Whole Genome Sequencing for Cancer

March 5, 2010 · Posted in Genetics of Disease, Tools of the Genome Trade 

By Hsien-Hsien Lei, PhD, HUGO Matters Editor

Last month, researchers at the Johns Hopkins Kimmel Cancer Center announced that they had successful sequenced the complete genomes of cancer patients. The sequences were analyzed using a technique called “personalized analysis of rearranged ends” or PARE. PARE can detect genome rearrangements that can then be used as cancer biomarkers indicating tumor growth. Cancer genomes can be used to identify:

  • Driver mutations that cause cancerous growth through mechanisms such as the alteration of gene expression
  • Mutations that are the same in different tumors of the same type
  • New drug targets based on the mutations identified in the cancer genome
  • Diagnostic tools based on a complete list of driver mutations in each cancer type
  • Effective drugs or a cocktail of drugs tailored to each individual based on their tumor profile of driver mutations

    (Source: The Scientist)

The results from whole genome sequencing of cancer patients can be used to “monitor the growth of tumors, determine appropriate levels of therapy, and show instances of recurrence.” (BioTechniques)

“Eventually, we believe this type of approach could be used to detect recurrent cancers before they are found by conventional imaging methods, like CT scans,” Luis Diaz, assistant professor of oncology at Johns Hopkins, said in a press release.

The Cancer Genome Atlas (TCGA), part of the National Human Genome Research Institute, is also working on using large-scale genome sequencing to study cancer. In June 2009, their Genome Sequencing Centers began including whole exome and whole genome data. And in July 2009, the Genome Sequencing Centers completed the first of 24 whole genome sequence analyses of glioblastoma multiforme and ovarian tumor samples. Here’s Dr. Raju Kucherlapati, Principal Investigator, Genome Characterization Center, The Cancer Genome Atlas, speaking about cancer genetics and genomics.


Recently, Amy Harmon of the New York Times explored targeted cancer therapies in a three-part series. She profiled Dr. Keith Flaherty who was in charge of clinical trials testing PLX4032 in melanoma patients.

Healthy cells turned cancerous, biologists knew, when certain genes that control their growth were mutated, either by random accidents or exposure to toxins like tobacco smoke and ultraviolet light. Once altered, like an accelerator stuck to the floor, they constantly signaled cells to grow.

What mattered in terms of treatment was therefore not only where a tumor originated, like the lungs or the colon, but also which set of these “driver” genes was fueling its growth. Drugs that blocked the proteins that carried the genes’ signals, some believed, could defuse a cancer without serious side effects.

Targeted cancer therapies also include gene therapy although this approach has thus far been unsuccessful. More information on targeted cancer therapies is available at the National Cancer Institute (link).


One Response to “Whole Genome Sequencing for Cancer”

  1. Pallavi Shukla on March 11th, 2010 2:43 pm

    The video of Dr. Raju was nice and very informative. I am an indian student working on genetics. Get to know about the new emerging field “Personalized medicine” through this video.

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