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Nexus copy number software version 7

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Nexus Copy Number Software version 7.0 is a bioinformatics tool designed for the analysis and visualization of copy number variations (CNVs) in genomic data. The software provides core functionality for processing and interpreting copy number information from high-throughput sequencing experiments.

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Lab products found in correlation

Agilent 4 180k microarrays, by Agilent Technologies (4 mentions) Feature extraction software, by BioDiscovery (3 mentions) Agilent 4x180k microarrays, by Agilent Technologies (2 mentions) G1471, by Promega (1 mentions) Feature extraction software, by Agilent Technologies (1 mentions) Genomic dna uls labeling kit, by Agilent Technologies (1 mentions)

Close spelling variants of this product

Nexus Copy Number software (23 citations) Nexus Copy Number (22 citations) Nexus software (11 citations) Nexus 7.5 (9 citations) Nexus Copy Number 7.5 (5 citations) Nexus-Copy-Number version 7.5 (4 citations)

8 protocols using nexus copy number software version 7

1

Array CGH Analysis of FFPE Tumors

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Tumor tissue was microdissected from 20 μm thick sections of formalin-fixed paraffin-embedded tissue. After deparaffinization, DNA was obtained by phenol/chloroform extraction. Array CGH was performed on Agilent 4×180k microarrays (Agilent, Santa Clara, CA, p/n G4449A) according to the manufacturer’s instructions. Commercially available normal human DNA (Promega, city, WI, p/n #G1471 or #G1521,) was used as a reference. The raw microarray images were processed with Agilent Feature Extraction software and analyzed with Nexus Copy Number Software version 7.0 (Biodiscovery, El Segundo, CA, USA) as described previously14 (link).
de la Fouchardière A., Tee M.K., Peternel S., Valdebran M., Pissaloux D., Tirode F., Busam K.J., LeBoit P.E., McCalmont T.H., Bastian B.C, & Yeh I. (2020). Fusion partners of NTRK3 affect subcellular localization of the fusion kinase and cytomorphology of melanocytes. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 34(4), 735-747.
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2

Targeted NTRK3 Copy Number Profiling

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This was carried out using 500–1000 ng of genomic DNA on Agilent 4×180k microarrays (Agilent, Santa Clara, CA). The raw microarray images were processed with Agilent Feature Extraction software, and analysed using Nexus Copy Number Software version 7.0 (Biodiscovery, El Segundo, CA). Segmentation was performed requiring at least 10 probes per segment and copy number status was defined by log2ratio as follows: gain >= 0.2, amplification >=0.7, loss <= −0.17, homozygous loss <= −0.75. Cases demonstrating copy number transitions with relative copy number increase of the 3′ portion of NTRK3 with sufficient residual DNA or tissue were selected for sequencing. Given the resolution of our aCGH platform, we included copy number transitions within 50 kb of NTRK3.
Yeh I., Tee M.K., Botton T., Shain A.H., Sparatta A.J., Gagnon A., Vemula S.S., Garrido M.C., Nakamaru K., Isoyama T., McCalmont T.H., LeBoit P.E, & Bastian B.C. (2016). NTRK3 kinase fusions in Spitz tumours. The Journal of pathology, 240(3), 282-290.
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3

Array Comparative Genomic Hybridization Analysis

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Array comparative genomic hybridization (CGH) was carried out with 1–1.5 μg of genomic DNA on Agilent 4×180K microarrays (Agilent, Santa Clara, CA, USA) according to the manufacturer’s instructions. Commercially available normal human DNA (Promega #G1471 or #G1521, WI, USA) was used as a reference. Scanned images were processed using Agilent Feature Extraction software. Analysis was performed with Nexus Copy Number Software version 7.0 (Biodiscovery, El Segundo, CA, USA).
Yeh I., de la Fouchardiere A., Pissaloux D., Mully T.W., Garrido M.C., Vemula S.S., Busam K.J., LeBoit P.E., McCalmont T.H, & Bastian B.C. (2015). Clinical, Histopathologic and Genomic Features of Spitz Tumors with ALK Fusions. The American journal of surgical pathology, 39(5), 581-591.
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4

aCGH Microarray Analysis and MET Sequencing

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aCGH was carried out with 500-1000 ng of genomic DNA on Agilent 4x180k microarrays (Agilent, Santa Clara, CA). The raw microarray images were processed with Agilent Feature Extraction software, and analyzed using Nexus Copy Number Software version 7.0 (Biodiscovery, El Segundo, CA). Cases demonstrating copy number transitions with copy number increase of the 3’ portion of MET and with sufficient residual DNA or tissue were selected for sequencing. A total of 74 cases were identified with gain of the distal portion of the long arm of chromosome 7 (including the 6 cases with MET copy number transitions). Of the 68 cases without copy number transitions in MET, 41 with sufficient residual DNA or tissue were selected for sequencing.
Yeh I., Botton T., Talevich E., Shain A.H., Sparatta A.J., de la Fouchardiere A., Mully T.W., North J.P., Garrido M.C., Gagnon A., Vemula S.S., McCalmont T.H., LeBoit P.E, & Bastian B.C. (2015). Activating MET Kinase Rearrangements in Melanoma and Spitz Tumors. Nature communications, 6, 7174.
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5

aCGH Microarray Analysis and MET Sequencing

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aCGH was carried out with 500-1000 ng of genomic DNA on Agilent 4x180k microarrays (Agilent, Santa Clara, CA). The raw microarray images were processed with Agilent Feature Extraction software, and analyzed using Nexus Copy Number Software version 7.0 (Biodiscovery, El Segundo, CA). Cases demonstrating copy number transitions with copy number increase of the 3’ portion of MET and with sufficient residual DNA or tissue were selected for sequencing. A total of 74 cases were identified with gain of the distal portion of the long arm of chromosome 7 (including the 6 cases with MET copy number transitions). Of the 68 cases without copy number transitions in MET, 41 with sufficient residual DNA or tissue were selected for sequencing.
Yeh I., Botton T., Talevich E., Shain A.H., Sparatta A.J., de la Fouchardiere A., Mully T.W., North J.P., Garrido M.C., Gagnon A., Vemula S.S., McCalmont T.H., LeBoit P.E, & Bastian B.C. (2015). Activating MET Kinase Rearrangements in Melanoma and Spitz Tumors. Nature communications, 6, 7174.
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6

Array CGH Analysis of FFPE Tumors

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Tumor tissue was microdissected from 20 μm thick sections of formalin-fixed paraffin-embedded tissue. After deparaffinization, DNA was obtained by phenol/chloroform extraction. Array CGH was performed on Agilent 4×180k microarrays (Agilent, Santa Clara, CA, p/n G4449A) according to the manufacturer’s instructions. Commercially available normal human DNA (Promega, city, WI, p/n #G1471 or #G1521,) was used as a reference. The raw microarray images were processed with Agilent Feature Extraction software and analyzed with Nexus Copy Number Software version 7.0 (Biodiscovery, El Segundo, CA, USA) as described previously14 (link).
de la Fouchardière A., Tee M.K., Peternel S., Valdebran M., Pissaloux D., Tirode F., Busam K.J., LeBoit P.E., McCalmont T.H., Bastian B.C, & Yeh I. (2020). Fusion partners of NTRK3 affect subcellular localization of the fusion kinase and cytomorphology of melanocytes. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 34(4), 735-747.
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7

aCGH Analysis of Genetic Alterations

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aCGH analysis was performed using CytoChip 4× 180K v2.0 (Agilent Technologies Denmark ApS, Glostrup, Denmark). The analysis was conducted according to the manufacturer’s instructions using 0.5 µg patient DNA from bone marrow cells at diagnosis and peripheral blood cells at remission, as described in [27 (link)]. After hybridization and washing, the oligo array was scanned at 2.5 µm with a GenePix 4400A microarray scanner. Initial analysis and normalization were then carried out with Agilent CytoGenomics version 3.0.6.6 (Agilent Technologies). For analysis and visualization, normalized log2 probe signal values were imported into Nexus Copy Number software version 7.5 (BioDiscovery, El Segundo, CA, USA) and segmented using the FASST2 segmentation algorithm with a minimum of three probes/segment. Regions of gains or losses contained within copy number variable regions (CNVs) were discarded. The human reference genome was NCBI build 37 (hg19). Bioinformatics analysis was performed by querying the UCSC database (UCSC database. Availabel online: https://genome.ucsc.edu, accessed on 15 March 2021).
, & Kjeldsen E. (2022). Congenital Aneuploidy in Klinefelter Syndrome with B-Cell Acute Lymphoblastic Leukemia Might Be Associated with Chromosomal Instability and Reduced Telomere Length. Cancers, 14(9), 2316.
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8

Genome-wide Copy Number Variation Analysis

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Isolated DNA was labeled using the Genomic DNAULS Labeling Kit (Agilent) and subsequently hybridized on Agilent SurePrint G3 Human CGH Microarrays 4 × 180 K (Agilent) according to the manufacturer’s protocol version 3.5. Briefly, 1 μg DNA of each cell line and 1 μg normal genetic reference DNA (Promega) were differentially labeled with ULS-Cy5 and ULS-Cy3 (both Agilent), respectively. After hybridizing and washing according to the manufacturer’s instructions, slides were scanned with microarray scanner G256BA (Agilent), and images were analyzed by Feature Extraction software version 10.7.1.1 (Agilent). The aCGH data were visualized and analyzed using Nexus Copy Number software version 7.5 (BioDiscovery). The correlation between average CGH copy number and average gene expression was performed using Pearson’s correlation with aCGH Log2 ratio probe mean values as the X-axis versus ASXL3 expression Log2 ratios as the Y-axis. The significance threshold was P < 0.05 (two-sided t test).
Shukla V., Rao M., Zhang H., Beers J., Wangsa D., Wangsa D., Buishand F.O., Wang Y., Yu Z., Stevenson H.S., Reardon E.S., McLoughlin K.C., Kaufman A.S., Payabyab E.C., Hong J.A., Zhang M., Davis S., Edelman D., Chen G., Miettinen M.M., Restifo N.P., Ried T., Meltzer P.A, & Schrump D.S. (2017). ASXL3 is a Novel Pluripotency Factor in Human Respiratory Epithelial Cells and a Potential Therapeutic Target in Small Cell Lung Cancer. Cancer research, 77(22), 6267-6281.
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