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Genotyping Only Projects: Genotype Sample QC

Genotyping Quality Control Procedures:

The following QC steps are performed on DNA samples prior to genotyping:

  • Concentration Validation:Sample concentrations are performed using the Quant-iT Broad Range dsDNA kit (Invitrogen) to measure DNA concentration.
  • Sample Sex Assay: Sample sex is confirmed using an ABI TaqMan assay specific for X/Y chromosomal regions prior to genotyping. A definitive sex genotype is generated for each sample. These data will be compared against the reported sex from the submitted sample manifest.

QC Report

After concentration verification and the sample sex assay, the investigator will receive an email and a report detailing any QC failures. Samples that fail QC are not eligible to proceed. QC issues will need to be resolved by the investigator before the project can proceed to genotyping.

Resolution of QC Failures

If a sample has failed due to a sex conflict or due to insufficient concentration, the investigator may submit a replacement sample by filling out a new manifest describing the replacement sample. Submission of replacement samples will delay the release of data for the project.

If a replacement sample is not available, a single sample may be excluded from the project. In cases where the failing sample is critical to the analysis (i.e. the proband in a trio), the entire family will be excluded.
Following sample QC resolution, the project can proceed to genotyping with passed samples.