Where can you get your cancer sequenced for mutations?

Question

Have a family member with recurrent metastatic breast cancer.   She wants to fight and I want to help her.  Where can I get her tumor sequenced to find out what is wrong with her genome like what mutations she has and how we can reverse the mutations?

please help.

Comments

please elaborate a bit - what is the utility of having your genome sequenced in this situation?  how does it affect cancer treatment?

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does this apply to all cancers? what about melanoma and colon cancer?

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Is this useful for prostate carcinoma?  that's the same as cancer right?

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Does this do all types of mutations in cancer?  Is it worth it to get sequence by two places?

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why is this good? can they kill the mutations in cancer, and the tumor goes away?

Answer 1

Seems like a lot of major academic hospitals are doing this - Stanford, UCLA, MGH and the Brigham in Boston, Sloan Kettering in New York, probably Baylor and U. Chicago, and someone already mentioned the Siteman Clinic at UW.

Just check with the biggest academic medical center in the nearest large metropolis. Really, the Cleveland Clinic also must be trying this.

Call up the oncology departments at these places, and be persistent.  I'm a little wary in general of these startups, like Foundation Medicine or 23 and me - who knows whether they will be around in 10 years with your data?

I think academic hospitals in contrast are very skilled at simply remaining in existence, and are very good about privacy (HIPAA) and stuff.

Comments

Actually, does the NIH do this?  Would it be free to you there?  That might be worth exploring.

Answer 2

CAFighter,

very sorry to hear about the breast cancer in your family.   I hope she is getting good medical care and advice.

I have worked in biotech for 10 years, and have a PhD in molecular biology and biophysics.

Cancer sequencing is now a reality as technology has really advanced to make this discovery financially practical.

The place that springs to mind is Foundation Medicine

http://www.foundationmedicine.com/

They are CLIA certified (Clinical Laboratory Improvement Amendents), which basically means they can accept actual patient samples for diagnosis, not just for research.

There are other competitors in the sequencing space out there, and you should definitely check out as well.

 

Comments

They accept patient samples but what is the relevant link for CAFighter?  Is it "molecular testing" under the "patient tab" on top.

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I just looked at the Foundation Medicine site myself, and it is not very clear.   It does not seem like there is an easy web registration with instructions.   Perhaps you should email them if you have a sample for them to sequence?

Answer 3

From this National Cancer Institute Article, it sounds like you can get your cancer genome sequenced at the University of Washington - Siteman Clinic.   But it might be just for one form of leukemia, not every cancer.  And I'm not sure whether this is being done for research, or whether it will actually guide some kind of treatment.

http://www.cancer.gov/ncicancerbulletin/071211/page5

 

Comments

this is interesting to file away ... but is one place better another?  it'd be nice to compare like price and accuracy of the sequence.  what if they miss something?  that's kind of scary.

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Good point justaddwater.   Obviously, price can be compared, but accuracy?  that seems like it is very tough.   Each sample seems to be about 10K, so would be difficult to get many sequencings done at different places.

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Maybe in a few years it will be still cheaper - the sequencing technology may be following an attentuated form of Moore's law.   The medical interpretation however, may not be getting cheaper.

Answer 4

It looks like Phoenix has an institute that does sequencing for tumors:

"... Translational Genomics Research Institute in Phoenix for sequencing on equipment made by Life Technologies Corp..."

The article that I read about this is here:

http://www.businessweek.com/news/2012-01-24/curing-cancer-relies-on-genome-map-guiding-medical-care.html

In this article, a woman with breast cancer found a mutation in mTOR.  She had triple negative breast cancer, one for which there is no good therapy.  I don't know if the sequencing contributed directly to her therapy though - looks like her oncologist put her already on Avastin and taxol, which aren't indicated clearly for tumors with mTOR mutations, but certainly not inconceivable that the targets of Avastin and taxol somehow impinge on the mutated mTOR.  The good thing was that she responded to the Avastin / taxol and Afinitor therapy.

Afinitor stands out a bit - not sure what it is.

Comments

mTOR/AKT/PI3k are members of a prominent cell survival and metabolism pathway, and are often mutated or activated in cancer.   PTEN is also part of this pathway, and also is mutated or truncated to overactivate this pathway.

Rictor and Raptor, genes in the mTOR complexes also sometimes are mutated.

Answer 5

Your family member won't be getting the entire tumor sequenced, but just the parts of the genome that are known to drive cancers out of control - I'm pretty sure Foundation Medicine is like that.  And not to get your hopes up too high, but only some of those mutations are going to be "actionable", meaning that there is some sort of treatment that's specific for it.  Reversing the mutation is definitely not possible!  But my people believe that this kind of information is important to add to your tools for fight this disease.  So all the best!

Answer 6

For those worried about the cost, it seems that there are new technologies that bring the sequencing of one genome to under $1000.  NPR had a news article on it:

http://www.npr.org/templates/story/story.php?storyId=144984317

The company is Life Technologies.  But again, many answers here have indicated that sequencing should be tied to the possibility of therapeutic benefit.  We're at the stage where it's possible to sequence a tumor's DNA, but not possible to say for certain what to do with the information.

Answer 7

What is the followup on this answer?   I have heard of Foundation Medicine now in several contexts, and apparently they have already sequenced a few hundred cancers of patients.   I think it is all self-pay not clear that insurance is covering anything.   I would love to see what there reports say, and how they are connecting DNA sequencing of the tumor to treatment options today?

http://online.wsj.com/article/PR-CO-20120327-903348.html

http://onespot.wsj.com/taxes/2011/10/18/7f037/foundation-medicine-closes-a-round-with

Comments

who pays for all this?   did Obama say health insurance has to cover this?

Answer 8

Foundation Medicine offers a comprehensive Cancer Genomic test that uses next generation sequencing.  They launched this test recently, and it has been used by a lot of patients.