Nexus copy number 7

Manufactured by BioDiscovery

Sourced in United States

The Nexus Copy Number 7.5 is a high-performance digital PCR (dPCR) system designed for accurate and precise copy number variation (CNV) analysis. It features a user-friendly interface, reliable performance, and advanced data analysis capabilities.

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Lab products found in correlation

Genomestudio v2011, by Illumina (2 mentions) Oncoscan ffpe assay, by Thermo Fisher Scientific (1 mentions) Chromosome analysis suite 2.0 chas, by BioDiscovery (1 mentions) Iscan reader, by Illumina (1 mentions) Human omniexpress 24 v1.0 beadchip, by Illumina (1 mentions) Cytoscan hd array, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

Nexus Copy Number (22 citations) Nexus 7.5 (9 citations) Nexus Copy Number Software version 7.0 (8 citations) Nexus-Copy-Number version 7.5 (4 citations) Nexus Copy Number 7.0 Discovery Edition software (3 citations) Nexus Copy Number Discovery 7.0 software (2 citations)

5 protocols using nexus copy number 7

Genome-wide Copy Number and LOH Analysis

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Genome-wide DNA copy number and LOH analysis was performed in 13 of 14 cases using the Affymetrix OncoScan FFPE assay (Affymetrix, CA, USA), which utilizes molecular inversion probe technology and is optimized to work on DNA derived from FFPE tissue samples [35 (link)].
Sample preparation, hybridization and scanning were performed according to the manufacturer's specifications. Analysis was performed using the Affymetrix Chromosome Analysis Suite 2.0 (ChAS) and Nexus Copy Number 7.5 software (Biodiscovery, Inc. CA, USA). All copy number alterations and regions of LOH recognized by the software were verified visually to determine erroneous calls and identify clonal or subclonal gains and losses not detected by the software. Analysis was restricted to gains and losses >1 Mb in length (Supplementary Table 4). Genomic alterations were reported based on the NCBI build 37 (hg19) of the human genome and cancer-associated genes were curated from the Cancer Gene Census (COSMIC v61 Release; http://www.sanger.ac.uk/genetics/CGP/Census/)

Ganapathi K.A., Jobanputra V., Iwamoto F., Jain P., Chen J., Cascione L., Nahum O., Levy B., Xie Y., Khattar P., Hoehn D., Bertoni F., Murty V.V., Pittaluga S., Jaffe E.S., Alobeid B., Mansukhani M.M, & Bhagat G. (2016). The genetic landscape of dural marginal zone lymphomas. Oncotarget, 7(28), 43052-43061.

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Comparative Analysis of CNV Detection Platforms

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For each array design raw data from two technical replicate experiments using NA12878 DNA were obtained directly from the manufacturer or a manufacturer-recommended service provider and analyzed independently. Two CNV call sets were generated for each array design; one based on the manufacturer recommended platform specific software and another based on the platform agnostic software Nexus Copy Number 7.5 (BioDiscovery, Hawthorne CA 90250, U.S.A.) [Additional file 5: Spreadsheet 1]. The details of each analysis are described below. All chromosomal coordinates for the resulting CNV calls are based on hg19.

Haraksingh R.R., Abyzov A, & Urban A.E. (2017). Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans. BMC Genomics, 18, 321.

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Chromosomal Microarray Analysis Protocol

Cited 1 time

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Chromosomal microarray analysis was performed using Human OmniExpress-24 v1.0 BeadChip (Illumina Inc., San Diego, CA, USA), which contains 716,503 genome-wide markers at an average spacing of 4 kb. It targets a minor allele frequency of 5%, as reported in the HapMap data. It includes SNPs within 10 kb of RefSeq genes, nonsynonymous SNPs (NCBI annotated), MHC/ADME SNPs, and sex chromosomes. DNA amplification, tagging, and hybridization were performed according to the manufacturer’s protocol, aided by the Tecan Freedom Evo (Tecan, Mannedorf, Switzerland). The array slides were scanned on an iScan Reader (Illumina, Inc., San Diego, CA, USA). All data collected were evaluated using Illumina Genome Studio v2011.1 software (Illumina, Inc., San Diego, CA, USA) and genome build GRCh37/hg19. Data were analyzed using Nexus Copy Number 7.5 (BioDiscovery, El Segundo, CA, USA). CNV classification was based on the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen) 2020 guidelines [21 (link)].

Maya I., Perlman S., Shohat M., Kahana S., Yacobson S., Tenne T., Agmon-Fishman I., Tomashov Matar R., Basel-Salmon L, & Sukenik-Halevy R. (2020). Should We Report 15q11.2 BP1-BP2 Deletions and Duplications in the Prenatal Setting?. Journal of Clinical Medicine, 9(8), 2602.

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Genome-wide SNP Array Analysis of NK Cells

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SNP microarray study was performed using the Affymetrix CytoScan HD array (Affymetrix, Inc. Santa Clara, CA) which contains 2.5 million markers, including 750,000 SNPs and 1.7 million non-polymorphic probes, with extensive coverage over 18,500 RefSeq genes, known cancer genes and 12,000 OMIM genes. In brief, 250 ng of genomic DNA for each NK cell line were hybridized to a CytoScan HD array according to the manufacturer’s protocols. Array data for copy number alterations (CNAs) and copy-neutral loss of heterozygosity (cnLOH) were analyzed using Affymetrix Chromosome Analysis Suite v.3.1 (ChAS) software and the Nexus copy number 7.5 (BioDiscovery Inc, El Segundo, CA) with a reference framework of NA33 (hg19). Regions of copy number alterations larger than 50 markers/400 kb for gain or 20 markers/100 kb for loss and copy neutral loss of heterozygosity (LOH) larger than 3 Mb are recorded. All CNAs were compared with known public databases of normal genomic variants (DGV).

Gu J., Reynolds A., Fang L., DeGraffenreid C., Sterns K., Patel K.P., Medeiros L.J., Lin P, & Lu X. (2016). Coexistence of iAMP21 and ETV6-RUNX1 fusion in an adolescent with B cell acute lymphoblastic leukemia: literature review of six additional cases. Molecular Cytogenetics, 9, 84.

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SNP Array Analysis of Thyroid Cancer Cell Lines

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SNP array analysis of all ATC cell lines except ATC17 and ATC18 and all three PTC cell lines was performed using the Illumina HumanOmni5-Quad BeadChip platform, 24:5 containing ~5 million markers (Illumina), according to the manufacturer's instructions. SNP array analysis of ATC17 and ATC18 and their matched normal control samples was performed with the Affymetrix Genome-Wide SNP Array 6.0 (Affymetrix) according to the manufacturer's instructions. Probe positions were extracted from the GRCh37 genome build and data was analysed using the Genome studio v2011.1 (Illumina) and Nexus Copy Number 7.5 (BioDiscovery, El Segundo, CA, USA) software. For ATC17 and ATC18, constitutional copy number variants were excluded based on comparison with the matched control sample. For the remaining cases, all copy number changes <1 Mb were compared with copy number polymorphisms listed in the Database of Genomic Variants (http://dgv.tcag.ca/dgv/app/home) or Nexus and excluded from further analysis if there was substantial overlap. Regions displaying loss of heterozygosity (LOH) were included as aberrant if they comprised at least 5 Mb or were part of another rearrangement.

Woodward E.L., Biloglav A., Ravi N., Yang M., Ekblad L., Wennerberg J, & Paulsson K. (2017). Genomic complexity and targeted genes in anaplastic thyroid cancer cell lines. Endocrine-related cancer, 24(5).

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