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Hours of Operation/Sample Dropoff

Monday - Friday: 9am-5pm
or call for special arrangements.

We provide a sample drop off freezer if no one is available to take your samples. Instructions and a form are available in the Main lab.

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Affymetrix Genotyping Arrays - Quality Control

Regardless of array type, a reference sample with genomic DNA provided by Affymetrix, is run with each batch of samples processed as a positive control. We keep track of the call rates and QC metrics for all samples and evaluate the performance of the control samples.

Genome Wide Array (5.0/6.0) Failure Statics:

The Facility has processed over 2,000 samples on both the 5.0 and 6.0 genome wide arrays. The Genotyping Console Software runs a quality control report which evaluates the 3,000 lowest performing SNPs on the array. These SNPs need to have a QC call rate of above 86% in order to guarantee a genotyping call rate of greater than 97% when analyzed with either BRLMM (5.0) or Birdseed (6.0). Our failure rate, defined by a QC Call rate lower than 86%, is minimal, with around 1 out of every 200 samples or more failing. Most of these failures are due to array issues, and the call rate almost always increases when the sample is rehybridized to a different array.

The latest version of Genotyping Console (v2.1) introduced a new QC metric for the 6.0 arrays, the contrast QC. The Facility began implementing this QC parameter in April, 2008. Contrast QC is a metric that captures the ability of an experiment to resolve SNP signals into three genotyping clusters. It utilizes a static set of 10,000 randomly chosen SNPs and measures the difference between peaks in contrast distributions produced by homozygote genotypes, and the valleys they share with the heterozygote peak, and reports the smaller of the two values. In a poor quality sample, the homozygote peaks are not well resolved from the heterozygote peak and the difference values approach zero. For a good quality sample, this metric is greater than 0.4. Read more about contrast QC.