Open AccessSingle cell on-chip whole genome amplification via micropillar arrays for reduced amplification bias
Author(s) -
Harvey C. Tian,
Jaime J. Benítez,
Harold G. Craighead
Publication year - 2018
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0191520
Subject(s) - multiple displacement amplification , loop mediated isothermal amplification , genome , microfluidics , dna , biology , human genome , genomics , genomic dna , computational biology , microbiology and biotechnology , genetics , dna extraction , polymerase chain reaction , gene , materials science , nanotechnology
Single cell whole genome amplification is susceptible to amplification biases that impact the accuracy of single cell sequencing data. To address this, we have developed a microfluidic device for the isolation and purification of genomic DNA from individual cells. The device uses a micropillar array to physically capture single cells and its chromosomal DNA upon extraction. The extracted DNA is immobilized within the micropillar array in a way that allows isothermal amplification. In this system, whole genome amplification of the single cell is carried out under a continual fluid flow within the microfluidic channel. We have demonstrated the process for amplification of individual human cancer cell genomes from the HeLa cell line. By sampling select gene loci along the human genome and performing whole exome sequencing, we demonstrate improved genome coverage and reduced amplification bias compared to amplification of single cells deposited in wells by fluorescence activated cell sorting.