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Microarray Services Quality Control

The core facility has performed a series of quality control experiments in order to optimize the entire process of DNA microarray procedural conditions including printing, labeling and hybridization.

One of the crucial factors in the manufacturing of the microarrays is the measurement of the uniformity of the arraying.

Quality control is an ongoing process in our facility. To date, the following factors were checked to assess the quality of the individual spots of the array:

  1. Uniformity of the arraying
  2. Uniformity of the spot size
  3. Saturation limits of the probe

Probes labeled with Cy3 were used to assess the morphology (diameter, shape, etc.) of the spots across the array. Intensities of the labeled probe were measured to determine the amount of the probe on each spot. In a comparative experiment, the labeling was reversed from probe to target to see if the intensities matched. Probes were spotted in a dilution series to assess the saturation. Additionally, probes were spotted several times in the same location to see if the probe concentration on the surface changed. Several self-self hybridizations (same probe and target) were used to quantitate and develop novel methods of quality control.

Quality Control (ppt)

Since acquiring the Affymetrix GeneChip system in September 2001, the core facility has successfully processed hundreds of probe arrays and serviced numerous laboratories at M. D. Anderson Cancer Center and Baylor College of Medicine. Prior to offering Affymetrix probe arrays related services, the facility personnel underwent extensive training including bench science and software training by qualified Affymetrix representatives. The training included hands-on instrumentation handling/trouble shooting and operation of the various components of the Affymetrix GeneChip system.

In order to check the reproducibility of sample preparation by the facility personnel and the data generated by the Affymetrix probe arrays, two identical total RNA samples were used for cRNA preparation on different days and hybridized to test three chips on different days. In addition to the variability introduced by the technique, this quality control experiment also checked for day-to-day variation.

Reproducibility of Data Generated by Affymetrix Probe Array (ppt)

Slides one and two are scatter plots using different data transformation. Slide one used original signal intensity data collected from MAS 5.0. Slide two used logarithm transformation of intensity data. The data showed high correlation coefficient in both cases (>0.9). Slide 3 is a summary of statistics for the two replicates, listing the minimum, maximum, mean, median and quantile value, etc.

The reproducibility of the protocols performed by the core facility is tested by repeating the same set of experiments every six to eight weeks. Human reference RNA is used to prepare target using the IVT and the dIVT protocols and hybridized to test chips (Affymetrix Inc., Santa Clara, CA). The data are compared with those generated in the previous runs of the same sample.


© 2009 The University of Texas M. D. Anderson Cancer Center