A microfluidic platform for high‐purity cell free DNA extraction from plasma for non‐invasive prenatal testing

Abstract

Objectives Increase the yield and purity of cell‐free DNA (cfDNA) extracted from plasma for non‐invasive prenatal testing (NIPT) as inefficiencies in this extraction and purification can dramatically affect the sensitivity and specificity of the test. Methods This work integrates cfDNA extraction from plasma with a microfluidic chip platform by combining magnetic bead‐based extraction and electroosmotic flow on the microfluidic chip. Various wash buffers and voltage conditions were simulated using COMSOL Multiphysics Modeling and tested experimentally. Results When performing the first wash step of this assay on the microfluidic chip with 300 V applied across the channel there was a six‐fold increase in the A260/A230 ratio showing a significant improvement (p value 0.0005) in the purity of the extracted sample all while maintaining a yield of 68.19%. These values are critical as a high yield results in more sample to analyze and an increase in A260/A230 ratio corresponds to a decrease in salt contaminants such as guanidinium thiocyanate which can interfere with downstream processes during DNA library preparation and potentially hinder the NIPT screening results. Conclusions This technique has the potential to improve NIPT outcomes and other clinically relevant workflows that use cfDNA as an analyte such as cancer detection.

A Review of Microfluidic Experimental Designs for Nanoparticle Synthesis

“…Furthermore, investigations of chemical syntheses in various microreactors configurations may also represent an important base for designing chips for other purposes. Specifically, fluid dynamics analyses may be of good use for researchers aiming to fabricate microfluidic platforms for emerging biomedical applications, including non-invasive diagnosis devices [ 108 , 109 , 110 , 111 , 112 ], cell culture media (organs-on-a-chip) [ 113 , 114 , 115 , 116 , 117 ], and precise drug-delivery systems [ 118 , 119 , 120 , 121 ].…”

Leveraging the fundamentals of heat transfer and fluid mechanics in microscale geometries for automated next-generation sequencing library preparation

“…NGS is a markedly valuable tool for diagnostics and discovery because it generates millions of reads and is exceedingly sensitive to nucleic acid mutations [9][10][11][12] . Unfortunately, while innovations in sequencing technology have reduced requisite cost, time, and workload, sample (library) preparation has largely remained rudimentary and labor-intensive [13][14][15][16] . Even for applications requiring less data, such as microbial whole genome sequencing (WGS) or RNA-seq, the majority of the total sequencing cost can be attributed to library preparation,…”

“…Consequently, expensive robotic liquid handlers dominate research and clinical applications in core laboratories, and small laboratories suffer from the bottleneck of labor-intensive manual protocols. Automation innovation for small laboratories is necessary to accelerate NGS-based research, eliminate sources of human error, and reduce hands-on time [13][14][15][16] . Our previous work started with the innovative concept of integrating liquid mixing steps with thermodynamically driven steps such as ligation and amplification via a single capillary tube heating system [13][14][15][16] .…”

“…Automation innovation for small laboratories is necessary to accelerate NGS-based research, eliminate sources of human error, and reduce hands-on time [13][14][15][16] . Our previous work started with the innovative concept of integrating liquid mixing steps with thermodynamically driven steps such as ligation and amplification via a single capillary tube heating system [13][14][15][16] . This work utilized magnetic bead motion through a microchannel for purification step, as needed by steps C and D in Fig.…”