Prior to submitting a proposal or samples to CCGD for OncoMap analysis, please read this document to ensure that your
samples will meet our sample submission requirements and to familiarize yourself with the OncoMap process.
ONCOMAP SAMPLE SUBMISSION REQUIREMENTS
Sample Number:
1) CCGD requires a minimum number of 30 samples. We cannot accommodate projects less than 30 samples as
our mutation calling algorithm requires sufficient background to detect outlier samples with mutations.
If you do not have 30 samples: please add additional samples to bring your total submission to 30. These
additional samples can be tumor, or matched or unmatched normals from the same tumor type. Importantly, all
samples submitted (per plate/batch of 30) must be of the same tissue collection format (e.g. all test samples
derived from cell lines means all additional samples should be derived from cell lines; all paraffin-embedded
samples need paraffin-embedded additional samples). Cell lines and fresh frozen samples can be used in the
same batch.
2) OncoMap is run in batches of 95 samples. If you submit >95 samples at once, they will be divided into batches
of 95.
General Submission Requirements:
1) Please submit all samples on a 96-well plate (not a tissue culture plate). To prevent evaporation, please seal
plate with plastic adhesive seal -not parafilm wrap or lids. Tubes will not be accepted. If you do not have a 96well plate or adhesive seal, we can provide these at Dana 1506.
2) Please submit any samples derived from paraffin-embedded blocks (FFPE) on a separate 96-well plate as
we process FFPE samples separately from cell lines and fresh frozen tissue. Cell line and fresh frozen DNA may
be placed on the same 96-well plate.
3) Please elute all DNA in water not TE. Salt and other contaminates increase the background on the mass
spectra.
Two sample submissions are required:
1) The first sample submission is solely for CCGD to quantify DNA using Picogreen. CCGD requires an in-house
quantification of DNA regardless of external sample quantifications. Please submit 2ul of each sample in a 96well deep well plate for quantification. This plate will not be returned to you. If you do not have a deep well
plate (where each well holds at least 500ul), we can provide these at Dana 1506.
2) Once you receive the quantification results from CCGD, please submit a sample plate that ONLY contains those
samples which have sufficient DNA concentrations and total DNA to run on OncoMap where sufficient total
DNA is 250ng/sample and sufficient concentration is 20ng/ul for samples derived from cell lines and fresh frozen
tissue and 10ng/ul for samples derived from paraffin-embedded blocks (FFPE). All concentrations must be
normalized based on CCGD’s Picogreen readings (eg: if submitting cell lines and our Picogreen reading is
100ng/ul, submit 12.5ul at 20ng/ul; if submitting all FFPE samples and our Picogreen reading is 100ng/ul, submit
25ul at 10ng/ul). If your samples do not meet our requirements they will be returned to you.
THE ONCOMAP PROCESS AND WHAT TO EXPECT:
1) Log in to http://ccgd.dfci.harvard.edu/ccgd/ (inside the DFCI firewall) or www.cancergenomediscovery.org
externally to register as a user and submit a proposal. Please specify in your proposal if you want OncoMap 3
Core only, or both OncoMap 3 Core and Extended panels.
2) Your proposal will be reviewed by a scientific committee and evaluated for scientific merit. You will be
contacted when the committee has evaluated your proposal (typically one week).
3) Once your proposal has been accepted, you will be sent an e-mail prompting you to fill out an online sample
submission form for the first sample submission( to quantify your samples). In addition, a price quote will be
sent- this should be signed and returned to CCGD.
4) Once CCGD receives your signed quote and online sample submission form we will e-mail you with sample
delivery instructions.
5) CCGD will quantify your samples’ DNA concentration and send you results along with instructions for the
second sample submission for OncoMap.
6) Once we receive this second submission, your samples will be put queued and we will provide you with a
turnaround time.
7) When OncoMap results have been analyzed by CCGD staff, you will be e-mailed an OncoMap report with a list
of candidate mutations. Upon review, we can facilitate meeting with CCGD staff to discuss your data and
validation plans.
8) We will queue your samples for hME validation, our lower throughput but higher sensitivity chemistry, to confirm
candidate mutations identified during the OncoMap run.
9) Upon completion, CCGD staff will e-mail you an hME validation report.
10) After reviewing your hME validation report CCGD staff will be available to meet with you to discuss data (and
next steps if necessary).
11) We request that remaining DNA is collected within 30 days following receipt of your validation report. Due to
space limitations we cannot store your DNA for longer than this.