Welcome to the Arthur and Rochelle Belfer Cancer Genomics Center.

The Belfer Center functions as the gateway facility for Array CGH at the Dana-Farber Cancer Institute and provides DNA in-data out services. Researchers will have immediate access to CGH arrays that provide an average of 3 Megabase coverage for both Human and Mouse based experiments. In the near future, the coverage will be increased to 1 Mb while maintaining the original 3 Mb BAC set to ensure data continuity.

In planning an experiment, the researcher should consider the size of the experiment and how it relates to the Belfer Center's throughput. Currently, the Belfer Center can process 6 experiments a day for a total of 24 a week. A single sample versus control comparison, done in duplicate, constitutes an experiment. Without exception, all comparisons are done in duplicate with dye swap and result in 4 replicate spots across two arrays for each of the 1000 BACs. Researchers considering larger experiments (>24) should state in their proposal whether they require their samples to be processed consecutively or not. The Belfer Center will make every effort to accommodate the needs of all researchers. In considering samples appropriate for Array CGH, researchers must be able to provide 5 mg of high quality Eco RI digested genomic DNA as described in the protocols section. For studies with human samples, a universal reference DNA will be used as reference. For studies with mouse tissues, researchers should provide appropriate reference DNA. The reference DNA should be from normal mouse tissue, preferably from the same mouse as the experimental sample. Alternatively, normal tissues from the same cohort or same genetic background are acceptable. Further, all samples should be provided in 1.5 ml microcentrifuge tubes at a concentration of 100 ng/ml. Each sample MUST also be accompanied by pre and post digestion agarose gel images in electronic format for quality control. DNA samples not prepared appropriately or of low quality will not be accepted for profiling experiments.

Once the samples have been prepared, the researcher can initiate an Array CGH experiment by selecting the Order Microarrays button and filling out the required fields. Following their submission, requests will be processed by the Belfer Center and positioned in the queue based on project size and any special experimental requirements (i.e. consecutive day processing). Once the project has been queued, the researcher will be sent Belfer Center tracking forms and barcodes to label their tubes. Labeled tubes should be submitted to the Belfer Center immediately to avoid any delay in their processing. If a researcheršs DNA is not received the week prior to their scheduled experiment, their experiment will be rescheduled as if it were a new submission.

The researcher will be notified via e-mail that data has been generated from their experiments. They will be provided with a hyperlink to their data on our server. Access to these data is restricted to the researcher only. Data on the server is in Read Only format. Researchers should download these data to their local computers for manipulation and analysis. The data provided to the researcher will include the original Cy3 and Cy5 Axon images, as well as, a GenePix Pro output file of quantified image data. The images are unaltered 16-bit tif files, while the quantified image output comes in the form of a tab-delimited spreadsheet. All data is provided without background subtraction or normalization and is as unaltered as we can provide it.

Thank you for your interest and we look forward to serving the Dana-Farber scientific community.