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Related Concept Videos

  1. Home
  3. Benchmarking Nanopore Sequencing For Cln2 (tpp1) Mutation Detection: Integrating Rapid Genomics And Orthogonal Validation For Precision Diagnostics.
  1. Home
  3. Benchmarking Nanopore Sequencing For Cln2 (tpp1) Mutation Detection: Integrating Rapid Genomics And Orthogonal Validation For Precision Diagnostics.

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Benchmarking Nanopore Sequencing for CLN2 (TPP1) Mutation Detection: Integrating Rapid Genomics and Orthogonal

Betül Teker1, Gökce Akan2, Hasan Hüseyin Kazan3

  • 1Institute of Health Sciences, Istanbul University, 34452 Fatih, Türkiye.

International Journal of Molecular Sciences
|June 13, 2025

View abstract on PubMed

Summary
This summary is machine-generated.

Oxford Nanopore sequencing accurately detects TPP1 gene mutations in CLN2 disease patients. This method, combined with enzymatic assays, enhances diagnostic precision for timely treatment of this rare neurodegenerative disorder.

Keywords:
CLN2DNA sequencingTPP1TPP1 enzyme activitycomprehensive carelong-read sequencing

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Area of Science:

  • Genetics and Genomics
  • Biochemistry
  • Rare Diseases

Background:

  • CLN2 disease, a rare lysosomal storage disorder, stems from TPP1/CLN2 gene mutations, leading to neuronal ceroid lipofuscinosis.
  • Impaired tripeptidyl peptidase 1 (TPP1) activity due to these mutations causes progressive neurodegeneration.
  • Early diagnosis and enzyme replacement therapy are crucial for managing CLN2 disease progression.

Purpose of the Study:

  • To evaluate Oxford Nanopore long-read sequencing (ONT-LRS) for detecting TPP1 gene mutations in Turkish CLN2 patients.
  • To assess the concordance of ONT-LRS with Sanger sequencing and TPP1 enzymatic activity assays.
  • To expand the understanding of TPP1 mutation spectrum in the Turkish CLN2 cohort.

Main Methods:

  • Targeted sequencing of the entire TPP1 gene (6846 bp) using Oxford Nanopore MinIon platform with a custom primer panel.
  • Validation of detected variants through Sanger sequencing.
  • Correlation of genetic findings with TPP1 enzyme activity measured in leukocytes and dried blood spots.

    • Main Results:

    • Four pathogenic/likely pathogenic TPP1 variants (c.622C>T, c.857A>G, c.1204G>T, c.225A>G) and 14 benign variants were identified.
    • Novel findings include the homozygous state of c.857A>G and compound heterozygous c.225A>G/c.622C>T variants.
    • Significantly reduced TPP1 enzymatic activity was observed in all affected individuals (p < 0.0001).

    Conclusions:

    • ONT-LRS provides a robust and cost-effective method for high-resolution TPP1 gene analysis.
    • Integrating molecular and biochemical data improves diagnostic accuracy for CLN2 disease.
    • This approach supports timely interventions, especially in regions with consanguinity and limited diagnostic resources.