Nexus copy number v9

Manufactured by BioDiscovery

Nexus Copy Number v9.0 is a bioinformatics software tool used for the analysis and visualization of copy number variations (CNVs) in genomic data. The software provides a comprehensive suite of algorithms and visualization options for the detection and interpretation of CNVs from various genomic profiling technologies.

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Lab products found in correlation

Qubit 2.0 fluorometer, by Thermo Fisher Scientific (2 mentions) Infinium ffpe qc kit, by Illumina (1 mentions) Infinium hd ffpe dna restoration kit, by Illumina (1 mentions) Genomestudio data analysis software v2011, by Illumina (1 mentions)

2 protocols using nexus copy number v9

Genome-wide SNP Profiling of FFPE Tumor Samples

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FFPE tissues were sectioned. Archived hematoxylin and eosin-stained tissue slides were evaluated by a pathologist for the area with at least 70% tumor cells for manual macrodissection using a needle tip or scalpel. A minimum amount of 200 ng of DNA extracted from each FFPE tissue was quantified by the Qubit® 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA) and qualified using the Infinium FFPE QC Kit before being processed with the Infinium HD FFPE DNA Restoration Kit (Illumina, San Diego, CA), all according to the manufacturers’ protocols.
SNP array was performed with the HumanCytoSNP FFPE-12 v2.1 DNA Analysis BeadChip (Illumina, San Diego, CA), according to the manufacturer’s instructions. This array contains approximately 299,140 SNP markers spanning the entire genome with an average probe spacing of 72 kb. The data were analyzed with GenomeStudio Data Analysis Software v. 2011.1 (Illumina, San Diego, CA) and Nexus Copy Number v9.0 (BioDiscovery, Inc., El Segundo, CA) using the reference human genome (hg19/GRCh37).

Sunpaweravong S., Bunbanjerdsuk S., Pongrujikorn T., Naktang C., Sunpaweravong P., Nitiruangjaras A., Dechaphankul T, & Jinawath N. (2019). Clonal relationship of synchronous head and neck cancer and esophageal cancer assessed by single nucleotide polymorphism-based loss of heterozygosity analysis. BMC Cancer, 19, 1174.

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Copy Number Profiling of Targeted Sequencing

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DNA copy number profiling of the targeted sequencing data was performed using NEXUS Copy Number, v9.0 (BioDiscovery, El Segundo, CA). CNA regions were defined by a rank segmentation algorithm. In the rank segmentation algorithm, we set a threshold for segmentation of p = 1.0E–6. The thresholds for copy number gain and loss were 0.3 and −0.4 on a log₂ scale, respectively. The thresholds for amplification and homozygous deletion were 1.0 and −1.0 on a log₂ scale, respectively.

Choi S.H., Jung S.H, & Chung Y.J. (2017). Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations. Genomics & Informatics, 15(4), 136-141.

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