High-throughput sequencing: a failure mode analysis

Background: Basic manufacturing principles are becoming increasingly important in high-throughput sequencing facilities where there is a constant drive to increase quality, increase efficiency, and decrease operating costs. While high-throughput centres report failure rates typically on the order of 10%, the causes of sporadic sequencing failures are seldom analyzed in detail and have not, in the past, been formally reported. Results: Here we report the results of a failure mode analysis of our production sequencing facility based on detailed evaluation of 9,216 ESTs generated from two cDNA libraries. Two categories of failures are described; process-related failures ( failures due to equipment or sample handling) and template-related failures ( failures that are revealed by close inspection of electropherograms and are likely due to properties of the template DNA sequence itself). Conclusions: Preventative action based on a detailed understanding of failure modes is likely to improve the performance of other production sequencing pipelines.