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Since the expected DNA yield stated in the Certificate of Analysis for the NIPT reference standards (HD860, HD861, HD862 and HD863) is ≥ 24 ng per 2mL, but 1mL is provided per tube, do I have to extract 2mL with the QIAamp Circulating Nucleic Acid Kit?

Correct, extraction is performed using the QIAamp Circulating Nucleic Acid Kit (Cat. No. 55114); using 2ml of cfDNA product per extraction column provided with the kit leads to ≥ 24 ng.