Wednesday, 7 November 2012

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.


  1. Hey there! Thank you for sharing your thoughts about breast cancer assay in your area. I am glad to stop by your site and know more about breast cancer assay. Keep it up! This is a good read. You have such an interesting and informative page. I will be looking forward to visit your page again and for your other posts as well.
    From the approximately 25,000 genes in the human genome, Genomic Health identified 250 candidate genes possibly associated with breast cancer tumor behavior. These genes were analyzed in more than 400 patients from three independent clinical studies in order to identify a panel of 21 genes strongly correlated with distant recurrence-free survival.
    HPLC sample fractionation for highest degree of purity & sensitivity with Breast Cancer Assay

  2. This comment has been removed by the author.

  3. Cancer is caused due to uncontrollable cell growth which keep on multiplying. This causes a tumor which affects other organs functionalities. There are more then 200 types of cancer which a human body can get affected. Cancer can be treated well if diagnosed in earlier stages. Treatment of cancer can be radiation, chemotherapy and immunotherapy.
    cancer centers in philadelphia

  4. Thank you for giving information on cancer treatment.It is really good and helpful for the people.Keep giving such a valuable information.I will wait for your next post.
    Regards:cancer treatment in india

  5. This comment has been removed by a blog administrator.

  6. This comment has been removed by a blog administrator.

  7. Cancer is a complex set of diseases. Each cancer is unique in the way it grows and develops, its chances of spreading depends on the way it affects one`s body and the symptoms one may experience . Several factors, including location and how the cancerous cells appear under the microscope, determine how cancer is diagnosed. best cancer treatment in India

  8. Pretty good post. I just stumbled upon your blog and wanted to say that I have really enjoyed reading your blog posts.

    breast cancer assay

  9. I like the helpful information you provide in your articles. I will bookmark your weblog and check again here frequently. I’m quite certain I will learn plenty of new stuff right here! Best of luck for the next!


Note: only a member of this blog may post a comment.