Concept explainers
The website CBioPortal (http://www.cbioportal.org) is an exceptionally useful program for visualizing the cancer genes and genomes of tumors from thousands of patients with different kinds of cancer that have been analyzed by whole genome sequencing and in some cases, by RNA-Seq.
Go the the CBioPortal site and click All under Select Cancer Study and in Enter
Gene Set type PTEN, then hit Submit. On the page that is returned you will see how the coding region of the PTEN gene is altered in tumors investigated in the various studies. Hitting the tab Mutations will let you see the details of these mutations relative to the PTEN protein, while the tab Expression lets you see how the gene’s expression (in terms of cDNA reads) is altered in individual tumor samples.
a. | Is PTEN an oncogene or a tumor suppressor gene? What kinds of evidence lead you to this conclusion? |
b. | What kinds of cancer are most likely to involve alterations of PTEN? |
c. | How would you identify patients whose tumor cells are particularly likely to have a somatic mutation in the PTEN gene that is outside of the coding region but nonetheless contributes to cancer by affecting the gene’s regulation? |
Now return to the CBioPortal home page. Again, select All under Select Cancer Study, but this time type ERBB2 under Enter Gene Set and then hit Submit. | |
d. | Is ERBB2 an oncogene or a tumor-suppressor gene? What kinds of evidence lead you to this conclusion? |
e. | Are any kinds of listed mutations in the ERBB2 gene almost certainly passenger mutations as opposed to driver mutations? What does it mean to be a passenger mutation? |
f. | If you were looking for regulatory mutations in the ERBB2 gene that are not in the coding sequence but that contribute to cancer, what attributes would you look for under the Expression tag? |
g. | In comparing your results with the PTEN and ERBB2 genes, how informative are missense mutations in these genes with respect to possible contributions of such mutations to cancer |
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Genetics: From Genes to Genomes
- Two genes associated with breast cancer, BRCA1 and BRCA2, were discovered in 1994 and 1995, respectively, and shortly thereafter, were patented by Myriad Genetics, a company based in Utah. Under the patents, testing for mutations in these genes could only be performed by Myriad, at costs from 300 to 3,000. Myriad also patented the process of analyzing the results of such tests, preventing anyone who obtains the sequence of their BRCA genes by other means (which itself would probably be patent infringement) from interpreting the information. The idea that genes can be patented has been a contentious issue from the beginning. Patents are not granted for products of nature, meaning that genes inside the body are not patentable, but biotech companies successfully argued that by removing a gene from the human body, purifying it, and then obtaining its DNA sequence, they created something not found in nature, and which is therefore a patentable invention. The U.S. Patent Office found the argument persuasive, but opponents argue that genes are parts of our bodies and can be identified but not invented. Biotech companies argue that without the protection offered by patents, they would have no incentive for research and development of diagnostic tests. In Europe, patents for BRCA1 and BRCA2 were revoked in 2004 because they did not meet the standards for a patent. After more than a decade of legal disputes, the patents were partially restored in 2008 on a very restricted basis. In the United States, a lawsuit, focused on the patents for the BRCA genes, was filed in May 2009. The suit challenges the basic idea that genes are patentable. In November 2009, the judge ruled that the lawsuit can proceed, and the case is moving forward. In March 2010, a federal court invalidated Myriad Genetics patent on these genes. In August 2011, the U.S. Court of Appeals reversed the lower courts decision and ruled that gene sequences isolated from cells are not a product of nature and are therefore patentable. The case went to the U.S. Supreme Court, which ordered the appeals court to reconsider the case. The Federal Appeals Court did not change its decision, and the case once again, went to the U.S. Supreme Court. A unanimous decision in June 2013 invalidated Myriads patents on the basis that isolating a gene from nature does not make it patentable. This is a landmark decision on gene patenting with widespread ramifications for the biotechnoloogy industry. Will this decision reduce the incentives for companies to invest in new diagnostic tests that would be used by cancer victims or those with serious genetic disorders?arrow_forwardthe task is to use this image to write a results section of a report about: Identification of Differentially Expressed Genes in Breast Cancer Using RNA-Seq. 1000 words would be bestarrow_forwardRetinoblastoma is an extremely rare cancer of the retina in the eye. The disease mainly affects children up to the age of 5 years because it can only occur while the nerve precursor cells are still dividing. In its nonhereditary form, a tumor usually occurs in only one eye; in its hereditary form, multiple tumors develop in both eyes.To explore the basis for these differences, a cDNA clone of the Rb gene was used to probe the structure of the gene in cells from normal individuals and from individuals with nonhereditary or hereditary retinoblastoma. As shown in the figure Part A, normal individuals have four restriction fragments (A, B, C, and D) that hybridize to the Rb cDNA probe, indicating that each restriction fragment encodes at least one Rb exon. Samples from fibroblasts and tumor cells of affected persons show some differences in the patterns of hybridization, with some bands missing entirely and some bands present at half intensity. The order of the restriction fragments in the…arrow_forward
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- A graduate student who has not taken BIOL 519 thinks they have discovered a new oncogene that could cause breast cancer. The student transfects cells with this oncogene and finds that the cells proliferate uncontrollably. The student next designs a PCR assay that will detect the presence of the oncogene in cancerous breast tissue. The student sets up the assay and analyzes the presence of the oncogene in normal and tumor issue samples (See data below). The student is disappointed to see that the potential oncogene is present at similar levels in both the normal and tumor tissue. Therefore, the student concludes that this gene is not an oncogene. Do you agree with this conclusion? Justify your answer (5-6 senetences max).arrow_forwardScientists carried out a microarray analysis to compare the gene expression of normal liver cells to that of cancer cells from a person with liver cancer. The scientists labeled the cDNA from the normal pancreatic cells with green fluorescent nucleotides. They labeled the cDNA from the cancer cells with red fluorescent nucleotides. The two cDNAs were mixed and allowed to hybridize to a microarray. Normal liver cells =Green Cancer cells =Red The DNA in that spot is the same in cancer cells and normal cells =Yellow Question: Gene alpha is turned on in all liver cells. In the cancer sample there is a nonsense mutation in this gene such that the protein terminates translation early but transcription is unaffected. What color is the alpha gene spot on the microarray? Answer: Yellow please explain why is the answer yellow?arrow_forwardthe context of this image is that it is from the GEO website and what to do is to write 500 words for the results section of a report using the image. the title is Identification of Differentially Expressed Genes in Breast Cancer Using RNA-Seqarrow_forward
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