Editors' note: Discrepancy in redetermination of SMN2 copy numbers in children with SMA

Abstract

In the article, “Discrepancy in redetermination of SMN2 copy numbers in children with SMA,” Drs. Schorling et al. evaluated the accuracy of initial SMN2 copy number determination by repeating genetic testing in 20 patients with spinal muscular atrophy (SMA) using Multiplex Ligation-dependent Probe Amplification (MPLA) analysis. They found that the results of the second testing were discrepant to initial testing in 45% of patients, concluding that reliability testing and quality control procedures are essential before SMN2 copy numbers can be used for clinical decisions and interpretation of outcome data. In response, Drs. Dangouloff et al. reported having observed high rates of discrepancy between the results for SMN2 copy number obtained from their laboratory and other laboratories where their patients were initially tested. They report finding an overall agreement rate of just 31% for SMN2 copy number for 35 patients when testing their samples using 2 different MPLA methods in their own laboratory. They conclude that better standardization of SMN2 copy number testing is needed before these results guide decision-making in the setting of newborn screening. Responding to these comments, the authors note that they switched from the P021-A2 kit the P021-B1 kit (both methods used by Drs. Dangouloff et al.) in March 2019 and found identical results when running 3 probes with variable SMN1 / SMN2 copies with both kits and found an extra copy of exon 1-6 in 12% of the 77 individuals whose samples they subsequently analyzed. They suggest that it is critical to use reliable controls with DNA isolated from the same tissue in every MPLA run. This exchange highlights the difficulties of standardizing quantitative genetic testing techniques across different laboratories—particularly for relatively rare diseases for which it may be challenging to build domain-specific laboratory expertise, but the results nevertheless guide potentially game-changing decisions for patients. In the article, “Discrepancy in redetermination of SMN2 copy numbers in children with SMA,” Drs. Schorling et al. evaluated the accuracy of initial SMN2 copy number determination by repeating genetic testing in 20 patients with spinal muscular atrophy (SMA) using Multiplex Ligation-dependent Probe Amplification (MPLA) analysis. They found that the results of the second testing were discrepant to initial testing in 45% of patients, concluding that reliability testing and quality control procedures are essential before SMN2 copy numbers can be used for clinical decisions and interpretation of outcome data. In response, Drs. Dangouloff et al. reported having observed high rates of discrepancy between the results for SMN2 copy number obtained from their laboratory and other laboratories where their patients were initially tested. They report finding an overall agreement rate of just 31% for SMN2 copy number for 35 patients when testing their samples using 2 different MPLA methods in their own laboratory. They conclude that better standardization of SMN2 copy number testing is needed before these results guide decision-making in the setting of newborn screening. Responding to these comments, the authors note that they switched from the P021-A2 kit the P021-B1 kit (both methods used by Drs. Dangouloff et al.) in March 2019 and found identical results when running 3 probes with variable SMN1 / SMN2 copies with both kits and found an extra copy of exon 1-6 in 12% of the 77 individuals whose samples they subsequently analyzed. They suggest that it is critical to use reliable controls with DNA isolated from the same tissue in every MPLA run. This exchange highlights the difficulties of standardizing quantitative genetic testing techniques across different laboratories—particularly for relatively rare diseases for which it may be challenging to build domain-specific laboratory expertise, but the results nevertheless guide potentially game-changing decisions for patients.