Quality control at Oxford Gene Technology

Tuesday 23 August 2011

Applications:: Genomic services

At Oxford Gene Technology (OGT), we pride ourselves on rigorous quality control (QC) at every step of the microarray process regardless of sample throughput. We provide a good laboratory practice (GLP)-like system comprising:

20 sample QC steps
>30 in-process QC checks
15 sign-off/validation steps.

All information is recorded in our Laboratory Information Management System (LIMS)

Sample QC

QC step	Equipment/ process	Checking/ validating
Initial	NanoDrop™ 8000 spectrophotometer	Concentration Salt and other contaminants
	Agilent 2100 Bioanalyzer/gel electrophoresis	Integrity RIN
Process	Gel electrophoresis	Digestion
	NanoDrop 8000 spectrophotometer	Concentration/yield Dye incorporation (specific activity
Final	DNA analytics/ laboratory management system (LIMS)	QC metrics: DLR spread Background noise: Red and green Signal intensity: Red and green Signal-to-noise: Red and green Reproducibility: Red and green processed signal Reproducibility with background subtracted: Red and green Area under ROC curve Median difference Error fraction

DLR: derivative log ratio; PMT: photomultiplier intensity; ppb: parts per billion; RIN: RNA integrity number;
ROC: receiver operating characteristic.

Equipment QC

Equipment	Element tested	Reason
Bravo™ liquid handling robot	Tartrazine	Calibration across 96-wells
Freezer	Temperature	Checks for power cuts and maintenance of constant temperature
Fridge	Temperature	Checks for power cuts and maintenance constant temperature
G-Storm™ (thermal cycler)	Engine + lid test Temperature	– Constant temperature across 96 wells
Hybridisation oven	Temperature Rotation speed	Maintenance of constant temperature and mixing across ovens
Little Dipper® (automated slide washing steps)	Temperature Ozone Touch-screen	Maintenance of constant temperature and washing conditions Calibration
Milli-Q® Water System	Sanitisation and water purity	–
NanoDrop 8000 spectrophotometer	Concentration	Calibration (uses known DNA)
Room environment	Ozone (ppb) Temperature	Minimisation in lab working areas –
Scanner	Confidence and PMT slides;ozone	Minimisation of variation in laboratory working areas
Workstation	Ozone (ppb)	Minimisation in lab working areas
Pipettes	Calibration	Accuracy
Generator	Diesel level	Maintain working order