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I have a question I would like to pose to the community. I have recently received access to a bench-top ion torrent DNA sequencer. Our idea is to use this machine to sequence the DNA from patient’s tumors in order to guide treatment options. My job is to identify a list of all currently used anti-neoplastic drugs along with their known targets (i.e., specific genes and mutations) and accession numbers. I would like to put these data in a table in which each row corresponds to a different drug.

For example, a row in the table might read (column names are indicated in brackets): [disease] breast cancer, [drug] trastuzumab, [drug target] HER2/neu receptor, [gene] ERBB2, [location] chr17:37844393-37884915, [mutation type] amplification, [accession number] ENSG00000141736. The pathologists would then be able to use this database in order to select appropriate genes for sequencing whenever they receive a tumor specimen. If the patient’s tumor had an amplified ERBB2 gene, they could be given trastuzumab.

Currently our study is in pre-planning stages (i.e., we won’t actually be testing this on patients any time soon). I would appreciate it if anyone could give me on advice on how to go about creating such a database. I am aware of online databases including COSMIC, Sanger's Cancer Gene Census, and the Potential Drug Target Database (PDTD), but they don’t have everything that I’m looking for. I am familiar with R and could use it to combine data from multiple sources if necessary. If anyone else has comments or suggestions for further reading that would also be appreciated. Thanks!

Note: This question has also been posed on a Research Gate forum: http://www.researchgate.net/topic/Cancer_Biology/post/Looking_for_a_cancer_drug_target_database_to_guide_sequencing_of_patient_tumor_DNA

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Would this question be better suited to healthcare-it? –  Rory M Jan 24 '12 at 14:07
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Have you tried looking at the NCI-60? Here's a (dated) paper but might serve as a good starting point: discover.nci.nih.gov/nature2000/paper/nature_v26_3_mar_2000.pdf –  jp89 Jan 24 '12 at 19:18
    
@RoryM I don't thinkg so, this is either our project or biostart.SE, rather the ours. –  Alexander Galkin Jan 24 '12 at 20:43
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This ma be a good start pharmgkb.org. I think biostar may be able to give you a good answer. –  bobthejoe Jan 24 '12 at 21:52
    
Is doing whole exome sequencing out of the question for your upcoming project? I feel like it'd crank up the chances of success for your project, and ... actually ... the exome isn't all that big, right? –  Steve Lianoglou Jan 25 '12 at 19:23
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Not sure if the exome sequencing is the way to go for this kind of tasks, especially if you have an idea of the mutations you might be looking for. Current arrays are pretty performant and are much more rapid and cheap.

For the data, you might consider having a look on The Cancer Genome Atlas. Otherwise Biological Networks might provide you the API for you if you aren't afraid of doing a little bit of Java to interface it with R.

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