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 Software

Non-FFPE samples enter the workflow at target prep stage.

Deliverables

As part of our Agilent aCGH service, you will receive:

  • Raw Data Files
    • .tiff scanned images
  • Extracted Quantitative Data Files from Agilent’s Feature Extraction software:
    • .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 and yield)
    • 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 e-mail.

Quality Control

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.

Yield:

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.

Integrity:

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 standardization.

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.

Turn-around Time

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

CC0400 Agilent Human 244A aCGH Array (1x244K)
CC0440 Agilent Human 105A aCGH Array (2x105K)
CC0390 Agilent Human 44K aCGH Array (4x44K)
CC0410 Agilent Mouse 244A aCGH Array (1x244K)
CC0460 Agilent Mouse 105A aCGH Array (2x105K)
CC0420 Agilent Mouse 44K aCGH Array (4x44K)
CC0430 Agilent Rat 244A aCGH Array (1x244K)
CC0450 Agilent Rat 105A aCGH Array (2x105K)

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