Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data

0Citations
Citations of this article
7Readers
Mendeley users who have this article in their library.

This article is free to access.

Abstract

Background: SNP arrays, short- and long-read genome sequencing are genome-wide high-throughput technologies that may be used to assay copy number variants (CNVs) in a personal genome. Each of these technologies comes with its own limitations and biases, many of which are well-known, but not all of them are thoroughly quantified. Results: We assembled an ensemble of public datasets of published CNV calls and raw data for the well-studied Genome in a Bottle individual NA12878. This assembly represents a variety of methods and pipelines used for CNV calling from array, short- and long-read technologies. We then performed cross-technology comparisons regarding their ability to call CNVs. Different from other studies, we refrained from using the golden standard. Instead, we attempted to validate the CNV calls by the raw data of each technology. Conclusions: Our study confirms that long-read platforms enable recalling CNVs in genomic regions inaccessible to arrays or short reads. We also found that the reproducibility of a CNV by different pipelines within each technology is strongly linked to other CNV evidence measures. Importantly, the three technologies show distinct public database frequency profiles, which differ depending on what technology the database was built on.

Cite

CITATION STYLE

APA

Lavrichenko, K., Johansson, S., & Jonassen, I. (2021). Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data. BMC Genomics, 22(1). https://doi.org/10.1186/s12864-021-08082-3

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free