title: Concurrent detection of targeted copy number variants and mutations using a myeloid malignancy next generation sequencing panel allows comprehensive genetic analysis using a single testing strategy.
abstract: Currently, comprehensive genetic testing of myeloid malignancies requires multiple testing strategies with high costs. Somatic mutations can be detected by next generation sequencing (NGS) but copy number variants (CNVs) require cytogenetic methods including karyotyping, fluorescence in situ hybidization and microarray. Here, we evaluated a new method for CNV detection using read depth data derived from a targeted NGS mutation panel. In a cohort of 270 samples, we detected pathogenic mutations in 208 samples and targeted CNVs in 68 cases. The most frequent CNVs were 7q deletion including LUC7L2 and EZH2, TP53 deletion, ETV6 deletion, gain of RAD21 on 8q, and 5q deletion, including NSD1 and NPM1. We were also able to detect exon-level duplications, including so-called KMT2A (MLL) partial tandem duplication, in 9 cases. In the 63 cases that were negative for mutations, targeted CNVs were observed in 4 cases. Targeted CNV detection by NGS had very high concordance with single nucleotide polymorphism microarray, the current gold standard. We found that ETV6 deletion was strongly associated with TP53 alterations and 7q deletion was associated with mutations in TP53, KRAS and IDH1. This proof-of-concept study demonstrates the feasibility of using the same NGS data to simultaneously detect both somatic mutations and targeted CNVs.
authors.affiliation: ARUP Laboratories, Salt Lake City, UT, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Shen
authors.affiliation: ARUP Laboratories, Salt Lake City, UT, USA.
authors.forename: Philippe
authors.initials: P
authors.lastname: Szankasi
authors.affiliation: ARUP Laboratories, Salt Lake City, UT, USA.
authors.forename: Maria
authors.initials: M
authors.lastname: Sederberg
authors.affiliation: ARUP Laboratories, Salt Lake City, UT, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Schumacher
authors.affiliation: ARUP Laboratories, Salt Lake City, UT, USA.
authors.forename: Kimberly A
authors.initials: KA
authors.lastname: Frizzell
authors.affiliation: ARUP Laboratories, Salt Lake City, UT, USA.
authors.forename: Elaine P
authors.initials: EP
authors.lastname: Gee
authors.affiliation: Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
authors.forename: Jay L
authors.initials: JL
authors.lastname: Patel
authors.affiliation: Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
authors.forename: Sarah T
authors.initials: ST
authors.lastname: South
authors.affiliation: Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
authors.forename: Xinjie
authors.initials: X
authors.lastname: Xu
authors.affiliation: Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
authors.forename: Todd W
authors.initials: TW
authors.lastname: Kelley
mesh_terms: D056915:DNA Copy Number Variations; D005260:Female; D019337:Hematologic Neoplasms / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D009363:Neoplasm Proteins / Q000235:genetics*; D000090243:Nucleophosmin
chemical_list: C000716967:NPM1 protein, human; D009363:Neoplasm Proteins; D000090243:Nucleophosmin
keywords: circular binary segmentation; copy number variant; molecular diagnostics; myeloid malignancies; next generation sequencing