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Updated: Nov 28, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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SnackVar: An Open-Source Software for Sanger Sequencing Analysis Optimized for Clinical Use.

Young-Gon Kim1, Man Jin Kim1, Jee-Soo Lee1

  • 1Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea.

The Journal of Molecular Diagnostics : JMD
|November 27, 2020
PubMed
Summary
This summary is machine-generated.

SnackVar is a new, user-friendly software for Sanger sequencing analysis. It accurately identifies genetic variants, offering a faster and cost-effective solution for clinical labs compared to existing tools.

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Area of Science:

  • Bioinformatics
  • Genetics
  • Clinical Diagnostics

Background:

  • Sanger sequencing remains crucial in clinical labs despite the rise of next-generation sequencing.
  • Bioinformatics tools for Sanger sequencing have lagged behind those for next-generation sequencing.

Purpose of the Study:

  • To develop a novel, user-friendly software named SnackVar for Sanger sequencing analysis.
  • To improve the efficiency and accuracy of variant identification in clinical settings.

Main Methods:

  • Development of a graphical user interface-based software, SnackVar.
  • Prestored reference sequences for precise variant description using Human Genome Variation Society nomenclature.
  • Validation using 88 known variants in insertion/deletion-rich genes (BRCA1, APC, CALR, CEBPA).

Main Results:

  • SnackVar achieved 98.9% agreement with previously reported variants.
  • Identified one false positive due to poor-quality trace files.
  • Analysis time was less than half that of commercial software.

Conclusions:

  • SnackVar is an accurate and efficient tool for Sanger sequencing variant analysis.
  • It offers a cost-effective alternative for clinical laboratories.
  • The software simplifies the identification and description of genetic variants.