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Systematic error monitoring

Alongside quality control checks for individual samples, batch monitoring is also in place to detect systematic errors should they arise. Plate-level and site-level quality control metrics are routinely evaluated for contamination, sex mismatch, and poor quality CNV calling issues, to ensure the genome is suitable for variant prioritisation.

  • Metrics for batch monitoring of contamination levels: Fraction of contaminated samples vs fraction of delivered samples is determined per plate. This will allow for investigation of adjacent wells in a plate for potential below-threshold contamination.
  • Metrics for batch monitoring of samples with sex mismatches: Fraction of samples with conflicting inferred and reported sex vs fraction of delivered samples is determined per plate. Using these metrics, issues such as unexpected plate rotation will be readily identifiable.