Cancer profiling: NGS is not the only tool in the box

Many groups are working on next-generation sequencing tests for mutation profiling of tumours. There are two main approaches, amplicon sequencing (reviewed in a previous post) and in-solution capture capture (reviewed here and here); both of which only look at DNA which is not immediately limiting, and tests are being commercialised (see my recent Foundation Medicines post).

Of course DNA and NGS is not the only assay that can be used. Other tests target more than this, e.g. FISH for DNA rearrangements, RT-PCR for gene expression or IHC for protein expression.

There are companies aiming to be as comprehensive as possible and one of them also has an interactive tool I thought you may not be aware of.

Cancer pathways: The Caris website has a nice interactive tool to look at Breast, Lung and Colon pathways and the drugs that impact treatment.

Caris Life Sciences have two main technologies, Target NOW and Carisome microvesicle technologies. They have also just selected the MiSeq and TruSeq Custom Amplicon for their sequence based analysis of FFPE tissue. In Illumina's press release Matt Posard said that Caris had completed over 40,000 molecular profiling tests.

Target Now is a molecular profiling service for personalised cancer medicine. It is based on markers identified in the literature which correlate with drug response and also identifies open clinical trials patients may be enrolled in. It is somewhat similar to the approach used by foundation Medicine and also by Illumina in their clinical sequencing tests. As well as identifying patient treatment options Target Now aims to suggest alternative therapies for patients where the standard of care is not an option, has been exhausted, or for cases of highly aggressive, metastatic, or rare tumours. You can see what is included in their Target Now Breast Cancer test here. It offers a mix of Sequencing, IHC, FISH/CISH, RT-PCR and RFLP. You can also download a sample report from their website.

Carisome technology is a blood based assay for circulating microvesicles (cMV) or exosomes that can act as cancer biomarkers. cMVs are nm-sized sub-cellular membrane-bound vesicles released by many cell types into almost all intracellular fluids, including blood. These can be proteomically profiled to determine cell-of-origin. Caris Life Sciences are commercialising cMV profiling as a potential tool for cancer diagnosis.

Their Executive Director Dr. Daniel Von Hoff (also physician in chief at TGen and Professor of medicine at Mayo) presented at this years ASCO. You can see his presentation on YouTube.