Quantitative evaluation of bias in PCR amplification and Next Generation Sequencing derived from metabarcoding samples

  1. Pawluczyk, Marta
  2. Weiss, Julia Rosl
  3. Links, Matthew G.
  4. Aranguren, M.E.
  5. Wilkinson, Mark
Book:
Proceedings of the 4th. Workshop on Agri-Food Research. WIA.15
  1. Artés Hernández, Francisco
  2. Egea Gutíerrez-Cortines, Marcos
  3. Fernández Hernández, Juan Antonio
  4. Baille, Alain
  5. Calatrava Leyva, Javier (coord.)

Publisher: Universidad Politécnica de Cartagena

ISBN: 978-84-608-5399-2

Year of publication: 2016

Pages: 103-106

Congress: Workshop on Agri-Food Research for young researchers (4. 2015. Cartagena)

Type: Conference paper

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Abstract

Unbiased identification of organisms by PCR reactions using universal primers followed by DNA sequencing assumes positive amplification. We used six universal loci spanning 48 plant species and quantified the bias at each step of the identification process from end point PCR to Next-Generation Sequencing. End-point amplification was significantly different for single loci and between species. Quantitative PCR revealed that Cq threshold for various loci, even within a single DNA extraction, showed 2000-fold differences in DNA quantity after amplification. Next Generation Sequencing (NGS) experiments in nine species showed significant biases towards species and specific loci using adaptor-specific primers. NGS sequencing bias may be predicted to some extent by the Cq values of Q-PCR amplification.

Data source: Dialnet