Abstract
BackgroundSNP 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.ResultsWe 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.ConclusionsOur 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.
Highlights
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
Characterization of CNV calls in NA12878 with arrays, long and short reads using a read-depth based score In this study we investigated and contrasted specific characteristics of CNV calls, derived from three different technologies - SNP arrays, short-read and long-read sequencing
To this end we assembled a large set of CNV calls for the well-studied NIST Genome in A Bottle individual of Northern European ancestry NA12878 [35]
Summary
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. Short reads enable a better digital estimation of copy numbers and improve the resolution for small variants (
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