. Matrix files were initially generated by collecting and comparing the laser-induced fluorescence emission of the labels specific to a particular STR kit, and raw data was processed to remove spectral overlap. The AmpFlSTR kits used in this work include Profiler Plus and COfiler, which are four-color kits used in tandem to address the core STR loci, as well as the five-color Identifiler kit, which contains each of the loci. In contrast to previous reports on multicolor detection for STR analysis on microchips, this detection system is characterized by a single filter and detector, and reports the first five-color genotyping application on-chip. This capability matches the portability and reduced scale of the microchip with the state-of-the-art in multicolor STR analysis kits.

Forensic DNA Analysis on Microfluidic Devices: A Review

The advent of microfluidic technology for genetic analysis has begun to impact forensic science. Recent advances in microfluidic separation of short-tandem-repeat (STR) fragments has provided unprecedented potential for improving speed and efficiency of DNA typing. In addition, the analytical processes associated with sample preparation--which include cell sorting, DNA extraction, DNA quantitation, and DNA amplification--can all be integrated with the STR separation in a seamless manner. The current state of these microfluidic methods as well as their advantages and potential shortcomings are detailed. Recent advances in microfluidic device technology, as they pertain to forensic DNA typing, are discussed with a focus on the forensic community.