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

Percy and Marion,

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

Julie

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.

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.