Integrated Microfluidic Systems for DNA Analysis

Abstract

The potential utility of genome-related research in terms of evolving basic discoveries in biology has generated widespread use of DNA diagnostics and DNA forensics and driven the accelerated development of fully integrated microfluidic systems for genome processing. To produce a microsystem with favorable performance characteristics for genetic-based analyses, several key operational elements must be strategically chosen, including device substrate material, temperature control, fluidic control, and reaction product readout. As a matter of definition, a microdevice is a chip that performs a single processing step, for example microchip electrophoresis. Several microdevices can be integrated to a single wafer, or combined on a control board as separate devices to form a microsystem. A microsystem is defined as a chip composed of at least two microdevices. Among the many documented analytical microdevices, those focused on the ability to perform the polymerase chain reaction (PCR) have been reported extensively due to the importance of this processing step in most genetic-based assays. Other microdevices that have been detailed in the literature include those for solid-phase extractions, microchip electrophoresis, and devices composed of DNA microarrays used for interrogating DNA primary structure. Great progress has also been made in the areas of chip fabrication, bonding and sealing to enclose fluidic networks, evaluation of different chip substrate materials, surface chemistries, and the architecture of reaction conduits for basic processing steps such as mixing. Other important elements that have been developed to realize functional systems include miniaturized readout formats comprising optical or electrochemical transduction and interconnect technologies. These discoveries have led to the development of fully autonomous and functional integrated systems for genome processing that can supply "sample in/answer out" capabilities. In this chapter, we focus on microfluidic systems that are composed of two or more microdevices directed toward DNA analyses. Our discussions will primarily be focused on the integration of various processing steps with microcapillary electrophoresis (μCE) or microarrays. The advantages afforded by fully integrated microfluidic systems to enable challenging applications, such as single-copy DNA sequencing, single-cell gene expression analysis, pathogen detection, and forensic DNA analysis in formats that provide high throughput and point-of-analysis capabilities will be discussed as well.

Profiling In Situ Microbial Community Structure with an Amplification Microarray

“…Furthermore, while traditional sample preparation, amplification, and microarray hybridization chemistries can be incorporated into a consumable via microfluidic transfer steps (9)(10)(11)(12)(13)(14)(15), the engineering, manufacturing, and quality control challenges of such consumables (and control instruments) scale with the complexity of the microfluidic architecture. An alternative approach for simplifying microarray technology for routine monitoring applications, then, is to minimize the biochemistry and processing steps that precede and interface with the microarray itself.…”

Technology Advancement for Integrative Stem Cell Analyses

“…The ability to observe cells in a high-throughput facility, or so-called ''lab-on-a-chip'' (e.g., microfluidic devices, microwells, and so on), provides critical and quantitative information about fundamental biological systems. [51][52][53][54] Microsystems including microwells or microhurdle-based docking with adequately controlled spatiotemporal resolution have been used for cell trapping and analysis and have also, been categorized as cell analytic technologies. ''Labon-a-chip'' devices and systems have become a conspicuous feature of cell analyses due to small reagent volumes, dynamic control of reagents, high throughput, biocompatibility, and sensitivity.…”

“…An integrated approach to iSCA should offer the ability to connect data about multiple aspects of the genetic, phenotypic, and operational variability and different states of stem cells. 53,129 Such integrated data with stem cells would offer new insights into the true diversity among populations of cells that is difficult to define with standalone analytical tools and bulk correlations.…”

Integrated Amplification Microarrays for Infectious Disease Diagnostics

“…Of these, nucleic acid tests based on real-time polymerase chain reaction (PCR) technology address many of the sensitivity and specificity challenges for infectious disease diagnostics, leading to widespread adoption of nucleic acid diagnostics in surveillance, epidemiology, and clinical practice over the last decade (e.g., [1,2,3,4,5,6,7,8,9,10,11]). The advent of integrated PCR systems [12,13,14,15] that address user needs for rapid analysis times and ease-of-use are likewise expected to expand and accelerate the adoption of molecular diagnostics in clinical practice, including point-of-care and point-of-use settings [16,17,18,19]. Integrated real-time PCR systems, however, typically comes at the cost of mid- to high-level multiplexing, or the ability to detect multiple microorganisms, nucleotide polymorphisms or drug resistance mutations from a single sample.…”