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CGH Services
 
  We have set up an in-house facility for processing NimbleGen arrays, and we offer these services on a cost-recovery basis. The services include specialty chip design, DNA labelling, hybridization, scanning and data analysis for deletion detection, SNP mapping, and general copy number investigations. We keep a couple of chip designs on hand, including HX3 whole-genome chips and Hawaiian/N2 SNP mapping chips; you may also have custom designs fabricated by NimbleGen and shipped to us for processing.

The descriptions elsewhere in this web site of the various CGH approaches available are good places to start thinking about your experiment. Please contact Don Moerman (moerman@zoology.ubc.ca) for specific advice or information on how to proceed once you have an idea of what you want to do.

 
Standard Chip Designs
  We are currently using two standard array designs, one an exon-centric whole-genome chip primarily used for deletion detection and validation, and one specifically for Hawaiian/N2 SNP-CGH mapping. These are designed to be synthesized on NimbleGen HX3 arrays, which allow three experiments to be done on a single chip.

CGH Array Design Name Notes
Whole genome 081002_CE_UBC_RZ_CGH exon-centric WS190
SNP Mapping 090127_Moerman_Map_v3_50mer Hawaiian/N2 SNP mapping

 
Pricing
  Basic pricing for CGH service is $1000 ($Cdn), and includes labelling of sample and reference DNA samples, hybridization, scanning, and data analysis. The actual cost is a little fluid due to exchange rate and the vagaries of DNA quality (specifically, low-quality or low-concentration DNA may require multiple labellings to obtain enough labeled DNA for an experiment; additional labellings are $160 each).

 
DNA Preparation and Shipping
 

Be sure to read the detailed section on DNA preparation, since the quality of the prep has the largest impact on the success of labelling and hybridization. At minimum we will require 5 micrograms of good-quality sample DNA at 100 ng/ul. We supply N2 or CB4856 reference DNAs, but you'll have to provide us DNA for any other reference strain.

Shipping should be done by courier (in our experience Federal Express is among the most reliable), on wet ice in a styrofoam box insert. To make things go as smoothly as possible, you should include documentation for the DNAs including the nature of the experiment, strain and reference genotypes, and DNA concentration and volume. Be sure to label things clearly. Shipments are best made on Tuesdays, and should be addressed to:

Mark Edgley
University of British Columbia
2350 Health Sciences Mall
Vancouver, BC V6T 1Z3
Canada
604-822-0221

Indicate on the waybill that shipment AND customs charges should be billed to the sender to protect us from unpleasant surprises, and email the courier waybill number to Mark so we can track the package (email address edgley@mail.ubc.ca).