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Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing

Filip Van Nieuwerburgh UGent, Sandra Soetaert UGent, Katie Podshivalova, Eileen Ay-Lin Wang, Lana Schaffer, Dieter Deforce UGent, Daniel R Salomon, Steven R Head and Phillip Ordoukhanian (2011) PLOS ONE. 6(10).
abstract
Here we demonstrate a method for unbiased multiplexed deep sequencing of RNA and DNA libraries using a novel, efficient and adaptable barcoding strategy called Post Amplification Ligation-Mediated ( PALM). PALM barcoding is performed as the very last step of library preparation, eliminating a potential barcode-induced bias and allowing the flexibility to synthesize as many barcodes as needed. We sequenced PALM barcoded micro RNA (miRNA) and DNA reference samples and evaluated the quantitative barcode-induced bias in comparison to the same reference samples prepared using the Illumina TruSeq barcoding strategy. The Illumina TruSeq small RNA strategy introduces the barcode during the PCR step using differentially barcoded primers, while the TruSeq DNA strategy introduces the barcode before the PCR step by ligation of differentially barcoded adaptors. Results show virtually no bias between the differentially barcoded miRNA and DNA samples, both for the PALM and the TruSeq sample preparation methods. We also multiplexed miRNA reference samples using a pre-PCR barcode ligation. This barcoding strategy results in significant bias.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
journal title
PLOS ONE
PLoS One
volume
6
issue
10
article_number
e26969
pages
6 pages
Web of Science type
Article
Web of Science id
000299081800053
JCR category
BIOLOGY
JCR impact factor
4.092 (2011)
JCR rank
12/84 (2011)
JCR quartile
1 (2011)
ISSN
1932-6203
DOI
10.1371/journal.pone.0026969
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
2941961
handle
http://hdl.handle.net/1854/LU-2941961
date created
2012-06-28 15:25:23
date last changed
2012-07-09 16:36:47
@article{2941961,
  abstract     = {Here we demonstrate a method for unbiased multiplexed deep sequencing of RNA and DNA libraries using a novel, efficient and adaptable barcoding strategy called Post Amplification Ligation-Mediated ( PALM). PALM barcoding is performed as the very last step of library preparation, eliminating a potential barcode-induced bias and allowing the flexibility to synthesize as many barcodes as needed. We sequenced PALM barcoded micro RNA (miRNA) and DNA reference samples and evaluated the quantitative barcode-induced bias in comparison to the same reference samples prepared using the Illumina TruSeq barcoding strategy. The Illumina TruSeq small RNA strategy introduces the barcode during the PCR step using differentially barcoded primers, while the TruSeq DNA strategy introduces the barcode before the PCR step by ligation of differentially barcoded adaptors. Results show virtually no bias between the differentially barcoded miRNA and DNA samples, both for the PALM and the TruSeq sample preparation methods. We also multiplexed miRNA reference samples using a pre-PCR barcode ligation. This barcoding strategy results in significant bias.},
  articleno    = {e26969},
  author       = {Van Nieuwerburgh, Filip and Soetaert, Sandra and Podshivalova, Katie and Wang, Eileen Ay-Lin and Schaffer, Lana and Deforce, Dieter and Salomon, Daniel R and Head, Steven R and Ordoukhanian, Phillip},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  language     = {eng},
  number       = {10},
  pages        = {6},
  title        = {Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing},
  url          = {http://dx.doi.org/10.1371/journal.pone.0026969},
  volume       = {6},
  year         = {2011},
}

Chicago
Van Nieuwerburgh, Filip, Sandra Soetaert, Katie Podshivalova, Eileen Ay-Lin Wang, Lana Schaffer, Dieter Deforce, Daniel R Salomon, Steven R Head, and Phillip Ordoukhanian. 2011. “Quantitative Bias in Illumina TruSeq and a Novel Post Amplification Barcoding Strategy for Multiplexed DNA and Small RNA Deep Sequencing.” Plos One 6 (10).
APA
Van Nieuwerburgh, F., Soetaert, S., Podshivalova, K., Wang, E. A.-L., Schaffer, L., Deforce, D., Salomon, D. R., et al. (2011). Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLOS ONE, 6(10).
Vancouver
1.
Van Nieuwerburgh F, Soetaert S, Podshivalova K, Wang EA-L, Schaffer L, Deforce D, et al. Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLOS ONE. 2011;6(10).
MLA
Van Nieuwerburgh, Filip, Sandra Soetaert, Katie Podshivalova, et al. “Quantitative Bias in Illumina TruSeq and a Novel Post Amplification Barcoding Strategy for Multiplexed DNA and Small RNA Deep Sequencing.” PLOS ONE 6.10 (2011): n. pag. Print.