QC Reason Messages

The qc_reason column in the NIPT Report displays a QC failure or warning when analysis results fall outside the expected range for an analytical QC metric. QC failures result in the suppression of supplementary report results and estimated fetal fraction and a value of INVALIDATED will be reported in the following NIPT report fields: class_auto, class_sx, anomaly_description and ff.

QC Reason Message	Description	Recommended Action
FAILED iFACT	individual Fetal Aneuploidy Confidence Test (iFACT)—QC metric that combines fetal fraction estimation with run metrics associated with coverage to determine whether the system has statistical confidence to make a call on a given sample.	Reprocess sample.
DATA OUTSIDE OF EXPECTED RANGE	The average deviation from euploid coverage is not consistent with the trained data distribution. Possibly caused by contamination or incorrect sample processing.	Reprocess sample.
FRAGMENT SIZE DISTRIBUTION OUTSIDE OF EXPECTED RANGE	The fragment size distribution is not consistent with the trained data distribution. Possibly caused by contamination or incorrect sample processing.	Reprocess sample.
FLOWCELL DATA OUTSIDE OF EXPECTED RANGE	Flowcell data are not consistent with the trained data distribution. Possibly caused by error in flowcell setup.	Reprocess sample.
FAILED TO ESTIMATE FETAL FRACTION	Unable to produce a valid fetal fraction estimate.	Reprocess sample.
SEQUENCING DATA OUTSIDE OF EXPECTED RANGE	Input sequencing data are not consistent with the trained data distribution. Possibly caused by contamination or incorrect sample processing.	Resequence flowcell.
UNEXPECTED DATA	The report generates a QC concern that does not correspond to any of the other QC reasons listed in this table.	Contact Illumina Technical Support.
NTC SAMPLE WITH HIGH COVERAGE	High coverage detected for an NTC sample (no DNA material expected). Possibly caused by contamination or incorrect sample processing.	Reprocess sample.
CANCELLED	Sample was canceled by a user.	Not applicable.
INVALIDATED	Sample was invalidated by a user.	Not applicable.