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Nucleic Acids Research Advance Access originally published online on March 20, 2009
Nucleic Acids Research 2009 37(8):e63; doi:10.1093/nar/gkp188
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Nucleic Acids Research, 2009, Vol. 37, No. 8 e63
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Flow cytometry for enrichment and titration in massively parallel DNA sequencing

Julia Sandberg, Patrik L. Ståhl, Afshin Ahmadian, Magnus K. Bjursell and Joakim Lundeberg*

School of Biotechnology, Division of Gene Technology, AlbaNova University Center, Royal Institute of Technology, 106 91 Stockholm, Sweden

*To whom correspondence should be addressed. Tel: +46 8 5537 8327; Fax: +46 8 5537 8481; Email: joakim.lundeberg{at}biotech.kth.se

Received October 19, 2008. Revised March 5, 2009. Accepted March 8, 2009.

Massively parallel DNA sequencing is revolutionizing genomics research throughout the life sciences. However, the reagent costs and labor requirements in current sequencing protocols are still substantial, although improvements are continuously being made. Here, we demonstrate an effective alternative to existing sample titration protocols for the Roche/454 system using Fluorescence Activated Cell Sorting (FACS) technology to determine the optimal DNA-to-bead ratio prior to large-scale sequencing. Our method, which eliminates the need for the costly pilot sequencing of samples during titration is capable of rapidly providing accurate DNA-to-bead ratios that are not biased by the quantification and sedimentation steps included in current protocols. Moreover, we demonstrate that FACS sorting can be readily used to highly enrich fractions of beads carrying template DNA, with near total elimination of empty beads and no downstream sacrifice of DNA sequencing quality. Automated enrichment by FACS is a simple approach to obtain pure samples for bead-based sequencing systems, and offers an efficient, low-cost alternative to current enrichment protocols.


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