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I began creating pottery in Junior year of high school and the thought of breaking a piece or it falling to its fragmented end off the end of the counter was a painful idea at best. It takes so much time and love to throw a bowl or cup, trim the foot and fire it twice over. For it to survive as a functioning piece of ceramics was a marvel to me. 

All that changed when I began this project. 

When I considered what type of project to do, I knew I would enjoy something artistic, especially if it involved my new found love of ceramics

SLA has had a ceramics class for 5 years and over time beginner pieces have accumulated in the studio. Pots, plates, and vases of all colors and sizes were left behind by students to collect dust. 

It should be said that I'd only done small scale mosaics in various art classes over the years-- I have never even done any piece of artwork this large. Using the 30-40 pieces left over from the ceramics class, I created a 13.5 sq ft mosaic. 

When I work with ceramic I am reminded that nothing is permanent and anything can be repurposed to make something completely new. The concept of recycling or "up-cycling" these pieces was a major concept for this project. I begin a piece by making many designs. I like having options and then choosing the one that speaks to me most. The design that I settled on, the silhouetted skyline of Philadelphia, was first and foremost something that means a lot to me, but also a manageable design for a beginner like myself. 

A combination of smashing the pieces with a hammer and throwing them into cardboard boxes allowed me to make usable tiles for the mosaic. 

When my work is going well, I am filled with a sense of vitality-- I don't feel anything but excitement for this project. Many times, I found myself most productive during the night time. My house was quiet and it felt like I was in my own little world. I never felt tired until I finished what I set out to do in a session of work. 

There is a sense of finality that comes with mosaic art because once it is glued and grouted it is permanent and cannot be changed. It was a huge challenge for my perfectionism because I had to sort through many tiles that were less than perfect and choose to use them. It was the beauty of recycling tiles instead of using tesserae- the unusual shape and thickness gives the piece its life. 

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https://sites.google.com/a/scienceleadership.org/one-island-two-worlds/

​Capstone Mentor: Matthew Kay 

Abstract

This was more a learning and growing experience for myself and the young teenagers involved than a project. Over the duration of the time I spent mentoring the kids, I forgot about the fact that I was doing a project for a grade. I felt more like I was doing something that was helping me become a better person. At the shelter, I helped the young kids deal with their hard life situations by writing. Over the time,  I also chimed in on helping them better understand basic every day mannerisms, like being respectful, grateful and polite. In the beginning, everything didn’t start off as lovely as it ended. The kids were very unkind to me and they would clearly express that they did not want to be in my “program”. They would openly express their dislike for what I was trying to teach them. I thought that they didn’t respect me because we were only 4 or 5 years apart in age but soon I realized what it actually was that disinterested the kids. I realized that the kids were being rude for 2 reasons. Reason one was that they didn’t have much discipline in their lives, which explained why they were so rude and they also, like all other teenagers, didn’t  want to sit and write and listen to someone talk for an hour. After this realization. I decided to take a different route into getting them to like what we were doing, which was use active games instead of writing exercise  to start off with. They enjoyed that after a long day of school, then they didn’t mind the writing as much. In the end every went well and I just hope that the kids took a lot from this experience. 

Dear Reader,

This cookbook was made to inform you about the power of food and how it affects our body. Every food out there has a power. These powers affect our bodies in positive or negative ways. I call fruits and vegetables power foods because they fuel our bodies the right way and provide the balance we need. I call unhealthy foods powerless foods because they take power away from us (our health) and they give no health benefits. A balanced diet is very important because our diet is what fuels the body. If the body is not balanced, health problems come about like diabetes, obesity, high blood pressure etc, and we get sick. The cure is in our food. If we eat right and feed our bodies what they need to function, we can be powerful people.

I hope this cookbook can make some people more aware of what they should eat and I hope it informs people about how crucial it is to have a balanced diet. 

Process Paper

For my senior capstone, I created a health food cookbook. This is not just a regular old cookbook, it is an instructional resource that I would like people to refer back to in order to remind themselves that a healthy diet is a key component to a hardy life. I chose to do this project because I found myself eating unhealthy and I see so many people eat unhealthy everyday. These people have no idea what some of these foods are doing to their bodies, and up until I did my research, I had no idea how foods effected my body. I wanted to make a cookbook to inform people that healthy foods didn’t all have to be nasty or bland. Eating healthy is not only beneficial for the body, it’s tasty and it makes the body run better, you can feel the difference. I put a note to the reader on the second page of my book, explaining to them why this book is so important for people to read if they are interested in learning the truth about food. Most food that people eat is out of bags, cans, boxes, and it is all processed and empty foods for the body, I like to call it powerless foods. I am well aware of the fact that people enjoy eating food, and that’s why they eat so much fattening food, to satisfy their cravings. But, over time, cravings can cause the body to become over weight and unhealthy. That’s why I have come up with healthy alternatives people can eat to sanctify their cravings, while eating healthy and fueling up the body with the right ingredients. 

I had to make sure that my capstone addressed all five of the SLA core values, inquiry, research, collaboration, presentation, and reflection. My project began with inquiry. I knew I wanted to do something with spreading awareness about healthy eating. I just didn’t know how I wanted to present my work. I asked myself a lot of questions about what I wanted to show in my capstone and how I wanted to show it. That’s where my research came in. I research different ways people have published their knowledge about healthy eating. I figured out that I wanted to construct and informative cookbook. I already had many of my own personal favorite recipes, but I also researched some more. I also had to research why certain foods are good or bad for the body. I collaborated with both of my mentors and kept them updated with everything I was doing. I especially collaborated with my grandmother a lot because we made all of the recipes together. I also collaborated with all of the people who were willing to try my recipes. My final collaboration with people with this capstone would be anyone who was to use and read my cookbook. I chose to present all of my work in book form. I have it as a PDF and as an actual hard copy document. I also have a few of my recipes on my health food blog I created on google. I can reflect on this project because I can take what I learned during this experience for the rest of my life. I now have more knowledge about food than I ever have before. This is very useful because I can now educate other people like my family and friends. 

There were many steps I took to complete this capstone. I first had to come up with the idea of a cookbook. Then I had to gather up all of my recipes and find more to make them my own by tweaking them. Then the fun part came in, I got to cook, make and eat all of these foods. I did extensive research about all of the power foods that were in each recipe. This is where all of my learning took place. Once I was done cooking and researching, I put all of my pictures, recipes, and information together to make my cookbook. 

I didn’t really bump into any major obstacles to complete my capstone. Whatever dishes I wanted to make, my grandmother and I made them, then I wrote about them. I used many resources to complete my capstone. I used some internet resources to learn about health benefits of the power foods. I used many healthy food resources to make my recipes. I also looked at some books and cookbooks to see what other people have done with it in the past. I am most proud of my information in my cookbook in this capstone. I spent many hours conducting intensive research in order to get all of my facts straight. I feel like if people actually take the time to read this book, it would be able to help many people, that is why I am so proud. I personally have learned so much from this process and I am so eager to share it with the public. I learned that the food that we eat has everything to do with how our body shapes, adapts, and functions. If I could do this whole capstone all over again, I would honestly do nothing differently. I am throughly satisfied with the way my cookbook turned out. SLA is a better place because I was a student here because I feel like as a student, I have a lot of useful information available to share with SLA. I showed this through the cookbook because unhealthy eating is a huge problem, even within the SLA community. If students and faculty took some time out to read this book, they would not only get awesome recipes, but wise advice about eating. They will also find out a lot about what they didn’t know about foods they probably eat everyday. 

Malik Tlili

ABSTRACT
For my capstone I decided to think outside of the box. The beginning of the 2nd quarter a guest speaker from the “Women’s way” organization inspired me to help make a change in the world starting with my community. My goal is to enlighten my community about sex trafficking in the US and heavily emphasize awareness of sex trafficking in Philadelphia. Before doing so I researched the topic and discovered a lot of newfound information. Sex Trafficking targets a specific group of individuals while creating an environment that surrounds the victim that makes it difficult for the victim to make their own decisions. I have decided to specifically enlighten the underclassmen with all of the new research I have found. On December 24, 2012 House Bill 235 mandated the advertisement of the Nation Human Trafficking Resource Center Hotline. Since then I have printed out hundreds of flyers and distributed them to my community as well as informing them about the hotline and it's benefits. My senior capstone is to document how well a community can come together in order to achieve a goal of creating a safe environment for victims of sex trafficking.


Annotated Bibliography

Blancarte, Jody. "Anti-Trafficking Program." SafeHorizon (2013): n.pag. Safe Horizon. Web. 31 Jan 2013.

<http://www.safehorizon.org/index/what-we-do-2/anti-trafficking-program-13.html?gclid=CMiSwOvpkrUCFVCd4AodSF8A9g>.

 Safe Horizon is an organization that provides alarming facts on sex trafficking in the U.S. It also provides a thorough description of what exactly sex trafficking is. This source is what framed the type of organization we would like to collaborate with.

 Vejar, Ellis. "Sex Trafficking In America." For the Sake of One (2012): n.pag. FSO. Web. 31 Jan 2013. <http://www.FortheSakeofOne.org/>.

This source has interactive features that make you view sex trafficking in obscure ways. This source provided me with more personal stories and information on sex trafficking in America. I used these stories in the awareness presentation my partner and I are creating.

Padmore , Theda. "Human Trafficking is an international problem." Active Activism with Global Impact (2013): n.pag. The Defender Foundation. Web. 31 Jan 2013. <http://thedefenderfoundation.org/>.

This organization is the second largest enterprise in the Nation. It targets the most vulnerable victims (ranging from 4 – 19) and provides shelters and other essentials that these girls are deprived of. This source is incorporated into my final project to provide the sense of variety for change. This is one of many organizations that are conveniently available.

Brooke , Axtwell. "Selling American Girls: The Truth About Domestic Minor Sex-Trafficking." Forbes (2013): n.pag. She Negotiates. Web. 31 Jan 2013. <http://www.forbes.com/sites/shenegotiates/2012/12/03/selling-american-girls-the-truth-about-domestic-minor-sex-trafficking/>.

This article is written on how women are “sold” all around the nation. It calculates how much on average these people make and how human trafficking has become so large in the black market. It provides statistics on how these women are taken out of society and given a price. This is just extra information for our presentation.

Glenn , Booker. "Advocacy and Public Policy." Message Agency (2013): n.pag. Women's Way. Web. 31 Jan 2013. <http://womensway.org/advocacy>.

Women’s Way is the organization we are going to partner with. It provides an advocacy program that overall empowers women. Women’s way also works with domestic violence (sex trafficking), which is what our capstone is heavily focused on. They provide clothing and other essential items that the victims of domestic violence (sex trafficking) lack.

Renata , Nicoulin. "The Victims." Polaris Project (2013): n.pag. A World Without Slavery. Web. 31 Jan 2013. <http://www.polarisproject.org/human-trafficking/overview/the-victims?

This source provides inside stories from victims of sex trafficking. It includes how someone is targeted to the struggles of overcoming their obstacles. The stories from the Polaris Project acquire inspiration in the final presentation.

ALEX, WIGGLESWORTH. "Officials discuss why Phill'ys 'poised to become major hub of human trafficking'." Club Metro (2012): n.pag. Metro U.S.. Web. 31 Jan 2013. <http://www.metro.us/philadelphia/local/article/1157934--officials-discuss-why-philly-s-poised-to-become-major-hub-of-human-trafficking>.

This article discusses how Philadelphia must respond to the corrupt actions around us. Statistics show that law enforcements are not the first to respond to cases of sex trafficking. Sex trafficking is popular in most common areas like restaurants, gas stations, and super markets. Philadelphia residents should be more aware and reporting what they see to the authorities.

Organ, Hugh, and Carl Hill. "Philadelphia Anti-Trafficking Coalition." PATCOALTION (2013): n.pag. Modern Day Slavery. Database. 31 Jan 2013. <http://www.patcoalition.org/index.html>.

The Philadelphia Anti-Trafficking Coalition provides services to victims around the city of Philadelphia. The Philadelphia Anti-Trafficking Coalition describes the misconception of sex trafficking and how it is modern day slavery. This organization is in partnership with Women’s Way where they create foundations to help victims in the city.

Dunn, Mike. "Philadelphia Officials Probing Problem Of Human Trafficking Here." PHILADELPHIA(CBS) (2012): CBS PHILLY. Database. 31 Jan 2013. <http://philadelphia.cbslocal.com/2012/12/11/philadelphia-officials-probing-problem-of-human-trafficking-here/>.

This article is of the Philadelphia Official’s response to the rise of sex trafficking around the city. Many people around the city misunderstand the circumstances that women undergo. Also Philadelphia officials describe how to identify victims of sex trafficking and this incorporated into the final presentation.

Machuga, Laurence. "Man charged with human trafficking in Philadelphia." Local/State (2012): ABC Action News. Database. 31 Jan 2013. <http://abclocal.go.com/wpvi/story? section=news/local&id=8860941>.

This article is of a local in Philadelphia who was convicted of allegedly raping and forcing an underage teen into sex trafficking. This article provides the story of the young girl and how high the rates of sex trafficking in Philadelphia. This will be used in our presentation to help reach to students to be aware.

D. Kristof, Nicholas, and Sheryl WuDunn. Half the Sky. New York: Little, Brown Book Group, 2010. Print.

Nicholas D. Kristof and his wife Sheryl WuDunn have first handedly experienced and viewed the issues/circumstances women in Asia and Africa go through. The Novel discusses the revolutionary actions taking place around the world such as Micro-credit. This Novel is what inspired the capstone as a whole.

Murtha, Tara. "For Americans in the Sex Trade, Still Little Hope Read more: http://www.philadelphiaweekly.com/news-and-opinion/For-Americans-in-the-Sex-Trade-Still-Little-Hope.html?page=3&comments=1&showAll=.

This article discusses the journey of 20 year old Mimi living in New York. She has struggled through the sex-trafficking enterprise in New York and she enlightens the property on the inside look of the victims in sex trafficking. This article was used to research the prospective of sex trafficking.

Edel, Lionel. "Sex trafficking, prostitution & backpage ads." WHYY (2012): n.pag. RadioTimes. Web. 31 Jan 2013. <http://whyy.org/cms/radiotimes/2012/03/16/sex-trafficking-prostitution-and-backpage-ads/>.

This source discusses sex trafficking not only in Philadelphia, but across the nation as a whole. The article discusses statistics of the amount of victims both boys and girls. It also provides alarming information of advertisements that promote sex trafficking. This source was use in order to get more information on sex trafficking in the U.S.

Ki-moon, Ban. "Human Trafficking - Modern Day Slavery." NOVA (2008): n.pag. Network of Victim Assistance. Web. 31 Jan 2013. <http://www.novabucks.org/humantrafficking.html>.

The NOVA organization provides a safe line for victims to call when in distress or in need of emergency. This network is a nationwide organization that provides hotlines and shelters for women and men to use. This source is used in the conclusion of our presentation where we will provide “options” for students to use.

Attorney Office, U.S. "Philadelphia Man Charged with Child Sex Trafficking ." Federal Bureau of Investigation (2012): n.pag. Philadelphia Devision. Web. 31 Jan 2013. <http://www.fbi.gov/philadelphia/press-releases/2012/philadelphia-man-charged-with-child-sex-trafficking>.

The Philadelphia Division recently convicted Rashaad McIntyre for childe pornography and sex trafficking. This bust was very recent, occurring on December 14, 2012. This raises the awareness that this is happening in our own city with great stealth. This source is used to disprove the belief of sex trafficking occurring in areas around local families.

 

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          All three of us have an interest in some branch of engineering, more specifically aerospace engineering which is very important in interstellar space science. We aim to gain a better/more in depth understanding of the engineering behind space science (i,e. an in depth look at the lunar landing module). A focus on astronomy gave us a well rounded introduction to the different areas of student we want to pursue after high school. In addition to astronomy we did a lesson oriented completely on Astrobiology which offers an extremely wide variety of sciences to be learned. We most focused on exoplanets (planets that exist outside of our solar system) and what type of technology it would take us to get there. We also focused on the actual term astrobiology, which is a the study of the evolution/future of life in the universe. While helping others who might have interest in some of the lessons we  taught, we also cultivated our own interest in the related sciences.          
           The mini-courses were comprised of both lectures and power-point presentations, with open discussion being the majority of the presentation. Each quarter we turned in a lesson plan to our advisor to show our topic for a certain week. Inquiry and research stem from us looking at real data from missions of the Apollo program, for example or us tracking the status of yet to be determined exoplanets by the Hubble or Kepler telescopes. Collaboration came directly from our interaction with each other and how we choose to present/teach each mini-course lesson. We also took suggestions on what topics want to be discussed the most. Presentation and reflection will both be prevalent in our  end of the year presentation via keynote or powerpoint. ​

Annotated Bibliography

1)

http://i.space.com/images/i/000/000/467/original/earth-like-planet-100929-02.jpg?1290541923 (image)

Cook, Lynette. earth-like-planet. 2012. space.com, Ca . Web. 30 Jan 2013. <http://i.space.com/images/i/000/000/467/original/earth-like-planet-100929-02.jpg?1290541923 >.

This image helps depict the concept of exoplanets in other solar systems. In the Gliese 581 solar system there are planets that have the potential of being habitable planets. This helps explain the significance of exoplanets and how they can shape our future. Another important fact is that it illustrates the similarities between the artist depicted Gliese 581 planet and Earth. A blue ocean with green land masses. Most people think of Earth from an outside view as a blue sphere with green spots on them. Not all habitable planets have to/will look like Earth, but it would be easier for humans to adjust if the planet was Earthlike.

2)

http://www.youtube.com/watch?v=BNLfNe12BKE  

Barlowe, Wayne, writ. Alien Planet. 2005. Web. 30 Jan 2013. <http://www.youtube.com/watch?v=BNLfNe12BKE >.

Alien Planet is a documentary that brilliantly explains the science behind an exoplanet. It actually is pretty futuristic especially with the artificial probes that explore a planet called Darwin IV. It really displays the biological sciences behind a different planetary system. In contrast it also helps paint a picture of how an entire solar system would have to be in order to become another Earth.

3)

http://herschel.cf.ac.uk/results/gliese-581

Gliese 581. 2011. Herschel Space Observatory, Cardiff. Web. 30 Jan 2013. <http://herschel.cf.ac.uk/results/gliese-581>.

This is an image of compiled data that has been used to make graphic of what Gliese 581 would actually look like as a solar system. It is used in my presentation to compare with the Alpha Centauri system. Gliese 581 is much different from Alpha Centauri and our own solar system because of the large amount of dust that orbits the star. These will be the two star systems that will be used for my part of the minicourse.

4)

http://www.space.com/18089-earth-size-alien-planet-alpha-centauri.html

Calçada, . Discovery! Earth-Size Alien Planet at Alpha Centauri is Closest Ever Seen. 2012. space.com, Lisbon. Web. 30 Jan 2013. <http://i.space.com/images/i/000/000/467/original/earth-like-planet-100929-02.jpg?1290541923 >.  

This Image that shows an artists depiction and an enhanced image of the star Alpha Centauri. However, this doesn’t show the fact that Alpha Centauri is a binary star system. I will elaborate on this during my mini course week because the students will be split between two groups Gliese 581 and Alpha Centauri. They will have to research facts on the two star systems and which one would be better to send our first probe to. This image helps compare some of the physical differences between Alpha Centauri and Gliese 581.

5)

http://upload.wikimedia.org/wikipedia/commons/3/33/ESO_-_The_Radial_Velocity_Method_%28by%29.jpg

The Radial Velocity Method . 2007. ESO , La Silla, Chile . Web. 1 Feb 2013. <http://upload.wikimedia.org/wikipedia/commons/3/33/ESO_-_The_Radial_Velocity_Method_(by).jpg>.

This image helps explain the radial velocity method that is used to detect exoplanets by astronomers. The image shows the normal light that is given off by a distant star and then the light given off by a star if it was being orbited by a planet. The orbit of the planet tugs at the star making the velocity of the star dip. Astronomers can tell that the velocity is changing periodically because the light of the star will appear blue when the orbit of the planet causes the star to go further and red when the pull of the planet causes the star to shift backwards. The image pretty much shows the doppler effect in contrast to stars and their orbiting planets.

6)

http://www.nasa.gov/multimedia/imagegallery/image_feature_793.html

Berry , Dana. White Dwarf Star Spiral . 2008. NASAWeb. 1 Feb 2013. <http://www.nasa.gov/multimedia/imagegallery/image_feature_793.html>.

This is a more common example of a white dwarf binary star system. I’m using this image in order to explain specifically what a binary star system is and how it is important for the study of exoplanets. White dwarf binary star systems are really no use to astronomers and space explorers because they have no relevance to colonizing planets.

7)

http://www.astrobiologia.pl/eana/esaexo.html

"EANA: ESA Exobiology." EANA: ESA Exobiology. European Astrobiology Network Association, n.d. Web. 31 Jan. 2013. <http://www.astrobiologia.pl/eana/esaexo.html>.The ESA (Europe Space Agency) gives an introduction into what Exobiology does and what required knowledge there is to know about exobiology, beyond the word "biology". Utilizing many different ways to backtrack or unveil possible extinct life forms from other planets.

8)    

http://www.nasa.gov/externalflash/human_space/

Hanger , Scott. "The Future of American Spaceflight." Tulsa : 2012. <http://www.nasa.gov/externalflash/human_space/>.

This source depicts the evolution of spaceflight technology and how it will be in the future. It was created in 2009 and was last updated in 2012.

9)

https://astrobiology.nasa.gov/articles/2012/10/19/the-color-of-an-exoplanet/

Scalice, Daniella . "Life in The Universe." NASA (2012): n.pag. NASA Astrobiology. Web. 1 Feb 2013. <https://astrobiology.nasa.gov/articles/2012/10/19/the-color-of-an-exoplanet/>.

This shows how the different color of exoplanets can lead to scientist discovering facts about the material content of the planets atmosphere.

10)

http://en.wikiversity.org/wiki/Topic:Exobiology

"Topic:Exobiology." - Wikiversity. Wikipedia, 30 June 2012. Web. 31 Jan. 2013. <http://en.wikiversity.org/wiki/Topic:Exobiology>.Astrobiology is an idea that's currently in the process. Scientist around the world believe that life is or was present in millions of other planets, however through all of the extensive searching, there's only been few evidence of extra-terrestrial life out there. It's more probable to find remnants of them here on earth still awaiting to be discovered.

11)

http://cmex.ihmc.us/sitecat/sitecat2/exobiolo.htm

"Exobiology: The Search for Life on Mars." Exobiology: The Search of Life on Mars. N.p., n.d. Web. 31 Jan. 2013. <http://cmex.ihmc.us/sitecat/sitecat2/exobiolo.htm>.Exobiologist looking for answers on how life came to be on Earth. With the belief that it all started with chemical compound on our planet at its infancy that led to self replication. However that being 4.5 billion years in the making, most of the evidence has been wiped away by erosion, therefore looking into Mars for possible evidence, a planet with a thin atmosphere and has suffered less extreme deformation to its surface.

This is the link to my project  http://globalizationofmusic.weebly.com/ 

http://ejam15.wix.com/erynj-islamglobal 

BENCHMARK - Globalization of Healthcare

Development of a Comprehensive Mutational Pannel as an Effective Tool for Personalized Diagnostic of Medullary Thyroid Carcinomas

 

Medullary Thyroid Carcinoma (MTC) originates from mutations in calcitonin-producing parafollicular C cells of the thyroid, is a rare malignancy, accounting for 3-4% of all thyroid carcinomas. It occurs in a hereditary form (HMTC, 25%) or in a sporadic form (SMTC, 75%). The prognosis for patients with MTC is poor, as the tumor metastasizes at early stages; and the only curative therapeutic option so far is radical surgery. Genetic analysis helps identify inherited cases at a stage where prophylactic surgery can be offered to carriers of such mutations to prevent the disease. This approach may also be used to determine better treatment options for patients who are already diagnosed with MTC.

The goal of this project was to develop a comprehensive mutational panel for the detection of clinically relevant mutations in MTC samples. A total of 143 mutations (nucleic acid variations) in 8 human genes were selected from numerous papers and public databases and included into the MTC mutational panel. The selection criteria were based on the coding mutations (mutations that occur in the coding area of the genes) that were reported to occur in MTC patients and considered functionally relevant. Some of the mutations included into the MTC mutational panel (such as BRAF gene V600E mutation) were also described in other types of thyroid cancer, but most of the mutations were unique to MTC (such as all RET gene mutations). The entire assay design was carried out using Sequenom's online design tools (ProxSNP and PreXTEND (https://www.mysequenom.com/Tools) and Assay Design software (v. 3.1)).

The final file comprised from 115 assays corresponding to all 143 mutations included into the MTC panel. This file will be further processed using the SEQUENOM® Mass-ARRAY iPLEX® platform for DNA genotyping of clinical samples by the cancer research scientists at the Abramson Cancer Center of the University of Pennsylvania.

 

References:

1. Millis, M. (2011, Summer). Medium-Throughput SNP Genotyping Using Mass Spectrometry: Multiplex SNP Genotyping Using the iPLEX® Gold Assay. Springer Protocols, 700. Retrieved August 20, 2012, from http://link.springer.com/protocol/10.1007%2F978-1-61737-954-3_5

This paper discusses and explains the basics of genotyping with the using MALDI-TOF Mass Spectrometry. This was the first paper that I have read right after being given the project. After fully interpreting this paper, I realized that I am going to be able to finish the project on my own. This paper served as a guide to me throughout the process of doing this project, as well as while writing the entire research report. In addition, this paper was used to make sure that I am not saying something that is factually incorrect.

 

2. Gabriel, S., Ziaugra, L., & Tabbaa, D. (2009, January 1). UNIT 2.12 SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform. Current Protocols in Human Genetics.

This paper describes in details the SNP genotyping method based on the Sequenom MassARRAY platform. It includes two step protocol (initial locus-specific PCR reaction, followed by single base extension using mass-modified dideoxynucleotide terminators) an assay structure and how using MALDI-TOF mass spectrometry identify the SNP allele. The paper is mentioned in the corresponded section of the Introduction.

 

 

3.      Ricarte-Filho, J., Ryder, M., Ghossein, R., Fagin, J., Chitale, D., Rivera, M., et al. (2009, June 1). Mutational Profile of Advanced Primary and Metastatic Radioactive Iodine-Refractory Thyroid Cancers Reveals Distinct Pathogenetic Roles for BRAF, PIK3CA, and AKT1. CANCER RESEARCH. Retrieved July 1, 2012, from

http://cancerres.aacrjournals.org/content/69

The paper describes profiling of 111 mutations in RET, BRAF, NRAS, HRAS, KRAS, PIK3CA, AKT1 genes in clinical poorly differentiated, anaplastic and radioactive iodine-refractory differentiated thyroid cancers. The genotyping method is based on the Sequenom MassARRAY platform. It was shown that RAS mutations were prevalent in primary PDTC, whereas BRAF was more common in metastatic PDTC and ATC. PIK3CA or AKT1 mutations were rare. The paper is mentioned in the corresponded section of the Introduction.

 

4. MEN2 Database. (n.d.). AURP Scientific Resource for Research and Education.. Retrieved July 12, 2012, from http://arup.utah.edu/database/MEN2/MEN2_display.php

This database was only used for its mutations list during the collection phase of the project.

 

5. Human BLAT Search. (n.d.). UCSC Genome Browser. Retrieved August 17, 2012, from http://genome.ucsc.edu/cgi-bin/hgBlat

The Human BLAT database was used for alignment of nucleic sequences. The sequences retrieved from COSMIC were inputted in the BLAT Database to be aligned with the rest of the nucleic sequence, as only a small part of it could be gathered from COSMIC.

 

6. Catalogue of Somatic Mutations in Cancer - COSMIC. (n.d.). Wellcome Trust Sanger Institute. Retrieved July 10, 2012, from http://www.sanger.ac.uk/genetics/CGP/cosmic/

This database was used to retrieve the nucleic sequences that were used as the base to be inputted in the BLAT database. As it is impossible to use BLAT database with only knowing the position of the mutation, COSMIC was used to retrieve the minimal part of the sequence required to find the full nucleic sequence for any particular gene.

 

7. Genetics of Endocrine and Neuroendocrine Neoplasias (PDQ®). (n.d.). National Cancer Institute. Retrieved July 12, 2012, from http://www.cancer.gov/cancertopics/pdq/genetics/medullarythyroid/HealthProfessional/Table4

This database was only used for its mutations list during the collection phase of the project.

 

8. OMIM Entry - # 171400 - MULTIPLE ENDOCRINE NEOPLASIA, TYPE IIA; MEN2A . (n.d.). OMIM - Online Mendelian Inheritance in Man . Retrieved July 19, 2012, from http://omim.org/entry/171400

This entry was used as the basis of understanding of the MEN 2A syndrome. It talks about the relationship between MTC and diseases such as pheochromocytoma, and about the basics of what MEN 2A syndrome actually is. In addition, it talks about what mutations are associated with the syndrome. It was specifically used for comparison with the MEN 2B and FMTC.

 

9. Jimenez, C., Hu, M. I., & Gagel, R. (2008, Spring). Management of Medullary Thyroid Carcinoma. Elsevier Saunders, ?, 15.

This MTC review was the first of many that I have read in the duration of this project. This review provided me with the basic information about MTC without which any attempt at actually finishing this project would have been obsolete. Many parts of the introduction are referred to this paper, as it was very influential. Similarly to many other sources, mutations were taken from this publication during the first phase of the project.

 

10. MacConaill, L Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples. PLoS ONE (2009). http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007887

This publication was one of many that were used only for its mutations. No part, except for the abstract, which contributed to the overall idea of the research report, has been read.

 

11. Ehsan Alvandi, Seyed Mohammad Akrami, Mohsen Chiani, Mehdi Hedayati, Babak Noori Nayer, Mohammad Reza Mohajeri Tehrani,et al. (2011, April 5). Molecular Analysis of the RET Proto-Oncogene Key Exons in Patients with Medullary Thyroid Carcinoma: A Comprehensive Study of the Iranian Population. Thyroid, 1. Retrieved September 1, 2012, from http://online.liebertpub.com/doi/abs/10.10

This publication was one of many that were used only for its mutations, and or one small piece of information. No part, except for the abstract, which contributed to the overall idea of the research report, has been read.

 

12. Moura, M., Cavaco, B., Pinto, A., & Leite, V. (2011, February 16). High Prevalence of RAS Mutations in RET-Negative Sporadic Medullary Thyroid Carcinomas. JCEM ONLINE, 95, 6.

This paper has shown a study where 64% of the patients that had Sporadic MTC were found to have a BRAF mutation in position 600. This is very unusual as this mutation is considered to be PTC specific. In addition, this publication has given additional context to this research report. Similarly to many other sources, mutations were taken from this publication during the first phase of the project.

 

13. OMIM Entry - # 162300 - MULTIPLE ENDOCRINE NEOPLASIA, TYPE IIB; MEN2B . (n.d.). OMIM - Online Mendelian Inheritance in Man . Retrieved June 19, 2012, from http://omim.org/entry/162300 

This entry was used as the basis of understanding of the MEN 2B syndrome. It talks about the relationship between MTC and diseases such as pheochromocytoma, and about the basics of what MEN 2B syndrome actually is. In addition, this entry talks about what mutations are associated with the syndrome. It was specifically used for comparison with the MEN 2A and FMTC.

 

14. hybridization, f. i., & (1989), I. e. (n.d.). OMIM Entry - + 164761 - REARRANGED DURING TRANSFECTION PROTOONCOGENE; RET . OMIM - Online Mendelian Inheritance in Man . Retrieved July 19, 2012, from http://omim.org/entry/164761

This entry was used as the basis of understanding MTC, and why the mutations RET gene are found in so many cases of MTC. Unfortunately, as with many other publications, no definitive answer was given. This entry was also used as a guide, to make sure that what I say about mutations in RET gene is factually correct.

 

15. RT-PCR., & (2003), M. e. (n.d.). OMIM Entry - # 155240 - THYROID CARCINOMA, FAMILIAL MEDULLARY; MTC . OMIM - Online Mendelian Inheritance in Man. Retrieved July 19, 2012, from http://omim.org/entry/155240

This entry was used as the basis of understanding of the FMTC syndrome. It talks about the relationship between MTC and diseases such as pheochromocytoma, and about the basics of what FMTC syndrome actually is. In addition, this entry talks about what mutations are associated with the syndrome. It was specifically used for comparison with the MEN 2B and MEN 2A.

 

16. Hazard, J., Hawk, W., & Crile, G. (1959, January 1). MEDULLARY (SOLID) CARCINOMA OF THE THYROID—A CLINICOPATHOLOGIC ENTITY. JCEM, 19. Retrieved June 26, 2012, from http://jcem.endojournals.org/content/19/1/152

This publication was the first time MTC was classified. The paper itself was not read by this applicant, however, due to its historic relevance, it was referred to in the first paragraph of the introduction.

 

 

17. Cakir, M., & Grossman, A. (2009, May 25). Medullary Thyroid Cancer: Molecular Biology and Novel Molecular Therapies. Neuro Endocrinology, 25.

This publication, alongside many MTC reviews, was used as the guideline for this research report. Many facts, such as information about Sporadic and Hereditary MTC were confirmed by this publication. Similarly to many other sources, mutations were taken from this publication during the first phase of the project.