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Copy-number analysis by base-level normalization: An intuitive visualization tool for evaluating copy number variations

Authors
 Hongkyung Kim  ;  Yeeun Shim  ;  Taek Gyu Lee  ;  Dongju Won  ;  Jong Rak Choi  ;  Saeam Shin  ;  Seung-Tae Lee 
Citation
 CLINICAL GENETICS, Vol.103(1) : 35-44, 2023-01 
Journal Title
CLINICAL GENETICS
ISSN
 0009-9163 
Issue Date
2023-01
Keywords
CABANA ; CNV visualization ; NGS ; candidate CNV ; confirmatory test ; single-base-level normalization
Abstract
Next-generation sequencing (NGS) facilitates comprehensive molecular analyses that help with diagnosing unsolved disorders. In addition to detecting single-nucleotide variations and small insertions/deletions, bioinformatics tools can identify copy number variations (CNVs) in NGS data, which improves the diagnostic yield. However, due to the possibility of false positives, subsequent confirmation tests are generally performed. Here, we introduce Copy-number Analysis by BAse-level NormAlization (CABANA), a visualization tool that allows users to intuitively identify candidate CNVs using the normalized single-base-level read depth calculated from NGS data. To demonstrate how CABANA works, NGS data were obtained from 474 patients with neuromuscular disorders. CNVs were screened using a conventional bioinformatics tool, ExomeDepth, and then we normalized and visualized those data at the single-base level using CABANA, followed by manual inspection by geneticists to filter out false positives and determine candidate CNVs. In doing so, we identified 31 candidate CNVs (7%) in 474 patients and subsequently confirmed all of them to be true using multiplex ligation-dependent probe amplification. The performance of CABANA was deemed acceptable by comparing its diagnostic yield with previous data about neuromuscular disorders. Despite some limitations, we expect CABANA to help researchers accurately identify CNVs and reduce the need for subsequent confirmation testing.
Full Text
https://onlinelibrary.wiley.com/doi/10.1111/cge.14236
DOI
10.1111/cge.14236
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Laboratory Medicine (진단검사의학교실) > 1. Journal Papers
Yonsei Authors
Kim, Hongkyung(김홍경)
Shin, Saeam(신새암) ORCID logo https://orcid.org/0000-0003-1501-3923
Won, Dongju(원동주) ORCID logo https://orcid.org/0000-0002-0084-0216
Lee, Seung-Tae(이승태) ORCID logo https://orcid.org/0000-0003-1047-1415
Choi, Jong Rak(최종락) ORCID logo https://orcid.org/0000-0002-0608-2989
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/197690
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