Agilent cytogenomics software

Manufactured by Agilent Technologies

Sourced in United States

Agilent CytoGenomics software is a tool designed for the analysis and interpretation of cytogenetic and genomic data. It provides a comprehensive suite of features for visualization, analysis, and reporting of genomic data generated from various laboratory techniques.

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CytoGenomics software (43 citations) Agilent CytoGenomics (6 citations) Agilent CytoGenomics software 4.0.3.12 (2 citations)

23 protocols using agilent cytogenomics software

Comprehensive Genomic Profiling of CTCs and cfDNA

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Two-color probe-based aCGH was performed using Agilent Oligonucleotide Arraybased CGH for Genomic DNA Analysis (Sure Print G3 Human CGH array, 4x180K) [32] (link). Data were analyzed using the Agilent Cytogenomics Software, and all CNAs were manually analyzed [32] (link). CNAs were then cross-referenced with publiclyavailable prostate cancer datasets using cBioportal [35] (link). The biological or clonality of CTCs genomic concordance (CNA present in CTCs were detected in cfDNA) and discordance (CNA present in CTCs, but not detected in paired cfDNA samples) were calculated by comparing CNA in CTCs and cfDNA. Next, to minimize the false positives result, stringent filtering criteria were applied by using a minimum 3+ contiguous probes distribution, and two independent calls were used to call a copy gain or loss event. Further, all genomic altered genes were assessed manually based on aCGH probe distribution within chromosomal aberrations region analyzed in the Agilent Cytogenomics Software. In addition, genomic agreement and This article is protected by copyright. All rights reserved. disagreement between 64 CTCs and paired cfDNA CNAs (gain versus no gain, or loss versus no loss) from combined radium and PROPHECY studies were independently analyzed by Cohen's Kappa method in Graph Pad prism software (Table S3).

Gupta S., Hovelson D.H., Kemeny G., Halabi S., Foo W.C., Anand M., Somarelli J.A., Tomlins S.A., Antonarakis E.S., Luo J., Dittamore R.V., George D.J., Rothwell C., Nanus D.M., Armstrong A.J, & Gregory S.G. (2020). Discordant and heterogeneous clinically relevant genomic alterations in circulating tumor cells vs plasma DNA from men with metastatic castration resistant prostate cancer. Genes, chromosomes & cancer, 59(4).

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Differential Labeling and CGH Microarray Analysis

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Sample DNA (CTC, whole blood, peritumoral normal liver, and tumor tissue) and reference DNA (Agilent, Santa Clara, CA) were differentially labeled with cyanine-3 (CY3) and cyanine-5 (Cy5) dyes using the GenetiSure Amplification and Labeling Kit (Agilent) according to the manufacturer’s protocol. Purified labeled DNA samples were prepared for hybridization, which took place on Agilent 8×60 K CGH microarray slides at 67 °C for 6 h. Following the hybridization, the slides were scanned using the Agilent SureScan Microarray Scanner (Agilent). Microarray images were analyzed using the Agilent CytoGenomics software (Agilent) and the Microarray text files were analyzed using R version 3.3.2 and the packages rCGH, limma, agilp, and snapCGH.

Court C.M., Hou S., Liu L., Winograd P., DiPardo B.J., Liu S.X., Chen P.J., Zhu Y., Smalley M., Zhang R., Sadeghi S., Finn R.S., Kaldas F.M., Busuttil R.W., Zhou X.J., Tseng H.R., Tomlinson J.S., Graeber T.G, & Agopian V.G. (2020). Somatic copy number profiling from hepatocellular carcinoma circulating tumor cells. NPJ Precision Oncology, 4, 16.

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Custom Array CGH of COQ6 Gene

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As we previously reported^{25 (link)}, we conducted custom array comparative genomic hybridisation for one patient. We selected the COQ6 gene and constructed probes for it and the regions surrounding it. We used a custom HD-comparative genomic hybridisation microarray, 8 × 15 K (Agilent Technologies), in accordance with the manufacturer’s instructions. We used Agilent CytoGenomics software (Agilent Technologies) to analyse chromosomal patterns within the microarray profiles.

Nagano C., Yamamura T., Horinouchi T., Aoto Y., Ishiko S., Sakakibara N., Shima Y., Nakanishi K., Nagase H., Iijima K, & Nozu K. (2020). Comprehensive genetic diagnosis of Japanese patients with severe proteinuria. Scientific Reports, 10, 270.

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Confirming WES Results via Chromosomal Microarray

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To confirm our WES results, we performed chromosomal microarray testing using the CytoScan HD chip (Affymetrix, Santa Clara, CA, USA) in accordance with the manufacturer's instructions. Moreover, we analyzed data with ChAS software (Affymetrix), which had a calling threshold of 20 consecutive probes encompassing at least 25 kb in length. Genomic DNA was extracted from the peripheral blood samples. The first strand of cDNA was synthesized with this DNA sample as a template and designed primers. Then, the cDNA fragments were amplified by PCR with the primers, labeled, and hybridized. We analyzed pathogenic CNVs using Agilent Cytogenomics software (Agilent Technologies).
All the reported CNVs were subject to the build 37 of human genome/hg19 on NCBI. The screened CNVs for comparative analysis had to meet the following conditions: (1) deletions ≥50 kb/25 markers; duplications ≥100 kb/50 markers; (2) <50% overlap with known segmental duplications (SD); and (3) not found in the control populations cataloged in the Database of Genomic Variants (DGV). We selected 178 individuals without heart disease from our local database as controls. Other controls were selected from the SNP database (https://www.ncbi.nlm.nih.gov/projects/SNP/), 1000 Genomes Project (1000G, https://1000genomes.org), and the DGV (https://dgv.tcag.ca/dgv/app/home).

Yang R., Zhang W., Lu H., Liu J., Xia Y., Liao S., Li X., Zhang X., Fan X, & Wang C. (2022). Identification of a Novel 15q21.1 Microdeletion in a Family with Marfan Syndrome. Genetics Research, 2022, 3556302.

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Genetic Diagnostic Workflow for Chromatinopathies

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Genetic analyses were performed for diagnostic purposes and no further authorization was required from the Ethical Committee. Informed consents for genetic testing and the publication of significant results were obtained.
The patient underwent firstly array-CGH (comparative genomic hybridization) analysis with the commercial Agilent 2 × 244 kit (following manufacturer’s instructions, using the ADM-2 algorithm for data analysis with Agilent CytoGenomics software) (Agilent Technologies, Santa Clara, CA, USA), with normal results.
A NGS (Next Generation Sequencing) multigene panel to screen 70 genes responsible for chromatinopathies was subsequently performed with a customised HaloPlex Target Enrichment NGS panel (Agilent Technologies, Santa Clara, CA, USA Agilent Technologies) [11 (link)]. Potentially pathogenic variants were confirmed with PCR amplification and Sanger sequencing. DNA from parents was analysed to assess inheritance.
The significance of candidate variants was classified according to the American College of Medical Genetics and Genomics criteria [12 (link)] using InterVar (http://wintervar.wglab.org/), Varsome (https://varsome.com/), CAVA and PMut prediction (http://mmb.pcb.ub.es/PMut/) tools. Sequence variants were described according to the Human Genome Variation Society nomenclature guidelines (https://varnomen.hgvs.org/).

Bigoni S., Marangi G., Frangella S., Panfili A., Ognibene D., Squeo G.M., Merla G, & Zollino M. (2020). Clinical Genetics Can Solve the Pitfalls of Genome-Wide Investigations: Lesson from Mismapping a Loss-of-Function Variant in KANSL1. Genes, 11(10), 1177.

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Array-Based Comparative Genomic Hybridization

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Approximately 1000 ng of WGA DNA was subjected to aCGH by GenetiSure Pre-Screen Array Kit 8x60K (Agilent Technologies, CA, USA), following the manufacturer’s instructions. The image on a chip was acquired with a G4900DA SureScan microarray scanner (Agilent Technologies, CA, USA) and analyzed with Agilent CytoGenomics software (Agilent Technologies) for chromosome gain or loss. Aberrations were detected by using default setting.

Huang C.E., Ma G.C., Jou H.J., Lin W.H., Lee D.J., Lin Y.S., Ginsberg N.A., Chen H.F., Chang F.M, & Chen M. (2017). Noninvasive prenatal diagnosis of fetal aneuploidy by circulating fetal nucleated red blood cells and extravillous trophoblasts using silicon-based nanostructured microfluidics. Molecular Cytogenetics, 10, 44.

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Mouse CGH Microarray Analysis for AML

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For the Array Comparative Genomic Hybridization (CGH array), we used the SurePrint G3 Mouse CGH Microarray Kit, 4 × 180 K (Agilent Technologies) and 1 µg of genomic DNA extracted from AML samples using Gentra Puregene Tissue kit (Qiagen). For analysis, we used the G2505 DNA microarray Scanner (Agilent Technologies) and the Agilent Cytogenomics software was used (version 2.7, Agilent Technologies, https://www.agilent.com/en/download-agilent-cytogenomics-software).

Hermetet F., Mshaik R., Simonet J., Callier P., Delva L, & Quéré R. (2020). High-fat diet intensifies MLL-AF9-induced acute myeloid leukemia through activation of the FLT3 signaling in mouse primitive hematopoietic cells. Scientific Reports, 10, 16187.

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Microarray-based Copy Number Variation Analysis

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Microarray slides were scanned with a DNA Microarray Scanner (Agilent Technologies). Data were received using the Agilent Feature Extraction software and Agilent CytoGenomics software. Data were analyzed using quantitative imaging methods and analytical software (Agilent CytoGenomics software, Agilent Technologies) to assist in identifying each targeted DNA sequence as a loss of copy number (deletion), a gain of copy number (duplication), or a normal copy number. CNVs were detected using the ADM-2 algorithm with filters of the minimal size of 200 kb in the region, >5 Mb of copy number LOH. Genomic positions were estimated using the human genomic reference sequence GRCh37.

Gajjar K., Patel A., Patel B.I., Chettiar S, & Jhala D. (2023). Array comparative genomic hybridization analysis of products of conception in recurrent pregnancy loss for specific anomalies detected by USG. Reproduction & Fertility, 4(2), e220092.

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Microarray Analysis of Copy Number Variations

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Array-CGH was performed on patient I1 using the Agilent Sureprint G3 Custom CGH microarray 2x400k (Agilent Technologies, Santa Clara, CA, USA) by Beijing Capitalbio Technology Corporation (Beijing, China). Genomic copy number changes at locus 17p13.3 in other family members (II1, II6, II8, III6, IV5, IV6) were further tested using a microarray with higher probe density (SurePrint G3 Human 1x1M; manufactured by Agilent Technologies, Santa Clara, CA, USA) by the Laboratory of Clinical Genetics of Peking Union Medical College Hospital. The experiment and data analysis were performed according to the manufacturer’s instructions. In brief, patient and control DNA were labeled and combined to hybridize to the 60-mer oligonucleotide-based microarray. The resulting fluorescent signals were automatically scanned by the Agilent SureScan Microarray Scanner. Agilent CytoGenomics software was then used to extract and translate the signal into log ratios for further analysis of copy number changes.

Shen Y., Si N., Liu Z., Liu F., Meng X., Zhang Y, & Zhang X. (2018). 17p13.3 genomic rearrangement in a Chinese family with split-hand/foot malformation with long bone deficiency: report of a complicated duplication with marked variation in phenotype. Orphanet Journal of Rare Diseases, 13, 106.

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Genome-wide CNV Analysis using CGH Microarray

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We applied an Agilent custom Human Genome CGH microarray 4 × 180 K (Agilent Technologies, Santa Clara, CA, USA) for CNV analysis. Array CGH experiments were performed using standard protocols provided by the manufacturer. The analysis was performed using Agilent CytoGenomics software (Agilent Technologies, version 2.5.8.11) [15 ].

Sun B., Yang M., Hou J., Wang W., Ying W., Hui X., Zhou Q., Yao H., Sun J, & Wang X. (2022). Chromosomal abnormalities related to fever of unknown origin in a Chinese pediatric cohort and literature review. Orphanet Journal of Rare Diseases, 17, 292.

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