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.
Cite this paper
Strom, C. , Anderson, B. , Peng, M. , Patel, U. , Braastad, C. and Sun, W. (2013) 1000 sample comparison of MLPA and RT-PCR for carrier detection and diagnostic testing for Spinal Muscular Atrophy Type 1. Open Journal of Genetics
, 111-114. doi: 10.4236/ojgen.2013.32014
  Lefebvre, S., Burglen, L., Reboullet, S., et al. (1995) Identification and characterization of a spinal muscular atrophy-determining gene. Cell, 80, 155-165.
 McAndrew, P.E., Parsons, D.W., Simard, L.R., et al. (1997) Identification of proximal spinal muscular atrophy carriers and patients by analysis of SMNT and SMNC gene copy number. The American Journal of Human Genetics, 60, 1411-1422. doi:10.1086/515465
 Mailman, M.D., Heinz, J.W., Papp, A.C., et al. (2002) Molecular analysis of spinal muscular atrophy and modification of the phenotype by SMN2. Genetics in Medicine, 4, 20-26. doi:10.1097/00125817-200201000-00004
 Ogino, S. and Wilson, R.B. (2002) Genetic testing and risk assessment for spinal muscular atrophy (SMA). Human Genetics, 111, 477-500.
 Pearn, J. (1978) Incidence, prevalence, and gene frequency studies of chronic childhood spinal muscular atrophy. Journal of Medical Geneticst, 15, 409-413.
 Wirth, B., Rudnik-Schoneborn, S., Hahnen, E., Rohrig, D. and Zerres, K. (1995) Prenatal prediction in families with autosomal recessive proximal spinal muscular atrophy (5q11.2-q13.3): Molecular genetics and clinical experience in 109 cases. Prenatal Diagnosis, 15, 407-417.
 Prior, T.W. (2008) Carrier screening for Spinal Muscular Atrophy. Genetics in Medicine, 10, 840-842.
 Prior, T.W., Nagan, N., Sugarman, E.A., Batish, S.D. and Braastad, C. (2011) Technical standards and guidelines for spinal muscular atrophy testing. Genetics in Medicine, 13, 686-694. doi:10.1097/GIM.0b013e318220d523
 (1 September 2012) http://www.mlpa.com/
 Gomes-Curet, I., Robinson, K.G., Funanage, V.L., Crawford, T.O., Scavina, M. and Wang, W. (2007) Robust quantification of the SMN gene copy number by realtime Taqman PCR. Neurogenetics, 8, 271-278.
 French, C., Li, C., Strom, C. and Sun, W. (2004) Detection of factor V Leiden mutation by a modified photo cross-linking oligonucleotide hybridization assay. Clinical Chemistry, 50, 296-305.
 Strom, C.M., Janeczko, R.A., Anderson, B., Redman, J., Quan, F., Buller, A., McGinniss, M. and Sun, W. (2005) Technical validation of a multiplex platform to detect 30 mutations in 8 genetic diseases prevalent in individuals of Ashkenazi Jewish descent. Genetics in Medicine, 7, 633-639. doi:10.1097/01.gim.0000187120.93597.16
 Strom, C.M., Janeszco, R., Quan, F., Wang, S.-B., Buller, A., McGinniss, M. and Sun, W. (2006) Technical validation of a Luminex based multiplex assay for 40 mutations in the cystic fibrosis transmembrane regulator protein. Journal of Molecular Diagnostics, 8, 371-375.