Stats

Since I pulled these stats we have completed four more projects.  So far we have earned 47, 523 points and have returned 63 results.  Not as good as some of the groups but I was running it on my laptop so I didn't leave it running all the time!

Reflections

Molly-I am so happy we had the opportunity to participate in this project for a couple reasons.  I have worked in healthcare for over ten years and was able to see the journey of many cancer patients.  Some were happy and some were very difficult to observe the direction their cancers took them.  Many of these patients I was close to and when they passed it was like loosing a family member.  I myself have also had my own cancer scare.  I have had so many abnormal looking moles removed I cannot even begin to tell you how many.  A year and a half ago I went in to have two more removed expecting the same outcome as all the times before, nothing wrong just preventative measures.  Boy was I wrong.  Coming from the generation that used any kind of oil you could find to sunbathe I really shouldn't have been surprised.  Both of those moles came back abnormal 1 step prior to cancer. When the reports came back I also found out the boarders were not clear and that I had to go see a specialist to have them removed again.  Now I go yearly to have all my moles measured and observed for any changes and removed if necessary, in fact I go Friday to get two more removed.  Hopefully the work we have done will help future cancer patients receive the treatment they need for a successful outcome!!

Zack-I really enjoyed working on this project over the last few months for a few reasons. The first of these would have to be that I got a real world understanding of how scientific research is adapting to the future of technology. It blew my mind to know that there were thousands of people working on these tasks to propel research and all they had to do was keep their computers charged. The second reason would have to be that it gave me a better understanding of tumor markers and tumor development without having to read it in a textbook or listen to it in a lecture. For me, experiential learning is much easier and much more worthwhile, and this definitely came in under that category. Even though we lost a member throughout the semester, I feel as though the project was relatively easy since we were all engaged and interested. I personally can't wait to check out the blogs from the next class in the future. 

Melissa- I enjoyed working on this project because I have learned more about how tumor markers can affect how tumors or even cancers may form.  For myself, I have had family members die of cancer that was not found until it was later in the progression.  I personally have a risk of tumors in my family, so I am personally cautious of what I do and how it would affect my life. I have a large birthmark on one of my arms which I have to watch because it could become a tumor marker and if that occurs I have to have it removed and all freckles/moles checked, which would be extremely time consuming.  It was also interesting being able to adapt technology to looking into how to cure or be able to adapt markers to help those with a higher risk for cancer or tumors themselves.  

Tumor Marker Questions
Title:  Intratumor Heterogeneity and Branched Evolution Revealed by Multi-region Sequencing
Journal:  The New England Journal of Medicine
Date:  March 8, 2012

1.     This is a multi-part question.  To answer it, you will need to go to www.ncbi.nlm.nih.gov and follow these instructions.

From the drop-down search menu, choose “Nucleotide.” Type mTOR in the box to the right and hit “Search”.

Click on the Rattus norvegicus mechanistic target of rapamycin (serine/threonine kinase) (Mtor), mRNA (sixth entry). On the right side of the page, click “Run BLAST.” On the next page, click the BLAST button at the bottom (and wait…).

1. Scroll down your results page.  Name ten other taxa (scientific and common names) that share some sequence identity with this Rattus gene?
2. What is Rattus? In an evolutionary sense, why study the mTOR gene in this animal?
3. What does wild type mTOR gene do in these animals?  Why is it conserved across so many disparate species?

1a.)        
                                 Scientific Name                                         Common Name

                                  Mus musculus                                              House mouse
                          Peromyseus maniculatus                                      Deer mouse
                            Mesocricetus auratus                                      Golden hamster
                              Cricetulus griseus                                         Chinese hamster
                      Ceratotherium simum simum                               White rhinoceros
                                 Homo Sapiens                                                   Human
                                 Equus caballus                                                   Horse
                              Saimiri boliviensis                              Black-capped squirrel monkey
                                  Pan paniscus                                                    Bonobo
                              Macaca fasicularis                                     Long-tailed macaque


1b.) Rattus is commonly known as the brown rat and is the organism often studied in laboratories around the world or kept as pets. The reasons why the mTOR gene is studied in these organisms are that they grow to sexual maturity rapidly and multiple generations can be studied in a relatively short period of time, allowing us to test for mutations and changes in the gene due to heredity.

1c.) The wild type mTOR gene codes for protein mammalian target of rapamycin, it is a serine/threonine protein kinase that regulates cell growth, cell proliferation, cell motility, cell survival, protein synthesis, and transcription. It is conserved in so many species because it is a crucial protein in the developmental process of mammals even though it can contribute to a group of health problems. For example, hyperactivity of the protein can cause Alzheimer's in mammals.

2.    Apply Darwin’s postulates to tumor adaptation in drug-resistant clones.

2.) Postulate 1 states that within a population, genetic variation will exist among tumors formed in individual organisms. Postulate 2 goes on to state that at least some of the genes will be heritable. Mutations within a tumor site will be passed on to other cells within the same tumor or other tumor metastases. Postulate 3 states that not all of these populations of tumor cells will survive. This is shown when certain drugs and therapies do not have an effect on certain areas of a tumor in an organism. Postulate 4 allows natural selection to take place within the tumor cells, slowly allowing the resistant portions to develop and form a more resistant tumor over time.

3. The authors assert that intratumor heterogeneity will influence medical decisions and personalized treatments.  Why, then, might it be important for an Oncologist to understand evolution?

3.) Understanding the evolutionary processes of tumor development would be important to an Oncologist because it is the only way to truly understand and provide proper treatment. By understanding this evolutionary process, Oncologists can provide individualized treatment plans and help prevent resistant tumors.

4.  Considering Figures 2C and 4B, explain how phylogenetics can contribute to the understanding of tumor heterogeneity and to the generation of better tumor markers.

4.) "Reconstructing tumor clonal architectures and the identification of common mutations located in the trunk of the phylogenetic tree may contribute to more robust biomarkers and therapeutic approaches."

Interview with Dr. David German

Dr. David S. German, MD has a specialization in orthopedic hand surgery. He works at the Midwest Plastic & hand Surgery in Saint Louis, Missouri. He has three board certifications: General surgery, hand surgery and plastic surgery.  He has worked with different skin problems, such as removal of birth marks. 

                While speaking with Dr. German,  he stated that there are different tumor markers for a specific tumor itself. Tumor markers are generated throughout the body which do not directly correspond with that area of the body.  Also, tumor markers are “predictions” or “precursors” to a tumor or a cancer itself. An example would be CA25 which is a protein that codes for ovarian or breast cancer.  CA25 is like a tumor marker which helps with the diagnosis of ovarian or breast cancer, but it has to be found in higher-than-normal amounts. It is not possible to monitor a patient without monthly blood  or urine test. The only other test that is possible is taking a piece of a tumor itself and that is how to test for tumor markers. There are different tumor markers, there only some that are linked to cancers.   Tumor markers are rarely enough to show that cancer is present in the body, imaging or other lab tests  will be requested to make sure it is cancer or a tumor.

                Dr. German has worked with birth marks in the past.  There is a ten to fifteen percent chance that the birth mark on the face is a cancerous. The birth mark sometimes works as a tumor marker for skin cancer. The determining factor is dependent on the location, color, and the size of the birth mark. The age of an individual be influential on how the likely a cancer would be detected.  Birth marks on the face are usually removed because it is the most common cause of cancer.  The birth mark is considered to be a tumor marker, but there has to be a certain type of mutation to a gene.  Dr. German gave the example of the elephant man, which he has, a higher risk of skin cancer issues and other tumor markers for different cancers.

                Many patients believe that if they go in for gene testing or figuring out if there is an issue with tumor markers, they will have cancer that goes along with it or that the insurance would be increased or that they would not be covered. 

Description of Mapping Tumor Markers

The idea of grid-computing is a broad collaboration of computer systems that are non-interactive.  The non-interactive systems involve large numbers of files which are collected as a resource to reach a common goal, such as trying to find a cure for a disease. There are different types of grids that are used being a single grid or clustered.  Many of the single grids are used for operating systems that retain information specific to a certain place, such as a library software.  There are many applications for grid-computing to solve Grand Challenge problems which include: protein folding, finance modeling, different simulations, and weather/climate modeling.  Universities use existing computers to handle their own long-running computation tasks which are considered as a form of distributed computing.  The volunteer computing has different ways such as: the resources can be trusted; which would assume that a PC does not return results that are intentionally wrong and will not falsify, therefore there is no need for replication. Also, there is no need for screensaver graphics, usually it is desirable to have a computation be completely invisible and out of the control of the user of the PC and then the deployment of the information is automated.  The grand vision is often presented as an analogy to power grids where users (or electrical appliances) get access to electricity through wall sockets with no care or consideration for where or how the electricity is actually generated. In this view of grid computing, computing becomes pervasive and individual users (or client applications) gain access to computing resources (processors, storage, data, applications, and so on) as needed with little or no knowledge of where those resources are located or what the underlying technologies, hardware, operating system, and so on are.

                For an understanding of the project, an introduction of Mapping Cancer Markers is important. First, Tumor markers, also known as biomarkers, are found in a higher amount in blood, urine, or even some individuals with cancer.  Tumor markers help physicians indicate cancer and the corresponding treatment.  The markers are mostly used to screen high-risk individuals because it helps to find cancer in healthy or high-risk individuals before symptoms are developed.  The tumor markers can help physicians to predict cancer behavior and respond, to heighten the patient’s chance of recovery. The recovery consists of a treatment plan, which tumor markers help to decide if chemotherapy or immunotherapy should be used after surgery or radiation therapy.  There are other tumor markers that help a physician choose a prescription regimen for each individual patient.  The markers will also allow physicians and their patients to monitor for a reoccurrence, which is significant for some patients due to a change within the count of tumor markers, which provides detection sooner.

                There are limitations of tumor markers. Physicians usually need other tests done, like a biopsy, to determine if there is a presence of a particular tumor marker is a cause for concern. Tumor markers can have an elevated level which may be caused by a condition or disease other than cancer, some individuals have tumor markers levels that may be higher than usual that do not have cancer.  There is variation in tumor markers over time which causes inconsistent results and the level of tumor marker may not rise until after the progression of the cancer which does not help in early detection.

                The tumor markers are tested via a blood or urine which is sent for analysis. The biopsy sample, is an example of a surgical specimen can also be used to find tumor markers. The tests have to have two requirements: specificity and sensitivity.  Specificity is important because if the test is not specific enough there could be a false positive which would mean an individual would have unnecessary tests and anxiety. Sensitivity is important as well, because it could suggest that a tumor is there or not all and would cause a false positive because the individual would not be responding to a treatment.
                Grid computing will help scientist screen to identify grouping of markers in the body to detect cancer which in the long run will help make cancer curable. The project will screen data extracted from tissue and blood samples from thousands of individuals or patients and will help to identify the characteristic chemical markers that are associated with certain types of cancers or tumor markers. This will also eventually help to determine the risk of developing certain cancers or tumors and will allow for a better treatment that is effective for a specific individual or patient.

                There are specific tumor markers in cancer and they can be found on the following website. http://www.cancer.net/all-about-cancer/cancernet-feature-articles/treatments-tests-and-procedures/understanding-tumor-markers  

http://www.cancer.gov/cancertopics/factsheet/detection/tumor-markers
http://www.worldcommunitygrid.org/research/mcm1/overview.do
http://www.youtube.com/watch?v=D6CIOqym2mw&noredirect=1
http://www.cancer.net/all-about-cancer/cancernet-feature-articles/treatments-tests-and-procedures/understanding-tumor-markers
http://labtestsonline.org/understanding/analytes/tumor-markers/tab/glance
http://mcr.umh.edu/downloads/tumor_markers-m.pdf