CGH Analysis with Agilent

The development of cancer is associated with gains and losses of DNA sequences throughout the genome. Array-based comparative genomic hybridization measures copy number variations at multiple loci simultaneously, providing an important tool for studying cancer and for developing diagnostic and therapeutic targets. DNAVision provides you with whole genome Comparative Genomic Hybridization (CGH).

Description of the work flow :

A) Sample reception

Incoming samples. All samples received are labeled with a unique internal ID number and recorded in a validated electronic laboratory system management database. They are checked to confirm package/sample integrity, appropriate shipping conditions and a confirmation of sample identity against the shipping manifest is sent by e-mail on the day of reception.

B) DNA extraction and QCs

If needed, DNA is extracted from any eukaryotic (animals or plants) sample stored in the following conditions.

Quantification and estimation of DNA purity is carried out.

Genomic DNA integrity is tested on a 1% or 2% agarose gel.

C) Labeling (CY3 and/or CY5) / hybridization and scanning

Genomic DNA fragmentation / Cy3 and Cy5 DNA labeling.

Purification of labeled DNA / measurement of DNA concentration and labeling with Nanodrop.

Hybridization and scanning.

D) Deliverables and Quality Controls

As the quality of  data is  key to  further analysis, in DNAVision we have validated our processes using control DNAs.

To ensure security, all information is provided in  electronic form on a DVD. Encryption is available on request. Data may also be delivered via  a secure dedicated web site.

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

• Raw data files
• Extracted quantitative data files from Agilent Feature Extraction Software:
  • .txt data files
  • .JPEG images
  • .PDF QC reports
• Analysis report tables:
  • Project description
  • DNA assessment data
  • Cy3 and Cy5 incorporation rates
• DNA analytics reports:
  • Post-hybridization QC report
  • Probe-based report of predicted Copy Number Variation (CNV)
  • Genomic information related to the CNVs

E) Biostatistical and Bioinformatical analyses

In addition to  the core service activities carried out in a high quality environment, we can also provide you with basic to in-depth data analysis to extract  the relevant information from your data. For  more details please go to Bioinformatics in DNAVision

F) Available Catalog Arrays and Custom arrays

We can provide you with arrays available from  Agilent.

We can also help you with the design and the processing of any custom microarray. Genomic variations include both gains and losses of chromosomal regions that often vary extensively in  size. Enhanced detection resolution via  high-density microarrays gives  the highest precision in mapping chromosome breakpoints and identification of micro-variations  not detected by other platforms.

With Agilent technology, DNAVision is able to use  custom arrays with resolutions of up to 190 bp.