The Final Week of the Final Frontier

Welcome to the last week of the rest of your lives!!!

Well, the last week of my project that is. I know week after week you all have been waking up every day and longing to read each new installment of this ten part series that is my blog. Not every week was as exciting to read about as some of the more action packed weeks, but I have tried to make each post interesting and fun to read. I have honestly really enjoyed writing them and dramatizing everything that I do. No one wants to read about some guy putting some data into a computer. The people want to read about a young man finding himself by endlessly punching in names after names after names and prescriptions after prescriptions after prescriptions into a small, square laptop that takes FOREVER to load (I mean seriously its 2017 get faster wi-fi) while simultaneously considering the fact that this really should be illegal or be breaking some existing laws like I am looking at a lot of medical information right now.

Anyways, this week in the office consisted of exactly what I did last week which included printing off the results from the five standard tests that are used to check for diabetes. Soo not really anything new happened. I got tighter with Sarah and shes a pretty cool person. Maybe if my project was longer then we could have been as tight as the OG power duo: Carol and I. Alas, I think it is time to move on. I had a lot of great experiences at this doctor's office and it has definitely helped me have a clearer image of what I want my career to look like. I have decided that I don't really want to be a doctor but do something in the field of medicine. I don't know exactly what that is but I am hoping to find out in college (right now I am planning on doing biomedical engineering but we will see).

Outside of the office this week, I finished the rough draft of my power point! The senior project is coming to a close and fast. I can feel it and it feels great. I think my presentation will be pretty good. I mean it will be on a topic that I have been doing research on and participating in for the past ten weeks so I don't think it will be very difficult to talk about. Still not entirely sure exactly what day my final presentation will be on. It's gonna be sometime in May. I can tell you that much. I don't think this is the last post that we are supposed to do. I think I make another one after this, but I could be wrong. Anyways, I had a good last week. I said goodbye to Sarah and Heather and everyone that I have grown to know and love at the office. I wish peace to the world and to everyone reading this post for my last week! Bye bye SRP!

Almost There

Hello avid readers and welcome to the penultimate week of my project!

I'm almost done with the 10 weeks of my senior project! wooooohooooo. These past 2 months have been an emotional roller coaster. There were some good times and there were some bad times. I learned a lot and grew emotionally, spiritually, and geopolitically. Even though Dr. Lalani's office has been a great source of training and knowledge, I think ten weeks is the perfect amount of time for a research project. This way I can become accustomed to and knowledgeable about something and leave before my on-site mentor runs out of things for me to do.

This week in the office went very similar to last week where I would print off the different files of patients that are needed by Heather and various companies that need to check that Lalani's office has followed the standard operating procedure for treating certain conditions. Once again, along with progress notes I printed out what those companies needed, the results from past tests. This week Heather explained to me what the results I was printing out were actually for, which made my life more interesting. Apparently, when a patient has newly diagnosed diabetes, they go through five tests to confirm that they have diabetes, so the doctors have more specific data about the patient's individual case of diabetes.

The five tests are called the Doppler, Nerve Conduction, Smart Skan, Thyroid Biopsy, and a Retinal Scan. I am not sure on the specifics of these tests or how they work, but I know that in a typical diabetes screening all five are utilized.  Similar to last week, I had to look for these five tests that were performed in the year 2016 in the files of the patients in addition to any progress notes that needed to be printed out. Why only 2016? I don't know but I'm sure companies have their reasons. Or maybe they don't have their reasons and they want these files as a joke, in which case this isn't a very funny prank. Anyways even though what I did in the office was not related to the PGX study, I still got to learn a bit about diabetes and continue helping Heather and the other office people with stuff that needs to be done and no one wants to do. Seriously, this one woman treats me like a saint every time I come in, because if I didn't print out this stuff then she would have to do it.

Outside of the office, I have slowly been putting together my power point for the final presentation. I will put the date of the presentation in my next post, because I am drawing a blank on when it is while I'm writing this post. I hope it goes well. It shouldn't be too hard. At least I don't think so. I mean even if it doesn't go well, what are they gonna do? Make me not graduate? On second thought, maybe that's how it works. Welp, we will find out. I gotta go now. I'll see you all next week!

New Person, Same Old Medicine

Hello internet users!

Feeling good? Yes? That's good. I am glad to hear it. It always makes me feel warm inside when I know that each and every one of my dedicated viewers is having a good time. If at any point in your life you are not having a good time, I want you to know that you can come to me and we can talk it out. I feel like we have gotten to know each other pretty well.

Anyways enough about you, let's talk about what you really want to read about: me. After the tragic loss of Carol last week, I had to look to new horizons to finish off my senior project in these final three weeks. My mom is friends with Dr. Lalani and she asked if there was something else I could do in his office. He gave me the number of a physician's assistant named Heather. I left Heather a voice mail pleading for some sort of structure in this chaotic spiral I was slowly descending into. She texted me and informed me of a new possible on-site mentor. Her name is Sarah and she is the professional and spiritual successor to Carol.

I may not have the same, witty rapport with Sarah that I had established with Carol, but her position in Dr. Lalani's office is essentially the same as Carol's was which means that I do relatively the same kind of tasks that I have become accustomed to. The only problem with coming into the office now is that all the work on the PGX study that needed to be done in the office was completed by me during my first four weeks of my project. So Sarah and Heather had to find new tasks for me to do. However, even though what I did this week in the office was not related to the PGX study, I still developed valuable skills in learning how to look at patients charts electronically and help Heather with tasks that make her life easier.

To explain what I did this week, first you have to understand that when a doctor visits a patient many of the important notes that they take are hand-written and then later scanned into the patients electronic charts to be kept on file. Now when these patients come back for a follow-up visit with Heather, the problem is that many times Heather does not have these hand-written notes (labelled as "progress notes") on hand. So, it was my job this week to take all the patients that she will see in the next few weeks and print out their progress notes and then attach these progress notes to their physical, paper charts, which Heather actually has. This way Heather has all of the information that she needs before she meets with her patients. If I didn't do this, then either Sarah or Heather would need to do it themselves and they don't got time for that. They have more important stuff to do. Or at least I would hope that they do. Also, I learned that insurance companies like to know what kind of tests have been performed on the patients, so in addition to the progress notes, I also had to print out a series of results of tests that were done on Heather's diabetes patients to then fax to the insurance companies.

All in all, it felt good to be back in an office, feel productive, and feel like I was actually helping someone with something, hopefully making their life easier. I printed out sooooo many progress notes. Lemme tell you, Heather is stacked with progress notes. She has all of the progress notes she could ever need. Well I hope you had a good time reading this. Catch ya next week!

Mourning the Loss of a Great Mentor

Hello everyone. Today is a sad blog post.

I know you all have gathered here today to be entertained by another one of Jack's amazingly comedic blog posts, but alas this one will be dreadfully serious. Today, we sit here at our individual computers and contemplate the loss of Jack's greatest mentor and friend, Carol. On Monday March 20th, 2017, Carol resigned from her position at Dr. Lalani's office to have a better life somewhere else. Although I know that somewhere deep down she would love to still work in the field of medicine, the petty, verbal kerfuffles between the coworkers she oh so despised finally got the best of her. She couldn't take it anymore. Years of being underappreciated finally beat her down and won a long war of attrition. The conflict ultimately climaxed when she finally had an epiphany at the end of her vacation and decided that she would not be returning to work on Monday.

In many ways, Carol quitting her job made my life harder. On one hand, I lost my on-site mentor, but more importantly I lost a friend. On the other hand, I learned a lot from Carol's actions. She told me before she left that in America it doesn't really matter how long you have worked somewhere or how good you are at your job, because if you do not have the proper credentials (i.e. college degrees) then you will not go very far in life. I think that this is a very important lesson to learn especially for people in high school, because you always hear about how important college is but not usually from someone who actually wishes that they had gone to school for longer. So, in the end, am I upset that Carol left? In the same way that you are upset when your dog is terminally ill and in pain and you have to put him/her down. You wish you did not have to live through the whole situation, but it's for the best. I know that Carol will be in a better place. She told me that her husband is some master tennis court builder or something so she is gonna try to get in on some of that action.

So since Carol was in-charge of everything I was working on in the office, I didn't get the opportunity to come in this week, but I'm working on being able to shadow a physician's assistant named Heather for the remaining 3 weeks which would be awesome. I would get to do more hands on stuff and see if interacting with patients is something that I would like to do as a part of my future profession. Instead of going in this week, I continued to do research on enzymes and their processes in the body. Apparently there are some medications like Humira which are not metabolized by the cytochrome p450 enzymes so they are just not tested for in the PGX study. I thought this was interesting, because it shows a shortcoming of the experiment.

Anyways, I just hope Heather is as much of a bro as Carol was. I hope to see you all next week with some interesting stories! LONG. LIVE. C@ROL.

Research as a Lone Wolf

I'M BACK. Hope you all missed me, because you know I missed sharing my life with you all. My spring break was pretty fun. I'm sure all of your spring breaks were pretty fun too. Honestly with nothing to do though sometimes I get a little crazy, so it feels good to be back.

Anyways, Carol is actually on vacation this week so if I went into the office there would not be anything for me to do, because she is in charge of all the PGX study stuff. So, I took this week to stay at home and research the different genetic and enzymatic processes behind the study so that I could better understand it and be able to explain it to others in the future.

So, to start my research (and I began to explain it in my Week 4 blog post if you want to refer to that), I looked at Cytochrome p450 which is a group of enzymes responsible for the metabolizing of a myriad of the most common drugs prescribed by doctors. Now it is important to understand these enzymes for the obvious reason that they deal with exactly what the PGX study hopes to accomplish which is to investigate which drugs metabolize well in the patient. Enzymes included in Cytochrome p450 are ones that start with the letters CYP. This is integral to know since half of the genes that are tested for in the PGX study start with the letters CYP and those genes code for the enzymes that start with the letters CYP.

In my Week 4 post I mentioned the CYP2C9 gene which codes for the enzyme of the same name. As it just so happens, some common drugs act as CYP2C9 enzyme inhibitors and if a patient is already a poor metabolizer of the drugs that are broken down by the CYP2C9 enzyme then they will experience adverse effects from those drugs. Looking at CYP2C9 as an example, we can understand more broadly how the study operates. By looking at the genetic code of a patient, we can see whether that patient is a poor, normal, or rapid metabolizer of 12 specific genes and then we can recommend the drugs that do not inhibit the production of the enzymes that the patient naturally does not produce very well.

Well, I can't divulge all of the information that I researched, because then this blog post would become more like a biochemistry paper instead of a blog post. However, learning about all of these biological mechanisms will make it much easier to explain everything when I inevitably have to present what I did over ten weeks in a power point. But I am glad I did the research, because it was actually pretty interesting. Soooooooooooo i'm done here I guess. See ya'll next week. Quick shout out to Dalton for leaving a dope comment. This gif is for you!

Get Schwifty!!!!!!

Why Are You Looking At My Blog?

IT'S SPRAAAAAAAAAAAAANG BREAK!!!!!!

Enzymes Are Pretty Cool

GOOOOOOOOOD MORNING VIETNAM!!! and hello there blog readers. 

How has your week been dear viewer? Oh, it's been not terrible? That's always nice to hear. You think this conversation is kind of one sided? Yeah, it is. Well, since you are here let me tell you what you want to hear: what happened in my life this week. In all honesty, not a terrible amount happened but nevertheless I will tell you all about it. 

Since I am essentially the only one in the office who knows really how to input the data from the PGX study (Carol forgot since I have been doing it for the past four weeks and she isn't too good with computers), Carol was going to have me train someone from the office on how to input the PGX data. BUT, apparently some people are too good to be trained by some kid in high school (or they were too busy but I wanted it to be more dramatic). So, I didn't end up training anyone which would have been cool, because I would have been able to showcase my expertise at looking at papers and then typing what is on the papers into a computer. 

Since no one wanted to be trained this week and their was no more data to input, I decided to learn why exactly these twelve genes were chosen and how exactly the tests work. 

If you take a look at this picture which I included in my last post, then you will see that 6 out of the 12 genes that are being tested for begin with the letters CYP. Now, why is that? That is exactly what I was trying to figure out this week by doing my own investigative research. It turns out that all of the genes listed in this study correspond to enzymes that have the same name. So, the CYP2C9 gene codes for the CYP2C9 enzyme. Super cool! Apparently, the CYP genes are all part of a family of genes called the cytochromes P450. These enzymes are produced in the liver, like many enzymes, and are responsible for the breaking down of over 100 different commonly used drugs. It all makes sense now!

As I got deeper and deeper into my research I realized how much chemistry and biology are related. For instance, the CYP enzymes are all proteins that need a cofactor called Heme to function. Heme has a very specific shape of four five-membered rings containing a nitrogen atom all connected by methine bridges (=CH-). Lower levels of Heme can result in a patient not being able to metabolize some drugs as effectively, because then the CYP enzymes will not function at the normal rate. 

Moving forward I am planning on doing more research into the biochemical properties of enzymes and how they relate to genes and their ability to metabolize common drugs. Hopefully doing this research will allow me to accurately explain the complicated science behind the PGX test. Next week I am taking my spring break so I will have a week off of my project. It should be fun. I am planning on relaxing pretty hard. I hope you all have a good time on spring break too! WOOOOOOOO SPRAAAANG BREAAAAAK 

They Will Come Back...They Always Come Back

Hello all! I had a pretty relaxed week. I hope you all did too.

My week was not super eventful, but I will still share it with you (partly because I have to). This week we had our first patient come back in for their post-90 day survey so that they could conclude the study. All of the patients have a strong interest in finishing the study, because if they do not follow through with it then they get charged something like $1000 because their insurance will only cover it if they finish the study. So, that's pretty cool. I was not actually at my site the day the person came in, but I got to look at the survey that the patient fills out when they come back in and I got to input that data into the same system where I inputted the pre-PGX data. Maybe next week I will be able to take a picture of an example survey but for now I will just describe it to you. Basically, the patient describes the condition that has been causing them harm/discomfort and that information is recorded. Then the patient describes the new medication that was prescribed to them and says whether or not it worked better as a treatment than the previous drugs that they used. That's pretty much it. Not that complicated. All of the post-PGX data is compiled into a system designed by the company administering the study and then their researchers compile and analyze that data. 

Oh, also I have pictures of what the results look like for the test and what the patient sees! Its a practice trial, so don't worry it's not a HIPAA violation (probably). 

Okay, so this first picture is just one of several pages where it gives a list of drugs associated with helping with certain kinds of illnesses (on this page it shows cardiovascular and diabetes). Based on the patient's genes it gives a detailed list of what drugs are ok to take and which ones are not. Every drug in the column titled "Standard Precautions" is ok for the patient to take. Every drug in the column titled "Use with Caution" will most likely react poorly in the patient's body and the drugs in the column titled "Consider Alternatives" are the drugs that the patient can take instead of the drugs in the "Use with Caution" column. Now that's pretty neat!

This second page is the actual results from the analysis of the genes. There are twelve genes listed here and next to each one it describes the genotype and phenotype of the patient with respect to that gene. For the gene CYP2C9, for example, it tells us that the patient is a normal metabolizer for drugs that rely on enzymes created by the CYP2C9 gene to function. This second page is very interesting to me and will be the focus of my future inquiries into how exactly the testing works. I have been doing some studying on my own to try to understand better how these 12 genes operate and how these 12 genes affect enzymatic activity. Once I achieve a better understanding of these phenomena, I will share it in a blog post. Maybe even next week! Well, I hope this post was enlightening. Have a good week/weekend/whenever you get around to reading this. Bye!

Oh, and here's a gif.

First Human Contact

Hello world! Welcome back!

Coming at you with my second blog post ever, I am here to update you on my life from the past week. I learned a little bit more about the study, but what I mainly learned about was how to work in an office.

Throughout this week, I scheduled the follow-up visits for the patients participating in the First Vitals study. After a patient's initial visit with the doctor where they get a mouth swab and state the drugs that have been giving them trouble, they come in for two follow-up visits. The first one is two weeks after the initial visit and that is the meeting where they receive the results from the mouth swab. Then after that meeting, there is another follow-up meeting which happens 90 days after the initial meeting, so that the patient can take a survey about whether or not the new drug that was recommended to them actually worked better. Since most of the patients who have already participated for the study are ready for their 90 day follow-up, I had to schedule them so that they could complete the study.

First, I became accustomed to the program that the office uses to schedule people which was pretty simple. I had to look at when a patient's next regular appointment was at this office (an appointment for something other than the study), and then schedule a short meeting with a nurse practitioner so that the patient could fill out the post 90 day survey after their regular appointment. So, after working to rearrange a bunch of schedules, I learn that the doctor (Dr. Lalani) did not actually want the survey to be taken on the same day as the patients' other appointments. I do not really know why he wanted it that way, because the way I did it made everything way easier but I digress.

So with this news that I had done everything wrong, I had to make a list of all of the patients who participated in the study and call them so that we could book an appointment with them on an entirely different day. Let me tell you about talking to random people and telling them things that they do not want to hear. It sucks. A lot. The first two patients I called were not very happy. The next seven patients that I called went straight to voice mail. The one saving grace is that I ended the day with a phone call from a very nice woman who was totally understanding so that was cool. I think the key to talking to them is using as many big, complicated words as possible to sound official. I got better at talking to them as I made more and more phone calls and once you hit them with a word like "pharmacogenomics" then they will usually listen. The trick is that you make them think that you know what you are doing.

Well, well, well. Here we are again at the end of another blog post. In short, I would say that this week I learned that I never want to go into customer service. With that eloquent summary, I will once again leave you with a gif that I like. So long!

Oh btw, I did actually get to swab a patient's mouth this week. It was pretty awkward I am not gonna lie. I sat down with Carol and this middle-aged woman who was having problems with her meds. I unsheathed the swab. I stared this woman straight in the eye and stuck her with the swab. And then I just started moving the swab up and down in her mouth, At first, it was gentle. I didn't want to break her face. But then Carol was like "No! You have to really get in there!" So then I started jamming this thing into her gums for like 30 seconds. Both my face and the patient's face were panic-stricken. You could feel the tension in the air. In the wake of the aftermath, I pulled the mouth swab out of her mouth like King Arthur pulling that one sword out of that rock in that one story and I looked back up at her face. I didn't know what to say so I thanked her and apologized at the same time. I'm like "Thanks and sorry for all that". She laughed and we all exited the room. So, yeah. It was kinda weird, but hopefully the next swab will go better.

Entering the Bowels of Inputting Data

Let me tell you about data. In an experiment, there is a lot of it. But how do researchers then take the raw data and analyze it to find interesting trends that they can turn into scientific findings? They compile the data electronically and then use various software to study it. But who gets the very important job of inputting this data so that smart people can analyze it? You guessed it. This guy (Me).

When I arrived to the endocrinology office for my SRP, I met with a physician's assistant named Carol and she is now essentially my mentor and I am her trusty side-kick. Together we fight crime and do whatever needs to be done to ensure that the First Vitals study continues and collects accurate data. My job for this week has been inputting pre-PGX data into a website designed to organize that data for this experiment. While performing this task, I have gained a much stronger understanding of how exactly the study operates and I will now relay the full experimental process to you in this blog post.

So, the process starts with a patient who is unhappy with a medication they are taking. Unhappy in this case could mean that either the medication is not working how it is supposed to work or it is giving the patient undesirable side-effects. So, they are recommended by a healthcare professional to participate in the First Vitals study (which is covered by insurance at the moment), so they come into the endocrinology office where I am interning. The patient fills out a survey where they are asked various questions about the medical problems they have and the drugs that they are upset with (this survey is the pre-PGX data). We then swab their mouth and this mouth swab is sent to some other location where their genome is tested for the presence or absence of 12 specific genes. Then based on the results from the genetic testing, healthcare professionals from the endocrinology office work with the people who tested for the genes to see why the patient's medication is not working properly but now in the context of those twelve genes. After this analysis is made, alternative recommended treatments are provided to the patients and then the patient can take that information to their regular doctor and ask for the new treatment. 90 days after the initial mouth swab, the patient comes in again and fills out a survey to determine if this alternative medication worked better (this survey is the post-PGX data).

So, my job for this first week was to input the pre-PGX data into a website so that specialists can later analyze it for trends and take a look at that patients medical history in the context of their genetic code. We do not have a lot of post-PGX data yet, because the study started in December, so I was only inputting pre-PGX data. Carol told me that next week I get to swab someone's mouth, so I am looking forward to that. It should be loads of fun.

Well, that was fun. I wrote my first blog post and did it on time! I will leave you with a gif. See you next week!

Jack Barth

Hey there, I'm Jack! Welcome to my first blog post and the beginning of a fantastic odyssey through the world of my ongoing senior project.

I am currently a senior at BASIS Scottsdale and this is my blog to document my time interning at Dr. Atul Lalani's office near Shea hospital in Scottsdale, AZ. I like listening to music, watching movies, taking long walks on the beach, and writing blog posts.  So, at any time during reading my blog posts, please feel free to comment any amazing movies you would like me to watch or albums for me to listen to. I listen to all kinds of music except for country, so, if you have a country album you would like to suggest, please keep it to yourself and the world will be a better place for it.

The high school where I have spent my past four years is BASIS Scottsdale. BASIS is actually the reason for the creation of this blog in the first place, because, instead of attending school in the third trimester of our senior year, all of the seniors take part in senior projects that they have designed to carry out research in fields that they are interested in. My senior research project, as you can tell from the title of this blog, is named Genes: The Final Frontier. The project involves me interning at an office of endocrinology to input data taken from the national First Vitals study. This study is under the subject of pharmacogenomics and is integral to the development of the field of health care in the years to come. The First Vitals study involves analyzing the genetic sequence of several patients to try to determine the best drug to use to treat those individuals' illness and limiting the amount of negative side effects that their treatments give them. The idea is that health care needs to transition from the previous mindset that one medication with work for everyone equally to the mindset that we need to take into account everyone's genetic code to accurately give them a treatment that will work best for them.

So, I hope that I have interested you in my project and you will continue to come back and see all of the new, exciting developments in my life. If you have any further questions, please leave them in the comments section or feel free to contact me through my email designated on the right side of this blog. Thank you for taking the time to read this and have a nice day!