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Finding Novel Cancer Treatment Options Using Molecular Testing – A Guest Post by Kim Pelak

I am pleased to feature a guest post written by Kim Pelak, Ph.D. Dr. Pelak is an old friend of dear daughter’s. Dear daughter and I have known Kim since she was in fourth grade (yours truly was one of her Girl Scout leaders) and even back then she was interested in genetics. We all knew Kim would be doing important work some day and she is. Recently Kim offered to write a guest post explaining a bit about her work, which involves helping to find cancer treatment options using molecular testing. Targeted medicine based on each individual patient’s genomic information is where the future of personalized cancer treatment is likely heading. Thank you, Kim, for sharing about the exciting work you do. 

Finding Novel Cancer Treatment Options Using Molecular Testing

by Kim Pelak, Ph.D

In recent years, the cost of DNA sequencing has dropped sharply.  The sequencing of the first human genome was announced with the completion of the Human Genome Project in 2001; it cost several billion dollars and took a multi-national team of scientists about 15 years to complete.  Now, a mere 13 years later, a human genome can be sequenced in less than a week for a couple thousand dollars.

This drastic reduction in the cost of sequencing has enabled the expanded use of genetic information in a clinical setting, as well as improved our understanding of genetic diseases such as cancer.

One of the areas where genomic information has already had an effect on medicine is the field of oncology.  There are two kinds of genetic alterations that play a role in cancer:

  1. Heritable familial risk factors, such as certain BRCA1 and BRCA2 alterations.  Many of these have been known for several decades, and they can lead to a high rate of cancer within a family, as well as cancers that can have an earlier age of onset.
  2. Acquired genetic changes.  These are mutations that occur over a person’s lifetime, either as a natural part of the aging process, or from environmental exposures such as sunburn or smoking.

As the cost of obtaining genetic information has decreased, tests for both types of alterations have increased in availability and improved in accuracy.

Some genetic changes are seen frequently in certain types of cancer, such as an acquired amplification of the Her2 receptor, which is seen in 15-20% of breast cancers.  Several drugs have been developed to target this change.  Interestingly, recent research has shown that Her2 is also altered in other cancers, including gastroesophageal, bladder, ovarian, and colorectal.  Drugs that were initially designed and FDA approved to treat this alteration in breast cancer have now been FDA approved for gastroesophageal cancer, and are currently under investigation for other cancer types. There are many other examples of similar genetic alterations across cancers in different tissues.

There is a paradigm shift in the cancer field; cancers are beginning to be classified and treated based on these molecular similarities, rather than their tissue of origin.

I work at a company called Foundation Medicine, which is at the forefront of using personalized, genetic information to impact patient care.  We receive biopsies of patient tumors, extract the DNA, and sequence several hundred of the genes that are most often mutated in cancer.  We then provide a personalized report that explains what is known about the mutations in each person’s cancer, focusing on acquired genetic changes.  We also list any targeted therapies (FDA approved or in clinical trials) that could be relevant for individual patients based on the molecular classifications of their cancers.

Our goal is to provide doctors and patients with therapeutic options for consideration.  Some patients’ molecular profiles have many targeted therapy options, while others have just a few or none at all.  Some patients’ molecular profiles will suggest therapies that are FDA approved in that patient’s tissue.  Others will suggest therapies that may be FDA approved in a different tissue, such as for patients with Her2 amplification in cancers other than breast cancer or gastroesophageal cancer.  Currently, about 82% of our reports have mutations that are “actionable,” meaning we are able to identify potential targeted therapies or clinical trials based on patients’ molecular profiles.

Research is beginning to show that patients with the same molecular profiles, but different cancerous tissues of origin, may derive benefit from the same therapies, regardless of the tissue for which these therapies were initially developed.  Without a comprehensive test, such as the one offered by Foundation Medicine, some patients would never know that they are good candidates for these targeted therapies.

Foundation Medicine’s first test went on the market in mid-2012, and we had sequenced tumors from more than 21,000 patients as of mid-2014.  The role of molecular testing in cancer treatment is growing, and the number of targeted cancer therapies on the market is increasing every year.  This shift is transforming cancer treatment and helping to identify therapeutic options that may not have otherwise been considered.  Although there is still much work to be done, personalized genomic medicine is becoming a valuable tool in the treatment of cancer.

Have you had genomic sequencing done, or do you know someone who has?

What are your thoughts on molecular sequencing and/or the paradigm shift?

What question or comment do you have for Dr. Pelak?

©2014 Jon Chomitz Photography 3 Prescott street, Somerville, MA  02143 617.625.6789


About the author:

Dr. Kim Pelak has been an employee at Foundation Medicine since July 2013.  Her primary responsibilities are to analyze patient genomic information, write patient clinical reports, and help develop software tools to enable an efficient reporting process.  The views expressed in this post are entirely her own and do not express the views of Foundation Medicine.  Her aunt is a breast cancer survivor, and her uncle and grandmother passed away from lung and pancreatic cancer, respectively. She has been interested in the human genome and personalized medicine since middle school, and received her Ph.D. in human genetics and genomics from Duke University in 2012.

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Beth L. Gainer

Wednesday 10th of December 2014

Great post, Kim! I think Jackie raises a really good question about the variability in cancer. I would like to know that as well.

You are doing so much to help others; it is such a wonderful thing.


Monday 8th of December 2014

Yay Kim! Keep up the great work! Exciting to see the science make such big advancements.

One question - how do you account for some of the variability in cancer? For example, a person's could have HER2+ breast cancer but maybe 80% of the cancer cells might have that receptor and 20% don't. Do you test samples from multiple biopsy sites? Or look for variability within the sample you get?

Lisa DeFerrari

Friday 5th of December 2014

Thank you for this very informative explanation of what's involved in molecular testing. It's amazing what can now be done in this area and especially as more targeted therapies start to become available (hopefully), it seems that this is something that would naturally start to have a big impact on how doctors and patients make treatment decisions.


Thursday 4th of December 2014

Kim, what an interesting post! I really enjoyed reading about the work you're doing and the difference you are making for people.

Alene Nitzky

Thursday 4th of December 2014

Questions: 1. How is this shift in identifying molecular profiles impacting the research for new drug therapies, which has been stagnant for decades? It seems like we have the same pool of drugs and we keep throwing them at different things, aside from a few targeted therapies that have emerged in recent years, we are still largely relying on the same basic chemotherapy drugs.

2. How can this knowledge about the human genome help us find a way to discover these potentially carcinogenic molecular profiles BEFORE cancer even begins? That seems like an equally important, if not more important, way to spend research dollars.

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