MLPA is a simple method for relative quantification of up to 45 nucleic acid sequences in a single reaction. NGRL Manchester developed MLPA data analysis spreadsheets for MRC-Holland kits, applying an objective measure of the quality of each sample based on the standard deviation of control fragment dosage quotients.

A standard deviation of >0.1 for the control ligation products of any sample indicates poor quality unreliable data that should be rejected. However, some MLPA kits do not have clearly identified control ligation products that are not expected to vary in dosage in the patient group being tested. For instance the Human Telomere kits P069 and P070 only contain probes for telomeres, any of which may show dosage anomalies in patients. In the first version of the spreadsheets for these kits, the standard deviation of all the ligation products was measured. Problems may arise if samples are positive for deletions or duplications of the telomere probes as the copy number loss or gain can affect the standard deviation measure and flag the sample as poor quality for rejection. Revised spreadsheets for these kits now avoid this problem; any deleted or duplicated telomere ligation product that gives a dosage quotient within a defined range is excluded from the quality measure calculation.