Sources of PCR-induced distortions in high-throughput sequencing data sets.

ABSTRACT: PCR permits the exponential and sequence-specific amplification of DNA, even from minute starting quantities. PCR is a fundamental step in preparing DNA samples for high-throughput sequencing. However, there are errors associated with PCR-mediated amplification. Here we examine the effects of four important sources of error-bias, stochasticity, template switches and polymerase errors-on sequence representation in low-input next-generation sequencing libraries. We designed a pool of diverse PCR amplicons with a defined structure, and then used Illumina sequencing to search for signatures of each process. We further developed quantitative models for each process, and compared predictions of these models to our experimental data. We find that PCR stochasticity is the major force skewing seque

SUBMITTER: Kebschull JM 

PROVIDER: S-EPMC4666380 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature