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Medical information is no longer stored in big binders in  doctors' offices - instead it’s stored on internet servers for easy retrieval, manipulation and  increased efficiency. If your family doctor orders drugs, the pharmacy has access to your personal and medical information in addition to your insurance information. If the doctor prescribes further tests, the lab has your test information plus your personal information. If you have to go to the hospital for some reason, the hospital asks for your medical history and your insurance company. Every place you go, your medical and personal history is required. All this information is available to the organizations by few clicks of the mouse.

In order to avoid any misuse of this information, all organizations in Ontario are bound by privacy laws outlined by the province’s Personal Health Information Protection Act (PHIPA). PHIPA defines “personal health information” as identifiable information relating to an individual’s health and care history. PHIPA prohibits use and sharing of personal health information. But... there is always a 'but' in this imperfect world...we are essentially moving towards an era where we can sequence our genome for a couple of hundred bucks, analyze it and make it part of our medical history...which might be stored on a server. Technological  improvements  have enhanced both the accuracy and predictive ability of genetic information. In addition  to improving  the results  of  genetic  tests,  developments  in  computer storage systems have made data more easily available. Data can effortlessly flow and  become  integrated  into  other  computer databases.

Once the genetic information is out there on the internet it is very difficult to make it unavailable. It's very easy to add a face to a gene sequence. You don't believe me? Well here is an article from the Washington Post about a boy who was conceived through anonymous sperm donation. When the boy turned 15 years he wanted to about his background and his heritage. He took a swab of the inside of his mouth and sent the swab to one of the commercial genetic testing services. The Y chromosome has short tandem repeats which are passed on from father to son almost unaltered. He later decided to further pursue his search and compared his Y chromosome to a database of sperm donors set up by Family Tree DNA of Houston. Today he and his biological father know about each other.

 

Yaniv Erlich at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts., wondered if this was a fluke or he can replicate this in his lab. In order to test his hypothesis, he did several experiments. His lab came up with an algorithm that is based on the individual’s  genetic markers called short tandem repeats which are present on the Y chromosome (males only). The team then searched genealogical databases like ysearch.org. The databases store information in a way that the surname corresponds to their individual genetic markers. The database only provides the last name of the people. Therefore, the team confirmed the correct names by cross-referencing the possible last names with public records of people of similar ages and locations. His repeated experiments lead him to conclude that putting your DNA on the internet can be dangerous.
 

http://vimeo.com/60165760

It is clear that these genetic advances are going to play an ever important role in our lives in the future. Bioinformatics can use all the genetic information for research in the field of drug development, antibiotic resistance, gene therapy and molecular medicine. Also, it gives bioinformaticians the ability to not only compare genes from one human being to another but also across species like with the fruit fly!! This comparison can be at any level- genes, SNPs, proteins, or RNA. Bioinformaticians love this kind of data but this at the same time will raise a host of privacy challenges that we are only beginning to understand. Genetic information holds more informational value as opposed to regular medical history. The information may be predictive of genetic predispositions that would otherwise be undetectable. The information may have a significant impact on the family, including offspring and group. The significance of the information may not be necessarily understood at the time of testing.

If an employer knows that an employee is likely to be diagnosed with cancer, the employer might not want to retain that employee. Similarly, a person who is known to have a high risk for a genetic condition may have difficulty obtaining insurance because he or she is likely to run up medical bills that would be costly to the insurance company. Because we cannot control our genes, it is unfair to discriminate against a person's genetic predispositions. In 2008 the Genetic Information Nondiscrimination Act (GINA) was passed into federal law in the U.S. With all the above mentioned concerns a lot of people don’t want to undergo genetic testing even if it is advisable by a physician. GINA is a strong and essential first step in the fight against genetic discrimination and misuse of medical information. GINA not only helps against health and employment discrimination but also ensures that biomedical research continues to advance and people have the peace of mind when undergoing genetic testing. However, Canada does not have equivalent legislation.

 Speaking of genetic testing, there are tons of private companies that have come up recently. They make some very interesting arguments about what our genes can tell us... and that shall be a topic for my next blog.

The human genome 'city' is made up of billions of DNA nucleotides. Humans have been able to sequence it, which produced enormous amount of data (several terabytes!!).  This terabyte of information was written in DNA language (A,C,G,T), and printed in books that were called the "Book of life". Even though the book has a story to tell, it is hard to translate it into any of the 6900 or so languages we know!


http://www.opont.hu/hirek3.php?k_hirAzn=27234&k_hirFl=201112&k_hirKat=7

 The Human Genome Project lead scientists to realize that only 2-3% (about 20,000 genes) of our genome provided the blueprint for protein synthesis. Though this size may sound insignificant, mutations in this region are thought to be the cause of most genetic diseases. The rest of the genome is better known in the scientific community as "junk DNA". We had very little idea of what the rest of the DNA did.


 
 To investigate the junk DNA, Human Genome Research Institute  at National Institutes of Health funded a five year project called ENCODE (Encyclopedia of DNA Elements) .The aim of  ENCODE was to determine which parts of the DNA were biologically active  and make an initial assessment of their functions. Just a few months ago, the results of ENCODE were published in several journals including Nature, Genome Biology and Genome Research. The project made use of a lot of bioinformatics tools to analyze this information.

  The ENCODE  team reported that they were able to assign biochemical functions to over 80% of the genome. That's huge!!! Initially what we thought was “junk” is actually beaming with life! ENCODE results indicate that this “junk DNA" regulates the protein synthesizing genes and evolutionary changes. Each cell in the human body has the same copy of the genetic code. The combination of various genes in the genetic code helps to define the physical characteristics of the cell and its function. It is also this region in the human genome that decides if a cell is going to be a liver cell as opposed to a cell in the eye.

 Now you are thinking "Okay, that was really cool, but how does it affect me?" Well, at present scientists know of only 147 cell types, attempting to say just what each part of the genome is doing in them. In the future we hope to gain the necessary understanding of every cell type and transcription factor in our body to ascertain the function of all of the "junk DNA". The field of Bioinformatics is making this enormous task relatively easy to handle. Bioinformatician are using genomic sequencing as a tool to detect the absence of a particular gene, or a mutation which may lead to a diagnosis of a genetic disease. Having said so, doctors will be able to:
• Diagnose a patient who presents with symptoms
• Help pregnant mothers who are concerned about potential abnormalities in their babies
• Detect inherited diseases which may appear later in life
• Help with genetic counselling for couples who want to have children
Thus, bioinformaticians and doctors will be able to help an individual to make lifestyle choices to deal with the disease, avoid the disease or to make informed decisions about having children.
Although I must add, if the genetic sequence of an individual has a gene for a particular disease, it does not necessary mean that s/he will develop it. It just means that s/he is prone to it and may need to take precautions. Having that power to understand what is going on at such a microscopic level in our genome and to be able to do something about it, is a revolutionary change in the field of medicine.
 
 Encode data  information is publicly available, making it easy for scientists all around the world to integrate this information into their research.  My next blog will be on genetic privacy and future implications of having genetic information available at your finger tips.

"Aditi, so what is it that you are studying at Seneca College?" is a common question that usually comes up in a social setting. When I report back saying "A graduate certificate in bioinformatics," I am greeted with blank expressions. I find people are not familiar with the field. Well, it is like how your grade school used to teach you new words, by breaking down words to build meaning: Bio is the study of life and living organisms, and informatics is gathering, manipulating, storing, recoding, and retrieving information. In essence, using computers to analyze biological data to uncover the mystery called DNA. DNA is made up of four chemical structures (adenine, thymine, cytosine and guanine), that are repeated over and over again billions of times. Understanding the order of these chemical structures can reveal the secrets about Evolution, animal diversity, diseases and potential cures. This does not mean we are curing AIDS or cancer in our laboratories, but definitely helping to get closer to it.  Speaking of which, Western University has come up with a preventative vaccine for HIV and is now approved by FDA for first phase of clinical trial! Bioinformatics helped biologists analyze data used to create this vaccine. We actually might have a 'possible' tool to combat a virus that has created relentless havoc, pain and suffering to the human mankind, for decades! Exciting, huh? Who knows, now we might be able to help find a cure for the common cold!

The field of bioinformatics is fairly new, which...would explain the blank expressions I keep receiving. It all started in 1990 when National Institute of Health (NIH) in the US initiated a project called the Human Genome Project. NIH in collaboration with international laboratories in 2003 successfully concluded the Human Genome Project and sequenced the entire human genome! It was a terabyte of information of just repeated A's, C's, G's and T's!! The need for understanding, managing such vast amount of data with the least amount of time, resources and human effort gave rise to the field of bioinformatics.

Oh! by the way, my name is Aditi (yeah, about time I introduced myself). I have finished my undergraduate degree in Health Science at the University of Ottawa. Currently, I am a student at Seneca College, pursuing a certificate in bioinformatics (as you all have guessed by now). How did I end up here? Well, it is a long story. In short, I owe it all to my strong background in science, my inquisitive nature and a very annoying sibling (a computer whiz kid), who shaped my interest in computers. Therefore, bioinformatics for me is like having the best of both worlds! A one year graduate certificate at Seneca College provides training to people who come from multi-disciplinary backgrounds in biology or computer science to acquire the skills needed to meet the demands of this field. I think my experience at Seneca College has been very informative and insightful. My goal through this blog is to share my experience with curious individuals like you and get the word out there about the field. My next blog will be about, what is sometimes referred to as "junk DNA" and how an international project called ENCODE brought the letters A, C, G, and T to life!

Over the past six months Donald A Wilson Secondary School’s Biotech club have been researching and collaborating with the University of Guelph, the Toronto Zoo, the Ontario Genomics Institute and Let’s talk Science to create interactive signs in order to promote awareness for DNA barcoding. These signs are planned to be placed around the Zoo at various locations and can be used alongside an activity for high school students. The Biotech club put aside time during our summer vacation in order to complete these signs with accuracy and care. We met at a local library once a week. While there we worked on the signs but also had lots of fun together in the process.

Throughout this project we have had the opportunity to travel to many different scientific organizations and labs. In July we went to the MaRs facility in Toronto to meet with Alison Symington from the Ontario Genomics Institute. While there, we talked about our signs and project as well as toured the Sick Kids’ Centre for Applied Genomics. It was so cool! 

In early July and late August we traveled to the University of Guelph where we met with representatives from Let’s Talk Science and the University of Guelph to go over their signs as well as perform some DNA Barcoding lab work. In this lab work we got to sample various fish fillets that all looked very similar. We then barcoded their DNA; it was very interesting to have the opportunity to perform this lab work. We also took some photographs of the fish to go on our sign about how DNA barcoding can be applied to prevent mis-identification of fish fillets.

In late July we had the opportunity to present our signs and ideas to the CEW (Conservation Education and Wildlife) committee at the Toronto Zoo.  The curators and staff of the Zoo were incredibly supportive of the idea. After our presentation we began to collaborate with zoo staff on our project.

Finally all of our hard work was seen by a select group when on Monday October 29th grade 11 students from Donald A. Wilson piloted the project at the Toronto Zoo. We placed temporary signs throughout the zoo to identify any areas that could use improvement in the signs before the final installment.

Overall we are all very excited about our work and hope the signs will enjoyed by the general public at the zoo. We are all very grateful for the support received for this project from:  The Biodiversity Institute, Let’s Talk Science, the Ontario Genomics Institute, the Toronto Zoo and the staff at Donald A. Wilson S.S. As of now, the signs are predicted to be permanent at the Toronto Zoo by September 2013. As a team we are so excited to see where our project will go in to future.  Having worked on it will definitely be a highlight of our high school career. 

The announcement of last week’s 2012 Noble Prize winners really got me thinking not only about science and innovation but also the people who have really revolutionized the field.  These researchers really think outside the box and instead of making incremental steps in moving science forward, they develop ideas that create paradigm shifts in scientific thinking.  One of these great innovators is Kary Mullis.  In 1983, Dr. Mullis had the idea to use a pair of primers (primers will be described in the video below) to bracket a desired DNA sequence and to copy it using DNA polymerase, a technique which would allow a small strand of DNA to be copied almost an infinite number of times.  One complication; however, was that the DNA polymerase used was destroyed by the high heat used at the start of each replication cycle and had to be replaced.  Mullis started to use the Thermophilus aquaticus (Taq) DNA polymerase to amplify segments of DNA. The useful thing about this protein/enzyme is that it’s heat resistant and would only need to be added once, thus making the technique dramatically more affordable and subject to automation.  This has led to PCR becoming  a common and often indispensable technique used in medical and biological research labs for a variety of applications:

a. DNA cloning for sequencing
b. Genetic testing
c. DNA fingerprinting in forensic sciences and paternity testing
d. Detection and diagnosis of infectious diseases
e. ART?

For more information on PCR make the leap and link to see this video

In March 2012, the Ontario Genomics Institute (OGI) launched a new funding program for high schools entitled the “Genomics Equipment Grant”.  This program was set up to support Ontario high school teachers who want to bring effective and innovative teaching of genomics into their classroom. OGI recognized that some teachers were under-resourced and did not have the equipment to teach genomics in their classroom so we responded by launching the program.  The first high school to receive a grant is  Lester B. Pearson Collegiate Institute, Scarborough.

After reviewing the numerous applications that were submitted to the Genomics Equipment Grant competition, it became apparent that many high schools were under resourced and OGI was amazed that many schools did not have PCR machines which are essential instruments in any modern molecular biology lab (PCR machines are expensive but can be found for about $2,500.00).  Although “DIY” PCR instruments exist at a much lower price they require users to build them before use.  OGI wants to work with a high school class to help get one of these instruments.  If you are interested in a DIY PCR project contact me dmccormac@ontariogenomics.ca and we can discuss potential collaborations.

Now that you learned how PCR works, we wanted to alert you to a contest that OGI is hosting.  The contest is an effort for OGI to try and keep students innovative and to aid them in their ability to translate scientific knowledge in a way that is understandable to most non-scientists (in a fun and artistic way).  OGI has recently obtained a “used” PCR machine which is in great condition and we are offering it up to any high school in Ontario that comes up with an innovative YouTube video/art project that ultimately uses PCR technology. 

Before you run off and start thinking about your project and video, I wanted to share with you some cool innovative projects that use this technology!
DNA11, a novel Canadian company makes works of art from your own DNA.  Just swab your cheek and send them a sample, and they create a unique piece of art to hang on your wall. The creations are colorful blown-up photographs of the agarose gel that is run after amplification of your DNA by PCR.  It has been done this in the past and here is an Andy Warhol inspired DNA portrait of my own DNA portrait that was printed on plexiglass:

 
Fun Project Ideas
Bio-Rad, a leader in PCR instrument and reagent sales, often puts out musical parodies of what PCR is all about:
 http://youtu.be/CQEaX3MiDow
http://www.youtube.com/watch?v=x5yPkxCLads&feature=related
There are also students illustrating what PCR technology is all about through dance
http://youtu.be/LCjPFmv7hh0

Don’t let these ideas be limiting, come up with your own!

Here’s MY DNA, AMPLIFY ME MAYBE???

Contest Guidelines
This contest is an effort for the Ontario Genomics Institute to try and keep students innovative and to aid them in their ability to translate scientific knowledge in a way that is understandable to most non-scientists (in a fun and artistic way). 

OGI has recently obtained a “used” PCR machine (pictured above) which is in great condition and we are offering it up to a high school in Ontario that comes up with an innovative YOU TUBE video/art project that ultimately uses PCR technology.

Eligibility:  Any high school in the Ontario public or Catholic school boards
Submission deadline: Tuesday, January 15, 2013
Submit your link to Kim Riley

Please provide the following information along with your submission:

Teacher’s name and grade(s), (plus telephone & email address)
Name of School
School address
Name of School Principal, (plus telephone no. & email address)

Any Questions:  please email Kimberly Riley or call 416-673-6587

Please note:  Schools that have a functioning PCR machine are not eligible to enter this contest.