Topic: Genetic & Molecular testing

My Oncologist is trying to organise genetic & molecular testing in the US (as we dont do it in Australia). She has suggested this company;

http://www.carislifesciences.com/about-us


am wondering if anyone has any suggestions or know which ones their Oncologist uses?

I have heard of FoundationOne (from MD anderson)

Thanks,
Tereas

Re: Genetic & Molecular testing

My husband's oncologist at the University of Chicago used Foundation Medicine in Boston.
http://www.foundationmedicine.com/

Re: Genetic & Molecular testing

I don't know where, but the trial I am in is using molecular testing. Eli Lilly is doing the trial at 3 cancer centers.

KrisJ
"Don't just have minutes in the day; have moments in time."
Any opinions I give are based on personal experiences, and are not based on medical knowledge. I strongly suggest receiving medical care and opinions.

Re: Genetic & Molecular testing

Hi folks,

I wanted to follow up on this thread and see if any others have done genetic testing by FoundationOne? 

Would love to hear of your experience with it.

Thanks,
Julie

5 (edited by PCL1029 Wed, 13 Nov 2013 18:20:44)

Re: Genetic & Molecular testing

Hi,

I did both the Foundation ONE and the Targeted Report.

In my opinion, The foundation One report about  the gene mutations of  a patient can provide, if available, the treatments or clinical trials that are mostly likely be of benefits to the patient's tumor unique situation.

Target report ,at the time I ordered  about 2 years ago, did not use the "next-generation sequencing" genomic profile but used  the old "staining techique and FISH " method.
My result, as others that were experienced and written on this board ,is that  there are  currently   no FDA approval regimen available;but 2 clinical trials(ie: one is p53 gene suppression and the other is related to CDK4/6 genes; one is IV ,the other is PO.) but are no guarantee  and my timing is not right at this point to pursuit either.
In short, both reports help me to prepare for future battles but not for the immediate horizon for my situation.But it may be of benefit to you if they actually find one that fit your tumor biology now; then all you have to do is taking that regimen or clinical trials  rather than try this and try that if the first one don't work.. 
I believe the more people to do the next-generation sequencing genomic profile ;the better for all of us in the future; I regard it more or less like as a" baseline Ct scan" when I first diagnosis.
God bless.

Please know that my personal opinion is not intended nor implied to be a substitute for professional medical advice. If  provided, information are for educational purposes.Consult doctor is a MUST for changing of treatment plans.

Re: Genetic & Molecular testing

I am in discussions with several people on this subject.  If you can hold off for a bit, I will try to update.
Hugs,
Marion

THIS INFORMATION IS NOT INTENDED NOR IMPLIED TO BE A SUBSTITUTE FOR PROFESSIONAL MEDICAL ADVICE. YOU SHOULD ALWAYS SEEK THE ADVICE OF YOUR PHYSICIAN OR OTHER QUALIFIED HEALTH CARE PROVIDER

Re: Genetic & Molecular testing

Percy and Marion,

Thanks to you both for the replies.  I will await for your update Marion.

Julie

8 (edited by marions Thu, 14 Nov 2013 15:57:02)

Re: Genetic & Molecular testing

I spoke with  Jimmy Lin MD, PhD, web presenter on Understanding Cancer in the Age of Genomics.  See:  http://www.cholangiocarcinoma.org/media.htm

It is difficult to understand what people can expect from genetic testing as it ranges from simple gene testing to the huge area of genomics, costing anywhere from 10 thousand to 200 thousand.  The later is is based on the different levels of testing i.e. 20 or 30 thousands genes or the entire genome comprised of millions of variations.

At the moment, I find it to be the "wild west" of genetic testing.  Too many questions have yet to be addressed.

Dr. Lin is preparing an additional web presentation for us.  Unfortunately, we have not been able to set the date and time as of yet but, I hope for it to be within the next few weeks. 

I will keep everyone posted, but please don't forget to remind me too.

Hugs,
Marion

THIS INFORMATION IS NOT INTENDED NOR IMPLIED TO BE A SUBSTITUTE FOR PROFESSIONAL MEDICAL ADVICE. YOU SHOULD ALWAYS SEEK THE ADVICE OF YOUR PHYSICIAN OR OTHER QUALIFIED HEALTH CARE PROVIDER

Re: Genetic & Molecular testing

The below was quoted by Dr. Lin, in response to your question:

Genomic profiling is performed at a variety of institutions and companies - all based on the same technology: Next Generation Sequencing. The two companies that provide the machines for the different companies are Illumina (which hold approx. 80% of the market) and Life Technologies. Many academic institutions offer their own NGS profiling test - usually based on a panel of genes, varying from 30 genes to up to 200. Institutions that have their own include MD Anderson, Memorial Sloan Kettering, Washington University in St. Louis, Brigham and Women's, among others. There are also commercial offerings of the similar service from companies such Foundation Medicine, PGDX, Caris, among others. Another company that is in the news is Myriad Genetics. Their test is for genetic predisposition of cancer, which the other test I discussed are mutations that are acquired later in life. Of the companies that provide this service, the largest is Foundation Medicine, which recently IPO'd. One drawback is they only sequence the tumor and does not compare the sequence with the normal tissue, which companies such as PGDX perform.
Depending on the tumor type and family history, the panel size may or may not be important. There are only a limited number that have targeted drugs or prognostic importance. However, if one wants to be comprehensive, there is the option of whole exome sequencing, which analyzes all the genes for the cancer - this service of course being more expensive. The ultimate test is whole genome sequencing and for now this is seldom performed due to its cost. The main company that does is the machine manufacturer itself, Illumina.

Sequencing is only the beginning as it provides the raw information. Like an X-ray or MRI, the interpretation is very important - perhaps even more important for molecular profiling. This is were bioinformatics companies that help with interpretation beyond what's just provided by the sequence providers can be helpful.

This is a vastly changing landscape and new companies are being started almost every week and new technologies are revealed also frequently. New sequencing technologies such as nanopore sequencing, which is so called third generation sequencing, is being developed as the state-of-the-art that will revolutionize the field once more. Companies working on this include Genia, Oxford Nanopore, among others.

Best,
Jimmy Lin, MD, PhD, MHS

THIS INFORMATION IS NOT INTENDED NOR IMPLIED TO BE A SUBSTITUTE FOR PROFESSIONAL MEDICAL ADVICE. YOU SHOULD ALWAYS SEEK THE ADVICE OF YOUR PHYSICIAN OR OTHER QUALIFIED HEALTH CARE PROVIDER

Re: Genetic & Molecular testing

Hi, Marion and Dr. Lin,

Thanks for the info. and I totally agree that " the interpretation is very important - perhaps even more important for molecular profiling."
In my case, one company recommend 5FU and the other one say no from the same tumor tissue.Therefore bioinformatics companies that help with INTERPRETATION beyond what's just provided by the sequence providers can be helpful.

God bless.

Please know that my personal opinion is not intended nor implied to be a substitute for professional medical advice. If  provided, information are for educational purposes.Consult doctor is a MUST for changing of treatment plans.