NanoVar : accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing

NanoVar : accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing

The recent advent of third-generation sequencing technologies brings promise for better characterization of genomic structural variants by virtue of having longer reads. However, long-read applications are still constrained by their high sequencing error rates and low sequencing throughput. Here, we...

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Bibliographic Details
Main Authors: Tham, Cheng Yong, Tirado-Magallanes, Roberto, Goh, Yufen, Fullwood, Melissa Jane, Koh, Bryan T. H., Wang, Wilson, Ng, Chin Hin, Chng, Wee Joo, Thiery, Alexandre, Tenen, Daniel G., Benoukraf, Touati
Other Authors: School of Biological Sciences
Format: Article
Language:English
Published: 2021
Subjects:
Science::Medicine
Structural Variants
SV Characterization
Online Access:https://hdl.handle.net/10356/147971
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Institution: Nanyang Technological University
Language: English
Description
Summary:The recent advent of third-generation sequencing technologies brings promise for better characterization of genomic structural variants by virtue of having longer reads. However, long-read applications are still constrained by their high sequencing error rates and low sequencing throughput. Here, we present NanoVar, an optimized structural variant caller utilizing low-depth (8X) whole-genome sequencing data generated by Oxford Nanopore Technologies. NanoVar exhibits higher structural variant calling accuracy when benchmarked against current tools using low-depth simulated datasets. In patient samples, we successfully validate structural variants characterized by NanoVar and uncover normal alternative sequences or alleles which are present in healthy individuals.

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