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