Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms.

ABSTRACT:

Background

Here we present an in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells with Exclusion Amplification (ExAmp) chemistry (HiSeqX, HiSeq4000, and NovaSeq). We also present a remediation method that minimizes the impact of such swaps.

Results

Leveraging data collected over a two-year period, we demonstrate the widespread prevalence of index swapping in patterned flow cell data. We calculate mean swap rates across multiple sample preparation methods and sequencer models, demonstrating that different library methods can have vastly different swapping rates and that even non-ExAmp chemistry instruments display trace levels of index swapp

SUBMITTER: Costello M 

PROVIDER: S-EPMC5941783 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature