Topic: Genomic Profiling

I thought to enclose the context of a conversation with Jimmy Lin, MD, PhD, MHS,  http://www.raregenomics.org and web presenter of "Understanding Cancer in the Age of Genomics"
http://www.cholangiocarcinoma.org/media.htm

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.

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: Genomic Profiling

Hi,  Marion,

I happen to notice that the above was your  messages #9,000 ;
Your devotion is obvious to all of us.

Congratulations

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: Genomic Profiling

Thanks for that Marion. And many many thanks indeed for every single one of your 9000 posts as well!

Hugs,

Gavin

Any advice or comments I give are based on personal experiences and knowledge and are my opinions only, they are not to be substituted for professional medical advice. Please seek professional advice from a qualified doctor or medical professional.

4 (edited by marions Mon, 09 Dec 2013 12:27:23)

Re: Genomic Profiling

And, thanks to the both of you as well.  We are in this together.  And, a huge thank you to each and everyone participating on this site.  This discussion board has been established by the members, as the wealth of information contained on this site is directly related to each and everyone's posting.
Additionally, we thank the numerous, other volunteers working behind and the scene but are less visible to the public at large.

Hugs to all you wonderful people,
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: Genomic Profiling

Marion, you know how I feel about you so I will not repeat what Percy and Gavin said except to say I want to be like you when I grow up. Hey! How do I do that since I am much older than you? I would have never done so well with Teddy without your help and then mentoring me on this Board. The world is a better place because of our Board touching so many lives. Thank you!

Teddy ~In our hearts forever~ATTITUDE is EVERYTHING
Any suggestion I offer is intended as friendly advice based solely on my own experience. Please consult your doctor for professional guidance.