Simple and efficient germline copy number variant visualization method for the Ion AmpliSeq™ custom panel.

Area of Science:

• Genomics
• Molecular Genetics
• Bioinformatics

Background:

• Next-generation sequencing (NGS) accelerates disease-causing gene mutation discovery.
• Focus has been on single-nucleotide variants and indels, but structural variations like copy number variations (CNVs) are increasingly recognized as important disease causes.
• Limited tools exist for multiplex PCR-based target genome enrichment for CNV analysis.

Purpose of the Study:

• To develop a simple and efficient method for copy number variation visualization specifically for Ion AmpliSeq™ target resequencing data.
• To assess the utility of this method in identifying CNVs in a large cohort.

Main Methods:

• Developed a copy number variation visualization method leveraging the uniform read length and position of Ion AmpliSeq™ multiplex PCR products.
• Utilized depth of coverage information from amplicon coverage matrices for copy number detection.
• Validated the method using positive controls and a large Japanese hearing loss cohort.

Main Results:

• Successfully confirmed known copy number loss in the STRC gene and copy number gain in trisomy 21 cases.
• Identified numerous gene copy number variants in a cohort of 2,475 Japanese hearing loss patients.
• STRC gene copy number loss was the most frequent CNV, found in 129 patients.

Conclusions:

• The developed copy number visualization method for Ion AmpliSeq™ data enables efficient CNV analysis for large sample comparisons.
• The method is straightforward, requiring only basic calculations with standard spreadsheet software.