Agilent aCGH Services
Gene deletions or amplifications are associated with many forms of cancer and are
frequent and early events in the oncogenesis process. Therefore, research that characterizes
the DNA copy-number variants in cells is important for the basic understanding of
mechanisms of oncogenesis, tumor progression, and metastasis. Agilent microarray-based
Comparative Genomic Hybridization (aCGH) is a powerful technique used to identify
and characterize DNA copy number variations across the genome. Learn more about
how we qualify our methods and staff.
Description of Services
Asuragen provides services on the Agilent array-based comparative genomic hybridization
(aCGH) platform and procedures to analyze DNA copy number variations using the 60-mer
oligonucleotide microarrays. Asuragen’s internal validation of the equipment and
procedures has further demonstrated that the technology is highly reproducible,
sensitive, specific, and robust to a wide range of FFPE samples.
The platform is a two-color fluorescent assay for which the detection of a copy
number variation is based on a relative comparison of the experimental DNA sample
to a reference DNA at the genomic locations interrogated by the probes on the array.
As always, the experimental design, including the selection of the appropriate reference
genome, is critical to the success of a project.
Workflow for Agilent aCGH services:
- Incoming DNA QC (click here for
sample prep services):
- Target preparation and enzymatic labeling
- Combined labeled experimental and reference genomes
- Data extraction and analysis using Agilent’s Feature Extraction
Non-FFPE samples enter the workflow at target prep stage.
As part of our Agilent aCGH service, you will receive:
- Raw Data Files
- Extracted Quantitative Data Files from Agilent’s Feature Extraction
- .txt data files
- .JPEG images
- .PDF QC reports
- .XML files available upon request
- Analysis Report Tables:
- Project Description
- DNA assessment Data (260nm/280nm, 260nm/230nm ratios, concentration
- Percentage of Labeling: A measure of Cy3 and Cy5 incorporation
- DNA Analytics Reports:
- Post-hybridization QC Report. CGH Metrics include: DLRspread values,
signal intensity, background intensity, Signal-to-Noise ratio, and reproducibility
- Probe-based report of predicted Copy Number Variation (CNV) aberrations
- Interval-based report of predicted CNV aberrations
- Asuragen applies Agilent’s recommended settings for CNV analysis based
on the DNA Analytics 4.0 CGH Module User guide
To ensure security, all information is provided in an electronic form on a DVD.
Encryption is available on request. Data may also be delivered via an FTP site or
No matter how robust the downstream processes, good data is dependent on sample
quality. Consequently, accurate measurement of sample quality is essential before
deciding if a sample merits further analysis. All samples prepared by Asuragen Services
are routinely qualified. Due to the partial degradation of nucleic acids from FFPE tissues,
special quality control measurements are used.
Nucleic acid yield is primarily dependent on the tissue type and mass (or volume)
but is often affected by disease status, chemical treatment, media, preservatives,
and tissue handling.
Although DNA is routinely stable in most sample types, formalin fixation does lead
to partial DNA degradation in FFPE samples. For this reason, Asuragen offers a wide variety
of services compatible with RNA and DNA from FFPE.
Asuragen’s rigorous procedures enable Asuragen to be the only service provider to
offer a Data Quality Guarantee.
If, for any reason, a qualified sample does not pass our process control specifications,
we will re-run the sample at no additional charge.
Read more about our
commitment to the best possible data quality, and our contributions to
in-process controls and
Sample Handling and Processing
All samples are received and entered into the analysis queue under a controlled
SOP to confirm package/sample integrity, appropriate shipping conditions (frozen
samples/dry ice, as appropriate), and individual confirmation of sample identity
against the shipping manifest and sample submission form and instructions.
Most projects are completed in two weeks or less. If you have a critical time requirement,
we can often meet your need for no additional charge.
Read more about our commitment to prompt turn-around times.
Additional Services Available from Asuragen
Available CGH Arrays
Human, Mouse, and Rat
Catalog Numbers for Agilent aCGH Services
Agilent Human 244A aCGH Array (1x244K)
Agilent Human 105A aCGH Array (2x105K)
Agilent Human 44K aCGH Array (4x44K)
Agilent Mouse 244A aCGH Array (1x244K)
Agilent Mouse 105A aCGH Array (2x105K)
Agilent Mouse 44K aCGH Array (4x44K)
Agilent Rat 244A aCGH Array (1x244K)
Agilent Rat 105A aCGH Array (2x105K)