The Baylor College of Medicine Human Genome Sequencing Center—a designated large-scale sequencing center of the National Human Genome Research Institute—is a member of The Cancer Genome Atlas project, an ambitious government-funded consortium created to identify cancer-causing genes.
Administered by the NHGRI and the National Cancer Institute, both branches of the National Institutes of Health, the goal of the nine-year Cancer Genome Atlas Project is to identify genetic changes and variations found in more than 20 types of cancer. The initiative was formed to facilitate a comprehensive and coordinated effort to establish a detailed catalog of genomic changes in specific types of tumors, with the long-term goal of improving the prevention, diagnosis and treatment of cancer.
The consortium, which studies up to 500 samples for each cancer type, has identified more than 100 new genes, to date. The Duncan Cancer Center conducted all tissue banking for the samples. Funded to the tune of $100 million annually, TCGA is leading the way in new understanding of the causes and progression of the disease.
Under the leadership of genomics expert Dr. Richard Gibbs, the Baylor center received a $114 million grant for research to identify every gene and mutation linked to 50 types of cancer. To date, the center’s work has led to sequencing in tumors of the colon, pancreas, kidney, breast and bladder.
A five-year collaboration between the Baylor College of Medicine Human Genome Sequencing Center and center members in the Michael E. DeBakey Department of Surgery identified two new pathways involved in pancreatic tumors that may lead to the development of new and earlier diagnostic tests for the disease.
The study was the first to report findings from primary tumors. Previously, only cell lines or tumors transplanted into mice had been used.
Sequencing found that mutations in the genes of 224 cancerous colorectal tumors disrupted the proper activity of a cellular pathway known to play a crucial role in cancer and embryogenesis. The study identified several new genes not previously suspected in the disease.
Researchers considered colon and rectal cancers as distinct and examined each separately, but they found that the two were extremely similar on a genomic level, excluding hypermutated tumors that had abnormally high rates of genetic mutations.
The results of this study may help explain why people with hypermutated tumors have a better prognosis that those whose tumors are mutated at lower rates.
Deep molecular analysis of 131 muscle-invasive tumors found recurring defects in 32 genes for bladder cancer, a form of the disease that currently has no targeted therapies. Many of the genetic abnormalities had previously been linked to other forms of cancer, but nine of the genes had never been reported as significantly mutated in any other cancer.
Researchers surveyed 400 cancerous kidney tumors to identify 19 mutated genes.
The study found that high-grade, high-stage clear cell kidney tumors undergo a metabolic shift suggestive of the Warburg effect in cancer. The Warburg effect refers to the fact that cancer cells generate energy in the absence of oxygen, whereas normal cells produce energy in the presence of oxygen.
In the first comprehensive genetic analysis of breast cancer, TCGA researchers evaluated tumors and tissue samples from 825 patients and identified four main subclasses of breast cancer.
The study, which focused on the most common types of breast cancer that are thought to arise in the milk duct, found that the four subtypes do not appear to develop from one another. In addition, one type of breast cancer was found to have many of the same properties as an aggressive form of ovarian cancer. •
All studies published in the journal Nature between 2012 and 2013.