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Sample quality control

For a small proportion of samples, the sequencing data are not of sufficiently high quality to make reliable CNV calls. Sample level quality control is performed based on the number and ratio of different call types and the proportion of common CNVs detected. If CNV data for a proband do not pass this quality control step, the family is flagged in the Interpretation Portal with one of the following flags:

Poor_quality_CNV_calls

If most of the CNV calls in the proband are expected to be of poor quality. This flag is applied when:

  • the count of autosomal PASS CNVs ≥ 600, or
  • the Log2(Loss/Gain) < -0.5

Suspected_poor_quality_CNV_calls

When a sample is suspected to have an increased number of poor quality CNV calls. This flag is applied when:

  • the count of autosomal PASS CNVs ≥ 200 or ≤ 50, or
  • the Log2(Loss/Gain) ≤ -0.3 or ≥ 1.2, or
  • the fraction of common autosomal PASS CNV calls is <= 0.4. For this purpose, a CNV is defined as common if it has 50% reciprocal overlap with a CNV from Conrad et al. 2010.