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Evaluation and comparison of three assays for molecular detection of spinal muscular atrophy

  • Liang Li , Wan-Jun Zhou , Ping Fang , Ze-Yan Zhong , Jian-Sheng Xie , Ti-Zhen Yan , Jian Zeng , Xu-Hui Tan and Xiang-Min Xu EMAIL logo
Published/Copyright: October 18, 2016
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Clinical Chemistry and Laboratory Medicine (CCLM)
From the journal Clinical Chemistry and Laboratory Medicine (CCLM) Volume 55 Issue 3

Abstract

Background:

Spinal muscular atrophy (SMA) is mainly caused by deletions in SMA-related genes. The objective of this study was to develop gene-dosage assays for diagnosing SMA.

Methods:

A multiplex, quantitative PCR assay and a CNVplex assay were developed for determining the copy number of SMN1, SMN2, and NAIP. Reproducibility and specificity of the two assays were compared to a multiple ligation-dependent probe amplification (MLPA) assay. To evaluate reproducibility, 30 samples were analyzed three times using the three assays. A total of 317 samples were used to assess the specificity of the two assays.

Results:

The multiplex quantitative PCR (qPCR) assay had higher reproducibility. Intra-assay CVs were 3.01%–8.52% and inter-assay CVs were 4.12%–6.24%. The CNVplex assay had ratios that were closer to expected (0.49–0.5 for one copy, 1.03–1.0 for two copies, and 1.50–1.50 for three copies). Diagnostic accuracy rates for the two assays were 100%.

Conclusions:

The multiplex qPCR assay was a simple, rapid, and cost-effective method for routine SMA diagnosis and carrier screening. The CNVplex assay could be used to detect SMAs with complicated gene structures. The assays were reliable and could be used as alternative methods for clinical diagnosis of SMA.

Keywords: gene copy number assay; genetic testing; neuronal apoptosis inhibitory protein (NAIP); spinal muscular atrophy; SMN1; SMN2
Corresponding author: Dr. Xiang-Min Xu, Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Tonghe 510515, Guangzhou, Guangdong, P.R. China, Phone: +86 20 61648293, Fax: +86 20 87278766
aLiang Li and Wan-Jun Zhou contributed equally to this work.

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This work was supported by the National Natural Science Fund of China (NSFC, No. 81101328), the Pearl River S&T Nova Program of Guangzhou (No. 2013J2200050) and the Innovation Promotion Program of Southern Medical University (No. CX2015N011).

  3. Employment or leadership: None declared.

  4. Honorarium: None declared.

  5. Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.

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Supplemental Material:

The online version of this article (DOI: 10.1515/cclm-2016-0275) offers supplementary material, available to authorized users.

Received: 2016-4-5
Accepted: 2016-8-29
Published Online: 2016-10-18
Published in Print: 2017-3-1

©2017 Walter de Gruyter GmbH, Berlin/Boston

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https://doi.org/10.1515/cclm-2016-0275
Keywords for this article
gene copy number assay; genetic testing; neuronal apoptosis inhibitory protein (NAIP); spinal muscular atrophy; SMN1; SMN2

Articles in the same Issue

  1. Frontmatter
  2. Editorials
  3. Targeting errors in microbiology: the case of the Gram stain
  4. Time for a holistic approach and standardization education in laboratory medicine
  5. Reviews
  6. Serum uric acid levels and risk of prehypertension: a meta-analysis
  7. Lactic acidosis: an update
  8. Mini Review
  9. Progress and impact of enzyme measurement standardization
  10. Opinion Paper
  11. Critical comments to a recent EFLM recommendation for the review of reference intervals
  12. IFCC Paper
  13. Quality Indicators in Laboratory Medicine: the status of the progress of IFCC Working Group “Laboratory Errors and Patient Safety” project
  14. Genetics and Molecular Diagnostics
  15. Evaluation and comparison of three assays for molecular detection of spinal muscular atrophy
  16. General Clinical Chemistry and Laboratory Medicine
  17. Risk analysis of the preanalytical process based on quality indicators data
  18. Analytical and clinical validation of the new Abbot Architect 25(OH)D assay: fit for purpose?
  19. Looking beyond linear regression and Bland-Altman plots: a comparison of the clinical performance of 25-hydroxyvitamin D tests
  20. Next-generation osmotic gradient ektacytometry for the diagnosis of hereditary spherocytosis: interlaboratory method validation and experience
  21. Diagnosis of sphingolipidoses: a new simultaneous measurement of lysosphingolipids by LC-MS/MS
  22. Monitoring nicotine intake from e-cigarettes: measurement of parent drug and metabolites in oral fluid and plasma
  23. Development of a rapid and quantitative lateral flow assay for the simultaneous measurement of serum κ and λ immunoglobulin free light chains (FLC): inception of a new near-patient FLC screening tool
  24. A real-world evidence-based approach to laboratory reorganization using e-Valuate benchmarking data
  25. Cancer Diagnostics
  26. Utility of proGRP as a tumor marker in the medullary thyroid carcinoma
  27. Cardiovascular Diseases
  28. Can non-cholesterol sterols and lipoprotein subclasses distribution predict different patterns of cholesterol metabolism and statin therapy response?
  29. Infectious Diseases
  30. Improving Gram stain proficiency in hospital and satellite laboratories that do not have microbiology
  31. Diabetes
  32. Volumetric absorptive microsampling at home as an alternative tool for the monitoring of HbA1c in diabetes patients
  33. Corrigendum
  34. EFLM Recommendation
  35. Corrigendum to: Recommendation for the review of biological reference intervals in medical laboratories
  36. Letters to the Editor
  37. Evaluation of the trueness of serum alkaline phosphatase measurement in a group of Italian laboratories
  38. Innovative software for recording preanalytical errors in accord with the IFCC quality indicators
  39. Mixing studies for abnormal coagulation screen – the current trend
  40. Identification of 5-fluorocytosine as a new interfering compound in serum capillary zone electrophoresis
  41. How to define reference intervals to rule in healthy individuals for clinical trials?
  42. Evaluation of the performance of INDEXOR® in the archive unit of a clinical laboratory: a step to Lean laboratory
  43. Evaluation of an automated chemiluminescent immunoassay for salivary cortisol measurement. Utility in the diagnosis of Cushing’s syndrome
  44. Analysis of hemolysis, icterus and lipemia in arterial blood gas specimens
  45. Comparison of three routine insulin immunoassays: implications for assessment of insulin sensitivity and response
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