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September 3, 2026Scientific ReportsOpen Access

A rapid LNA-PCR assay from blood lysate without DNA purification for the diagnosis of homozygous SMN1 deletion in spinal muscular atrophy

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Key result

Direct LNA-PCR from blood lysate yields ~95% sensitivity for detecting homozygous SMN1 deletions.

  • Sensitivity 95.00%
  • 95% CI 86.3-98.4
  • n=792

Why the study?

Many molecular diagnostic methods for spinal muscular atrophy require DNA purification and complex workflows that increase turnaround time and cost.

Does a direct LNA-PCR assay from blood lysate accurately detect homozygous SMN1 deletions in individuals suspected of SMA compared to MLPA?

Population

792 individuals including SMA patients, validated healthy controls, SMA carriers, and clinical controls

Comparison

Direct LNA-PCR from blood lysate vs MLPA reference standard

Design

Diagnostic accuracy study

Authors

GAGökçe Güllü AmuranMaltepe UniversityBPBüşra PolatMarmara UniversityDTDilşad TürkdoğanMaltepe University

Discussion

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Implication

May accelerate SMA diagnosis in limited settings; leaves open accuracy and utility pending prospective validation.

Key Points

  • To develop and validate a rapid, simplified direct locked nucleic acid polymerase chain reaction (LNA-PCR) assay for detecting homozygous SMN1 deletions directly from blood lysate without DNA purification.
  • Tested peripheral blood samples from 792 individuals (61 MLPA-confirmed SMA patients, 45 MLPA-validated healthy controls, 56 MLPA-validated carriers, and 630 clinical controls).
  • Performed direct real-time PCR in a 10 µL volume using 2.5 µL of unpurified blood lysate with LNA-modified primers targeting SMN1 and β-actin as an internal control.
  • Correctly detected 57 of 60 MLPA-confirmed homozygous SMN1 deletion cases, achieving a sensitivity of 95.00% (95% CI: 86.3–98.4%).
  • Demonstrated a specificity of 100% (95% CI: 96.5–100%), a positive predictive value of 100% (95% CI: 93.7–100%), a negative predictive value of 97.14% (95% CI: 92.1–99.1%), and an overall diagnostic accuracy of 98.15% (95% CI: 94.7–99.6%).
  • Classified the single compound heterozygous patient as SMN1-positive, consistent with the expected limitation of real-time PCR in identifying point sequence variants.

Study Design

Type

Observational (n=792)

Multicenter

No

Structured PICO

Does a direct LNA-PCR assay from blood lysate accurately detect homozygous SMN1 deletions in individuals suspected of SMA compared to MLPA?

P
Population
792 individuals, including 61 MLPA-confirmed SMA patients, 101 MLPA-validated controls/carriers, and 630 clinical controls, evaluated for a rapid direct LNA-PCR diagnostic assay.
E
Exposure
Direct locked nucleic acid polymerase chain reaction (LNA-PCR) assay from blood lysate without DNA purification
C
Comparator
Multiplex ligation-dependent probe amplification (MLPA) as the reference standard
O
Outcome
Diagnostic accuracy (sensitivity, specificity, positive predictive value, negative predictive value) for detecting homozygous SMN1 deletionssurrogate

Main Result

Effect estimate: Sensitivity 95.00% (95% CI 86.3-98.4)

The direct LNA-PCR assay provides a rapid, reliable, and cost-effective method for detecting homozygous SMN1 deletions directly from blood samples without DNA purification, facilitating broader SMA molecular testing.

Limitations

  • Inability to identify sequence variants, such as in compound heterozygous patients who are classified as SMN1-positive.
  • Not reliable for carrier identification or quantification of SMN1 gene copy numbers due to overlapping grey zones.
  • Inability to identify sequence variants (compound heterozygous patients are classified as SMN1-positive)
  • Potential technical artifacts causing false negatives in single replicates
  • Method may be ambitious for quantification of SMN1 gene or carrier identification

Cite This Study

Amuran et al. (2026) conducted an observational in Spinal Muscular Atrophy (n=792). Direct LNA-PCR assay vs. Multiplex ligation-dependent probe amplification (MLPA) was evaluated on Diagnostic accuracy for detecting homozygous SMN1 deletions (Sensitivity 95.00%, 95% CI 86.3-98.4). The direct LNA-PCR assay from blood lysate without DNA purification demonstrated 95.00% sensitivity and 100% specificity for detecting homozygous SMN1 deletions in spinal muscular atrophy.

synapsesocial.com/papers/6a9934ea636c6408cfa7c9f5https://doi.org/10.1038/s41598-026-69572-6
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Also Consider

Synapse has enriched 5 closely related papers on similar clinical questions. Consider them for comparative context:

  1. 1Locked nucleic acid (LNA) based PCR approach for the diagnosis and screening of spinal muscular atrophy2026
  2. 2A new line method; A direct test in spinal muscular atrophy screening for DBS2023 · 2 citations
  3. 3A rapid and easy-to-use spinal muscular atrophy screening tool based on primers with high specificity and amplification efficiency for SMN1 combined with single-stranded tag hybridization assay2024 · 3 citations
  4. 4A Single-Tube Nested PCR Method for SMN1 Deletion Detection in Spinal Muscular Atrophy2026
  5. 5Analytical validation of the amplification refractory mutation system polymerase chain reaction-capillary electrophoresis assay to diagnose spinal muscular atrophy2024 · 2 citations