Quality control at Oxford Gene Technology

Tuesday 23 August 2011

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


Salt and other contaminants
  Agilent 2100 Bioanalyzer/gel electrophoresis


Process Gel electrophoresis Digestion
  NanoDrop 8000 spectrophotometer


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


Constant temperature across 96 wells
Hybridisation oven


Rotation speed
Maintenance of constant temperature and mixing across ovens
Little Dipper® (automated slide washing steps)




Maintenance of constant temperature and washing conditions

Milli-Q® Water System Sanitisation and water purity
NanoDrop 8000 spectrophotometer Concentration Calibration (uses known DNA)
Room environment

Ozone (ppb)


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
LIMS validation (by pin authorisation) Consumable tracking
Element controlled
Control DNA addition
Digestion setup
Digest incubation
Addition of random primers
Labelling setup
Labelling incubation
NanoDrop – validation of labelling efficiency
Adding of hybridisation buffer
Hybridisation incubation
Start hybridisation
Complete hybridisation
Scanning and feature extraction
FTP transfer and upload of QC metrics
Consumables tracked by lot number and expiry date
Backing plate
Hybridisation master mix
GE Plate 1
GE Plate 2
Random primer
Digestion master mix
Reference DNA batch
Female control batch
Labelling master mix (Cy5)
Labelling master mix (Cy3)
Wash buffer
Process tracking
Process controlled
Barcodes: Sample arrival tracking
Barcodes: Sample usage tracking
Monitor sample processing: Checks correct time has elapsed for each process
Sample throughput: Checks target for number of samples processed

Find out more

For more information about any OGT product or service, please contact us.