title: Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies.
abstract: Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversity at all levels, from genetic variation and expression to ecological community assemblage. However, the number of reads produced per sequencing run far exceeds the number required per sample for many applications, compelling researchers to sequence multiple samples per run in order to maximize efficiency. For studies that include a PCR step, this can be accomplished using primers that include an index sequence allowing sample origin to be determined after sequencing. The use of indexed primers assumes they behave no differently than standard primers; however, we found that indexed primers cause substantial template sequence-specific bias, resulting in radically different profiles of the same environmental sample. Likely the outcome of differential amplification efficiency due to primer-template mismatch, two indexed primer sets spuriously change the inferred sequence abundance from the same DNA extraction by up to 77.1%. We demonstrate that a double PCR approach alleviates these effects in applications where indexed primers are necessary.
authors.affiliation: School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, United States of America.
authors.forename: James L
authors.initials: JL
authors.lastname: O'Donnell
authors.affiliation: School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, United States of America.
authors.forename: Ryan P
authors.initials: RP
authors.lastname: Kelly
authors.affiliation: School of Marine and Environmental Affairs, University of Washington, Seattle, Washington, United States of America.
authors.forename: Natalie C
authors.initials: NC
authors.lastname: Lowell
authors.affiliation: Center for Ocean Solutions, Woods Institute for the Environment, Stanford University, Stanford, California, United States of America.
authors.forename: Jesse A
authors.initials: JA
authors.lastname: Port
mesh_terms: D017931:DNA Primers / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity
chemical_list: D017931:DNA Primers