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Updated: Sep 9, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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Visual Inspection of Sequencing Data for Diagnosis: Practical Guide to Structural Variant Analysis Using Integrative

Benjamin Ganne^1,2, Clément Hersent³, Vincent Gatinois^3,4

¹Unit of Chromosomal Genetics and Research Platform Chromostem, Department of Molecular Genetics and Cytogenomics, Site Unique de Biologie (SUB), Montpellier CHU, Montpellier, France. benjamin.ganne@chu-montpellier.fr.

Methods in Molecular Biology (Clifton, N.J.)

|August 30, 2025

Abstract

None:

Next-generation sequencing (NGS) has revolutionized clinical genomics, enhancing structural variant (SV) analysis, especially found in chromothripsis. This guide focuses on key steps of SV interpretation using IGV, detailing methods for assessing SV veracity and distinguishing true SVs from artifacts. This resource aims to aid clinicians and researchers in effectively interpreting NGS-derived SV calling data to improve diagnostic accuracy and patient care.

Keywords:

Bioinformatics Chromothripsis Copy number variation IGV Structural variation

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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