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.
Yang
George S
GS
Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Suite 100, 570 West 7th Avenue, Vancouver, BC, Canada. gyang@bcgsc.ca
Stott
Jeffery M
JM
Smailus
Duane
D
Barber
Sarah A
SA
Balasundaram
Miruna
M
Marra
Marco A
MA
Holt
Robert A
RA
D001331:Automation; D001709:Biotechnology / Q000191:economics / Q000295:instrumentation / Q000379:methods*; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D017931:DNA Primers; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015723:Gene Library; D015233:Models, Statistical; D010957:Plasmids / Q000378:metabolism; D032107:Populus / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*; D012984:Software
D017931:DNA Primers