Concurrent detection of targeted copy number variants and mutations using a XXXX next generation sequencing panel allows comprehensive genetic analysis using a single testing strategy.

@entity18258 @entity5 @entity72622 @entity16719 @entity9604 @entity11626 @entity984 @entity471 @entity876 @entity818 @entity14538 @entity8102
UNASSIGNED: Currently, comprehensive genetic testing of @entity5 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 @entity471 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 @entity72622 and @entity16719 , @entity876 deletion, @entity9604 deletion, gain of @entity18258 on 8q, and 5q deletion, including @entity14538 and @entity8102 . We were also able to detect exon-level duplications, including so-called @entity11626 ( @entity11626 ) partial tandem duplication, in 9 cases. In the 63 cases that were negative for mutations, targeted CNVs were observed in 4 cases. Targeted @entity471 detection by NGS had very high concordance with single nucleotide polymorphism microarray, the current gold standard. We found that @entity9604 deletion was strongly associated with @entity876 alterations and 7q deletion was associated with mutations in @entity876 , @entity984 and @entity818 . This proof-of-concept study demonstrates the feasibility of using the same NGS data to simultaneously detect both somatic mutations and targeted CNVs.
