SegSeq

[…] in normal samples according to our panel of normal bams, and a threshold of greater than 1% in the Exome Aggregation Consortium (ExAC) database.Copy number alterations (CNAs) were first detected with SegSeq for 31 WGS, and GATK4 Alpha for 283 WES. GISTIC2.0 was performed to identify significantly amplified or deleted genomic regions. Hierarchical clustering was used to identify sample subtypes. St […]

[…] X-38.45 X. The mapping rate of clear data ranged from 97.03 to 97.27%, and the genome coverage ranged from 99.83% to 99.85 (Additional file : Table S5).For CNV detection, we employed a MATLAB packet, SegSeq. Only two de novo CNVs were identified in the proband. However, both CNVs were reported as polymorphisms in the Database of Genomic Variants (DGV).Single Nucleotide Variants (SNVs) were detecte […]

[…] 00 Genomes Project data have been shown to predict accurate copy number values due to its capability of high-resolution CNV calls []. There have been several approaches based on RD, such as MAQ [, ], SegSeq [], mrFAST [] and CNVnator []. CNVnator can overcome some disadvantages, including unique regions of the genome [, , ], poor breakpoint resolution [, , , ], and detect different sizes of CNVs, […]

[…] lysis Toolkit. Point mutations were identified by MuTect, a Bayesian algorithm; short insertions and deletions determined by local assembly. To detect DNA copy-number alterations (CNAs), we performed SegSeq11 to infer somatic CNA in genomes on the basis of WES reads. Copy numbers < 1.5 were considered to indicate deletions, and those > 2.5 were considered amplifications by comparison to process ma […]

[…] pment of computational methods for estimating copy number alterations (CNAs). Many tools have been developed for estimating CNAs from WES data based on paired normal-tumor samples such as CNV-seq [], SegSeq [], ADTEx [], CONTRA [], EXCAVATOR [], ExomeCNV [], Control-FREEC (control-FREE Copy number caller) [], and CNVseeqer []. For example, VarScan2 [] is a computational tool that can estimate soma […]

[…] sequencing across each lung tumor and liver metastasis. Matched normal tail DNA was used as a control. We were particularly interested in recurrent changes enriched in metastatic tumors. We employed Segseq [] and CNVseq [] to identify CNV changes. We did not find recurrent examples of metastasis-specific enrichment or newly acquired genetic amplifications in Mycl or deletions of Pten in the liver […]