Purpose: To compare the accuracy of a commercially
available MLPA kit with a laboratory developed RT-PCR assay for the detection
of SMN1 and SMN2 copy numbers in clinical samples. Methods: We developed and
validated a laboratory developed real time PCR based test capable of detecting
SMN1 and SMN2 copy numbers in individuals. We also validated an MLPA kit
purchased from MRC Holland for the same purpose. We then analyzed a series of
1027 anonymized samples using both technologies. When discrepant results were obtained,
each sample was re-analyzed at least twice using both platforms. Results: Five
samples did not yield results in either assay. For SMN1 copy number analysis, 2
RT-PCR assays revealed indeterminant results and all 1020 other
samples were concordant for SMN1 copy number. There were 9 discrepancies in
SMN2 copy number determination mostly due to a variability in MLPA analysis. Conclusion:
Both MLPA and RTPCR assays give a reliable estimate of SMN1 copy number and are
therefore appropriate for population based carrier screening for Spinal Muscular
Atrophy Type 1. The MLPA kit has a low incidence (<1%) of underestimating
the SMN2 copy number by 1 copy, but this inconsistency is of little clinical
significance and can be overcome by replicate testing.
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