The arrays for CGH consist of linker-adapter PCR representations of BAC clones printed on a substrate. Each clone contains at least one STS (Sequence Tagged Site) and is mapped to the human genome sequence. Clones containing unique sequences near the telomeres and clones containing genes known to be significant in cancer and medical genetics are included. Hybridization to these arrays allows detection of single copy gains and losses compared to diploid even in the presence of normal cell contamination. Construction of the printing solutions from BACs, the arrangement of BACs in the printing plates, and the quality assurance steps we follow in producing our arrays are all outlined in the Protocols/SOP section of this web site. Complete hybridization instructions are also available in our Protocols/SOP section. Three to five hundred nanograms of genomic DNA from test specimens are typically used for analysis, however good results can be obtained with considerably less. Most of our arrays are printed on chromium-coated slides. We also routinely print on commercially available coated glass slides, including slides from Corning, Full Moon Biosystems, Telechem, Schott, Amersham, and others.
1.4MB BAC Array pricing >
We also carry a smaller human BAC array (HumArray3.2) that contains 2464 BAC clones spotted in triplicate, with an average spacing between clones of 1.4Mb. The spot spacing on our arrays is 125mm center-to-center and the entire array is 13.5mm X 13.5mm. We print two arrays on one 1” x 3” slide, and each array can be hybridized to a different sample. Our arrays are usually in stock.
Our mouse BAC arrays contain 2896 BAC clones spotted in triplicate, with an average spacing between clones of approximately 1Mb. The spot spacing on the arrays is 130mm center-to-center and the entire array is 12mm X 12mm. We print two arrays on one 1” x 3” slide, and each array can be hybridized to a different sample. Limited quantities of Mouse BAC arrays are usually in stock.
The Core from time to time designates arrays with modest flaws as practice arrays. These arrays typically have >90% of the arrayed clones intact and are very useful for beginners to familiarize themselves with the hybridization and imaging steps at a reduced cost. Limited quantities of practice arrays are usually in stock.
We are pleased to offer complete Array CGH “DNA to Data” processing. The Array Core will fluorescently label test DNA supplied by the investigator, and in-house normal reference DNA. The test and reference DNAs will be hybridized to a BAC array, and the resulting CGH data will be provided in Excel spreadsheets for use by the investigator, along with the raw array images.
Investigators can have arrays printed from reagents prepared in their labs. Printing can be accomplished from 96, 384, 864, and 1536 well microtiter plates. Arrays are routinely printed on a variety of substrates including poly-lysine, amino silane, and chromium coated microscope slides, as well as commercial slides from Corning, Full Moon Biosystems, Telechem, Schott, Amersham, and others. DNA, cDNA, and oligonucleotides can be suspended in a variety of buffers including phosphate, SSC, DMSO, etc. Investigators can specify additional substrates and printing buffers.
Printing requests can typically be accommodated with 7-10 days advance notice. Depending on the project, consultation charges may also apply.
CCD Imaging System The Core has a custom 4 Megapixel CCD Imaging System for use with our chromium-coated substrates and with glass slides. The system can image an area of 20mm X 20mm in a single frame, each pixel corresponding to 10mm on the array. Filter sets allow independent imaging of DAPI, Fluorescein, Cy3, Cy5, or their spectral equivalents. Acquisition of images for the standard CGH measurement (DAPI, Cy3, and Cy5) typically takes 45 seconds or less. No significant bleaching occurs during imaging.
Machine time may be reserved through Outlook scheduling software. Contact the Array Core for Outlook access and password information.
Imaging Equipment and Software For investigators who wish to use the 4M pixel CCD Imaging system, we offer training on the operation of the imager and its QED software. A one-hour session should provide all the information and hands-on training needed. Pricing for this training is $70.87/hour for UCSF investigators and affiliated institutions. Our academic pricing for investigators is $87 per hour and reflects our higher handling and administrative costs. Please see Pricing for details.
Labeling, Hybridization Techniques, Imaging Equipment, and Software Detailed protocols for the production, hybridization, and analysis of the BAC arrays are available on this website. We have found that users save considerable time and money by first receiving instruction in hybridization techniques and processing a test array before analyzing research samples. Hybridization training and consultations can be arranged by contacting Greg Hamilton. In our experience, after brief training and several practice hybridizations, everyone is able to obtain high-quality results with BAC arrays. Pricing for this training is $501.36 for UCSF investigators and $612.00 for investigators from other academic institutions. Please refer to Pricing for further information.
A searchable database of core facilities at all UCSF campus locations, provided by the Clinical and Translational Science Institute at UCSF, is available here.