High-throughput sequencing: a failure mode analysis.

Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Suite 100, 570 West 7th Avenue, Vancouver, BC, Canada. gyang@bcgsc.ca

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.

PMID: 15631628 [PubMed - indexed for MEDLINE]

PMCID: PMC546001