Rapid multiplex DNA amplification on an inexpensive microdevice for human identification via short tandem repeat analysis

• Published in: Analytica chimica acta Vol. 980; pp. 41 - 49
• Main Authors: DuVall, Jacquelyn A., Le Roux, Delphine, Thompson, Brandon L., Birch, Christopher, Nelson, Daniel A., Li, Jingyi, Mills, Daniel L., Tsuei, An-chi, Ensenberger, Martin G., Sprecher, Cindy, Storts, Douglas R., Root, Brian E., Landers, James P.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 08.08.2017
• Subjects: Centrifugal microfluidics; DNA; Electrophoresis, Microchip; Forensic Genetics; Human identification; Humans; Microsatellite Repeats; Nucleic Acid Amplification Techniques; Polyester-toner microdevice; Polymerase Chain Reaction; Short tandem repeat-based polymerase chain reaction; Centrifugal microfluidics; Polyester-toner microdevice; Human identification; Short tandem repeat-based polymerase chain reaction
• ISSN: 0003-2670; 1873-4324
• DOI: 10.1016/j.aca.2017.04.051

Forensic DNA analysis requires several steps, including DNA extraction, PCR amplification, and separation of PCR fragments. Intuitively, there are numerous situations where it would be beneficial to speed up the overall DNA analysis process; in this work, we focus on the most time-consuming component in the analysis pipeline, namely the polymerase chain reaction (PCR). Primers were specially designed to target 10 human genomic loci, all yielding amplicons shorter than 350 bases, for ease of downstream integration with on-board microchip electrophoresis. Primer concentrations were adjusted specifically for microdevice amplification, resulting in well-balanced short tandem repeat (STR) profiles. Furthermore, studies were performed to push the limits of the DNA polymerase to achieve rapid, multiplexed PCR on various substrates, including transparent and black polyethylene terephthalate (Pe), and with two distinct adhesives, toner and heat sensitive adhesive (HSA). Rapid STR-based multiplexed PCR amplification is demonstrated in 15 min on a Pe microdevice using a custom-built system for fluid flow control and thermocycling for the full 10-plex, and in 10 min for a smaller multiplex consisting of six core CODIS loci plus Amelogenin with amplicons shorter than 200bp. Lastly, preliminary studies indicate the capability of this PCR microdevice platform to be integrated with both upstream DNA extraction, and downstream microchip electrophoresis. This, coupled to the use of reagents that are compatible with lyophilization (lyo-compatible) for PCR, represents the potential for a fully integrated rotationally-driven microdevice for complete forensic DNA analysis. [Display omitted] •Demonstrated 15 min amplification of 10 STR markers for human identification.•Demonstrated potential for integration of microchip PCR with upstream liquid DNA extraction.•Proved feasibility of 10-plex PCR amplification on multiple microdevice substrates.