News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel

News, Analysis, Trends, Management Innovations for
Clinical Laboratories and Pathology Groups

Hosted by Robert Michel
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Goal is to map genetic, transcriptomic, and epigenomic changes in various cancer types

Surgical pathologists are likely to gain great benefit from a worldwide research collaboration that has $500 million in funding, and whose participants plan to identify and publish data about the genetic complexities involved in at least 50 different types of tumors. It is a research project that will directly contribute to the development of new and more precise clinical laboratory tests.

This research is being conducted by geneticists from around the globe. They are collaborating to describe the genomic, the transcriptomic, and the epigenomic changes in 50 tumor types. Expectations are that this research will produce an unprecedented leap in knowledge and launch a new age in cancer research.

This research project is led by the International Cancer Genome Consortium (ICGC). Scientists from 13 jurisdictions have each committed to sequencing up to 500 tumor specimens and matched control samples. The ICGC’s goal is to analyze 25,000 tumor genomes.

A New Era of Scientific Cooperation That Benefits Anatomic Pathology

ICGC members want to produce the definitive cancer genomic data set by working together more efficiently than the individual nations could on their own. ICGC collaborators created a common set of standards by which all participants will code and store the samples while maintaining the privacy of the individual donors.

Another notable feature is that the researchers agreed to not seek patents or other intellectual property rights for the data they produce. Instead, all of this data will be freely distributed through the ICGC’s data portal on the ICGC website.

Early findings from these research efforts are already available. As of November 25th 2010, the ICGC portal contains data from:

  • 22 cancer projects,
  • 12 cancer types,
  • 2,599 donors, and,
  • 4,037 samples.

Academic pathologists will be interested to learn that the data portal offers both “quick” and “advanced” search capabilities. The data is displayed in bar chart format. Data listed include:

  • Simple somatic mutations (SSM): 111,026
  • Copy number mutations (CNM): 3,628
  • Structural rearrangements (SR): 2,849
  • Genes affected by SSM: 23,125
  • Genes affected by non-synonymous coding SSM: 2,860
  • Genes affected by synonymous coding SSM: 1,186
  • Genes affected by frameshift coding SSM: 127
  • Genes affected by stop gained SSM: 220
  • Genes affected by noncoding RNA SSM: 6,995
  • Genes affected by 5’ UTR SSM: 201
  • Genes affected by 3’ UTR SSM: 684
  • Genes affected by intronic SSM: 8,819
  • Genes affected by CNM: 23,594
  • Genes affected by SR: 1,834

The Data Coordination Center (DCC) at the Ontario Institute of Cancer Research (OICR) in Toronto, Canada, was selected by the ICGC to store the massive amount of data being produced by the researchers.

Turning Research into Clinical Practice That Can Be Used by Medical Laboratories

Dr. Tom Hudson

Dr. Tom Hudson, Ontario Institute for Cancer Research (

“The ICGC was formed to identify cancer mutations for most of the major tumor types across the world, and to make the data rapidly available to develop new diagnostics and therapies to improve patient survival,” said Thomas J. Hudson, M.D., President and Scientific Director of the Ontario Institute for Cancer Research in a Dark Daily interview.

“It’s been known for decades that at the microscopic level, all cancer cells have a large number of mutations,” Hudson added. “While some cancer mutations have been studied extensively—and in some cases have become targets for new therapies, such as Herceptin for some forms of breast cancer and Gleevec for leukemia—there exists a large repertoire of unknown cancer genes.

“From the perspective of the cancer patient, it seems increasingly likely that selecting drugs that are based on a combination of pathology and mutation profiles will result in better clinical responses and increased survival,” Hudson continued. “The establishment of new diagnostic platforms that will perform high-quality genomic analyses—particularly sequencing of a large number of cancer genes in cancer patients—will be critical to the adoption of a ‘personalized medicine’ approach to patient management.”

Hudson also noted that the technology platforms currently used in genome centers for cancer genome sequencing have not been designed for use by pathology groups and clinical laboratories. However, there are many biotech companies actively designing systems for use in medical laboratories and pathology groups that will address their needs for rapid turnaround, reproducibility, reliability, and validity.

“The implementation of standard operating procedures and training of personnel in Clinical Laboratory Improvement Amendments (CLIA) laboratories should be possible. However, the management of the large datasets and preparation of mutation reports that are interpretable by clinicians are issues that require significant effort,” Hudson concluded.

The list of partners worldwide signing on to produce genomic data for the ICGC continues to grow. Funding organizations on four continents (North America, Europe, Asia and Australia) have committed to 37 projects totaling more than $500 million.

Funded projects include sequencing tumors found in the:

  • bladder,
  • blood,
  • bone,
  • brain,
  • breast,
  • cervix,
  • colon,
  • head,
  • neck,
  • kidney,
  • liver,
  • lung,
  • pancreas,
  • prostate,
  • oral cavity,
  • ovary,
  • rectum,
  • skin,
  • soft tissues,
  • stomach, and,
  • uterus.

Pathologists and clinical laboratory managers know that diagnostic testing for cancer is going to be a high growth area of laboratory medicine. As the ICGC meets its goal of 25,000 tumor genomes—and development of genomic diagnostic tools catches up with the research—the medical laboratory industry will be poised to deliver great value in earlier detection of cancer, along with the necessary genetic tests and molecular diagnostics assays that can help physicians determine the most appropriate therapies for individual cancer patients.

—Michael McBride

Related Information:

International Cancer Genome Consortium Plans to Sequence 25,000 Cancer Genomes

Cancer Genome Researchers Band Together

International Cancer Genome Consortium

ICGC Data Portal

International Cancer Genome Consortium (ICGC) Goals, Structure, Policies and Guidelines

The Dark Report: Scripps’ Tumor Board Finds Value in Digital Imaging of Slides

World map image provided by the ICGC