Assessing genetic polymorphisms using DNA extracted from cells present in saliva samples

<p>Abstract</p> <p>Background</p> <p>Technical advances following the Human Genome Project revealed that high-quality and -quantity DNA may be obtained from whole saliva samples. However, usability of previously collected samples and the effects of environmental conditions on the samples during collection have not been assessed in detail. In five studies we document the effects of sample volume, handling and storage conditions, type of collection device, and oral sampling location, on quantity, quality, and genetic assessment of DNA extracted from cells present in saliva.</p> <p>Methods</p> <p>Saliva samples were collected from ten adults in each study. Saliva volumes from .10-1.0 ml, different saliva collection devices, sampling locations in the mouth, room temperature storage, and multiple freeze-thaw cycles were tested. One representative single nucleotide polymorphism (SNP) in the catechol-<it>0</it>-methyltransferase gene (COMT rs4680) and one representative variable number of tandem repeats (VNTR) in the serotonin transporter gene (5-HTTLPR: serotonin transporter linked polymorphic region) were selected for genetic analyses.</p> <p>Results</p> <p>The smallest tested whole saliva volume of .10 ml yielded, on average, 1.43 ± .77 μg DNA and gave accurate genotype calls in both genetic analyses. The usage of collection devices reduced the amount of DNA extracted from the saliva filtrates compared to the whole saliva sample, as 54-92% of the DNA was retained on the device. An "adhered cell" extraction enabled recovery of this DNA and provided good quality and quantity DNA. The DNA from both the saliva filtrates and the adhered cell recovery provided accurate genotype calls. The effects of storage at room temperature (up to 5 days), repeated freeze-thaw cycles (up to 6 cycles), and oral sampling location on DNA extraction and on genetic analysis from saliva were negligible.</p> <p>Conclusions</p> <p>Whole saliva samples with volumes of at least .10 ml were sufficient to extract good quality and quantity DNA. Using 10 ng of DNA per genotyping reaction, the obtained samples can be used for more than one hundred candidate gene assays. When saliva is collected with an absorbent device, most of the nucleic acid content remains in the device, therefore it is advisable to collect the device separately for later genetic analyses.</p

Robust acoustic particle manipulation: a thin-reflector design for moving particles to a surface

Existing ultrasonic manipulation devices capable of pushing particles to a surface (“quarter-wave” devices) have significant potential in sensor applications. A configuration for achieving this that uses the first thickness resonance of a layered structure with both a thin reflector layer and thin-fluid layer is described here. Crucially, this mode is efficient with lossy reflector materials such as polymers, produces a more uniform acoustic radiation force at the reflector, and is less sensitive to geometric variations than previously described quarter-wave devices. This design is thus expected to be suitable for mass produced, disposable device

Modelling of particle paths passing through an ultrasonic standing wave

Within an ultrasonic standing wave particles experience acoustic radiation forces causing agglomeration at the nodal planes of the wave. The technique can be used to agglomerate, suspend, or manipulate particles within a flow. To control agglomeration rate it is important to balance forces on the particles and, in the case where a fluid/particle mix flows across the applied acoustic field, it is also necessary to optimise fluid flow rate.To investigate the acoustic and fluid forces in such a system a particle model has been developed, extending an earlier model used to characterise the 1-dimensional field in a layered resonator. In order to simulate fluid drag forces, CFD software has been used to determine the velocity profile of the fluid/particle mix passing through the acoustic device. The profile is then incorporated into a MATLAB model. Based on particle force components, a numerical approach has been used to determine particle paths. Using particle coordinates, both particle concentration across the fluid channel and concentration through multiple outlets are calculated.Such an approach has been used to analyse the operation of a microfluidic flow-through separator, which uses a half wavelength standing wave across the main channel of the device. This causes particles to converge near the axial plane of the channel, delivering high and low particle concentrated flow through two outlets, respectively. By extending the model to analyse particle separation over a frequency range, it is possible to identify the resonant frequencies of the device and associated separation performance.This approach will also be used to improve the geometric design of the microengineered fluid channels, where the particle model can determine the limiting fluid flow rate for separation to occur, the value of which is then applied to a CFD model of the device geometry

Multi-modal particle manipulator to enhance bead-based bioassays

By sequentially pushing micro-beads towards and away from a sensing surface, we show that ultrasonic radiation forces can be used to enhance the interaction between a functionalized glass surface and polystyrene micro-beads, and distinguish those that bind to the surface, ultimately by using an integrated optical waveguide implanted in the reflector to facilitate optical detection. The movement towards and immobilization of streptavidin coated beads onto a biotin functionalized waveguide surface is achieved by using a quarter-wavelength mode pushing beads onto the surface, while the removal of non-specifically bound beads uses a second quarter-wavelength mode which exhibits a kinetic energy maxima at the boundary between the carrier layer and fluid, drawing beads towards this surface. This has been achieved using a multi-modal acoustic device which exhibits both these quarter-wavelength resonances. Both 1-D acoustic modelling and finite element analysis has been used to design this device and investigate the spatial uniformity of the field. We demonstrate experimentally that 90% of specifically bound beads remain attached after applying ultrasound, with 80% of non-specifically bound control beads being successfully removed acoustically. This approach overcomes problems associated with lengthy sedimentation processes used for bead-based bioassays and surface (electrostatic) forces, which delay or prevent immobilisation. We explain the potential of this technique in the development of DNA and protein assays in terms of detection speed and multiplexing