Control for stochastic sampling variation and qualitative sequencing error in next generation sequencing.

ABSTRACT:

Background

Clinical implementation of Next-Generation Sequencing (NGS) is challenged by poor control for stochastic sampling, library preparation biases and qualitative sequencing error. To address these challenges we developed and tested two hypotheses.

Methods

Hypothesis 1: Analytical variation in quantification is predicted by stochastic sampling effects at input of a) amplifiable nucleic acid target molecules into the library preparation, b) amplicons from library into sequencer, or c) both. We derived equations using Monte Carlo simulation to predict assay coefficient of variation (CV) based on these three working models and tested them against NGS data from specimens with well characterized molecule inputs and sequence counts prepared using competitive multiplex-PCR am

SUBMITTER: Blomquist T 

PROVIDER: S-EPMC4673681 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature