Agilent CytoGenomics software statistics

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Agilent CytoGenomics software specifications

Information


Unique identifier OMICS_00701
Name Agilent CytoGenomics software
Software type Package/Module
Interface Command line interface
Restrictions to use License purchase required
Biological technology Agilent Technologies
Operating system Unix/Linux
License Commercial
Computer skills Advanced
Stability No
Maintained No

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Agilent CytoGenomics software in publications

 (20)
PMCID: 5746144
PMID: 29224250
DOI: 10.1002/sctm.17-0041

[…] (kurabo industries, osaka, japan, http://www.kurabo.co.jp/). arrays were analyzed through the agilent scanner and the feature extraction software (v8.1). graphical overview was obtained using the agilent cytogenomics software (v2.9.2.4)., total rna was extracted using universal rna purification kit (eurx, gdansk, poland, https://eurx.com.pl/) according to manufacturer's protocol. the reverse […]

PMCID: 5712079
PMID: 29213331
DOI: 10.1186/s13039-017-0343-3

[…] 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., approximately 1000 ng of wga dna was used for library […]

PMCID: 5708077
PMID: 29187220
DOI: 10.1186/s13041-017-0335-6

[…] gender of patients whose dna samples were analyzed., the data processed by feature extraction software were evaluated using the aberration detection method 2 algorithm with a threshold of 6.0 with agilent cytogenomics software (ver. 2.7.8.0). to analyze individual arrays, the following standard aberration filters were used: minimum of three contiguous supra-threshold probes and minimum of 0.25 […]

PMCID: 5135744
PMID: 27980677
DOI: 10.1186/s13039-016-0298-9

[…] array was acquired using the agilent laser scanner g2565ca (agilent technologies, california, usa) and analyzed with the agilent feature extraction software (v10.10.1.1.). results were analyzed by agilent cytogenomics software (v2.5.8.11)., the presence of the duplication was confirmed in the patient and searched in his relatives through mlpa (multiplex ligation probe amplification) […]

PMCID: 5107627
PMID: 27834075
DOI: 10.3343/alm.2017.37.1.88

[…] using the sureprint g3 hmn cgh+ snp 4×180k microarray according to the manufacturer's protocol v7.3 (agilent technologies, santa clara, ca, usa). the resulting images were analyzed using the agilent cytogenomics software v.2.9.1.3 (assembly grch37/hg19)., the patient had (n = 30 metaphases) an 8p+ with a g-banding pattern suggestive of a rec(8)dup(8q)inv(8)(p23q22) (). fish revealed […]


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Agilent CytoGenomics software review

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Vijay Lakhujani

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Desktop
A nice tool for work flow based automated analysis of patient samples on CGH micro array platform. Writing this review as I have extensively worked on this tool on a daily-basis.

1. User friendliness:
A moderate amount of video tutorials are available for the first time users which can be found here:
http://www.genomics.agilent.com/article.jsp?pageId=3293

Though it takes some time to get familiar with the basics, a good hands on for few days is enough to get started. The analysis wizards are quite intuitive in terms of what input files and parameters will be required. Visualization and interpretation requires a good knowledge of CGH micro array analysis.

2. Level of automation:
A good level of automation could be achieved wherein the samples being directly scanned via micro array scanners could be directed to be analysed as they are available to the software. Pre-defined analysis methods are available for a quick analysis and visualization and later users can modify the params accordingly. Multiple samples can be analysed at once and reports could be generated in fairly automated manner.

3. Ease of installation and up gradation:
This tool is supported on variety of windows versions and mac. A dedicated development team is always trying to launch new versions supported on latest versions of mac and windows. The memory requirements and storage capacities are high and hence require fairly high end PC's. Data backup is an issue and many a time it is very difficult to reload previously analysed samples. Up gradation is user friendly, and is also assisted sometimes by the development team or the Agilent software support team.

4. Support for non-Agilent samples:
The software comes bundled with another tool called "Agilent Feature Extraction" which extracts the signals into human readable raw data. Some of the versions support extraction and analysis of non-Agilent arrays like that of Illumina. However, it is recommended exclusively for analysis of Agilent microarray CGH and CGH+SNP arrays.

5. Data Administration:
Standard level of administrative roles are available to be assigned to a large/small team wherein each member designated for particular task can have their own set of functionalities. for e.g. the admin can define the scope of activities for a "technician" or "scientist" wherein say the technician cannot sign off a sample, whereas the scientist can. The administrator has all roles of a technician and scientist along with full database control access; he/she can also change the roles.

6. Data analysis and visualization:
This software supports detecting copy number changes (CNCs), copy-neutral loss of heterozygosity (LOH), and uniparental disomy (UPD) SurePrint G3 CGH+SNP microarrays. Visualization is fairly easy for a person with moderate knowledge of working with computers. However, the software as they say is only meant for research purposes (not diagnosis). That being said, a good knowledge of the underlying biology is must to interpret the results. Assistance is available via webinars and a technical team.

7. Extent of customization:
Advertised a one stop solution, the software is quite customizable in terms of preparing customized analysis methods (tweaking the parameters) and the final reports including options for sections, headers footers and image logo.

8. Support and development:
Extensive development is being done and new versions are available on regular intervals with bug fixes. 24X5 support is available by phone and email.

Pros:
- Fairly easy usage
- good visualisation
- moderate customisation
- 24 X 5 support service

Cons:
- not suitable / recommended for diagnostic purposes
- high end pc requirements, large memory consumptions
- difficult to backup data and restore
- reverse compatibility is not good