title: Using ERDS to infer copy-number variants in high-coverage genomes.
abstract: Although there are many methods available for inferring copy-number variants (CNVs) from next-generation sequence data, there remains a need for a system that is computationally efficient but that retains good sensitivity and specificity across all types of CNVs. Here, we introduce a new method, estimation by read depth with single-nucleotide variants (ERDS), and use various approaches to compare its performance to other methods. We found that for common CNVs and high-coverage genomes, ERDS performs as well as the best method currently available (Genome STRiP), whereas for rare CNVs and high-coverage genomes, ERDS performs better than any available method. Importantly, ERDS accommodates both unique and highly amplified regions of the genome and does so without requiring separate alignments for calling CNVs and other variants. These comparisons show that for genomes sequenced at high coverage, ERDS provides a computationally convenient method that calls CNVs as well as or better than any currently available method.
authors.affiliation: Center for Human Genome Variation, Duke University, Durham, NC 27708, USA. mingfu.zhu@duke.edu
authors.forename: Mingfu
authors.initials: M
authors.lastname: Zhu
authors.forename: Anna C
authors.initials: AC
authors.lastname: Need
authors.forename: Yujun
authors.initials: Y
authors.lastname: Han
authors.forename: Dongliang
authors.initials: D
authors.lastname: Ge
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Maia
authors.forename: Qianqian
authors.initials: Q
authors.lastname: Zhu
authors.forename: Erin L
authors.initials: EL
authors.lastname: Heinzen
authors.forename: Elizabeth T
authors.initials: ET
authors.lastname: Cirulli
authors.forename: Kimberly
authors.initials: K
authors.lastname: Pelak
authors.forename: Min
authors.initials: M
authors.lastname: He
authors.forename: Elizabeth K
authors.initials: EK
authors.lastname: Ruzzo
authors.forename: Curtis
authors.initials: C
authors.lastname: Gumbs
authors.forename: Abanish
authors.initials: A
authors.lastname: Singh
authors.forename: Sheng
authors.initials: S
authors.lastname: Feng
authors.forename: Kevin V
authors.initials: KV
authors.lastname: Shianna
authors.forename: David B
authors.initials: DB
authors.lastname: Goldstein
mesh_terms: D000465:Algorithms; D056915:DNA Copy Number Variations; D017353:Gene Deletion; D015894:Genome, Human; D060005:Genotyping Techniques; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D054928:Validation Studies as Topic