Comparison of Gene Expression and DNA Copy Number Data to Identify Amplicons in Breast Cancer

Abstract:
Breast Cancer is one of the primary causes of death in women in the world. Many genes have been implicated in the predisposition to this disease. In this experiment, chromosomal copy number changes were analyzed alongside gene expression. Using CGH technology, changes in DNA copy number in four tumors were used to detect areas of DNA Amplification. Gene expression levels found on 250k SNP arrays were inspected to match areas of increased expression with the previously found amplicons. Areas of correlated expression were sought in the hopes of locating specific genes being over-expressed, with the possibility they are driver genes of the amplicon, and therefore possible oncogenes. Of the eighteen amplicons found, four yielded posivtive correlation results (correlation hugher than 0.6 within a 1 megabase genomic window). The amplicons on Chromosomes 17, 12, 8, and 6 were analyzed in more detail.

I can now honestly say that I am FINISHED with my dissertation, as I submitted it for printing this morning. I still need to do our "portfolio entry" (they love making us 'reflect', as practice for later), as well as fill out a questionnaire, pick up the printed version, and hand it in; but the hard bit is over! Today is alll relaxation, and getting ready for the parties of the week.

If anyone wants to check out the full dissertation (no idea why you would), drop me a line and I'll send it your way.

-AMiB

Quick Update

As the Dissertation deadline for submission draws closer and closer, I realize more and more that I have NO IDEA what I'm writing about. I have a general idea as to the topic and I understand some of the more basic, broad things that I am reading in these articles (all for my intro), but for every 1 thing I read that I understand, there must be 5 more that I have no idea what the hell is going on. I have resigned to just pretend like I know what I'm doing, keep writing a bunch of random words down on paper, and hope for the best.

One things for sure - I'm definitely not going into research.

Fake memories...

hmm...saw this on a friend's blog, decided to see if anyone here would give it a go!

If you read this, if your eyes are passing over this right now, (even if we don't speak often) please post a comment with a COMPLETELY MADE-UP AND FICTIONAL memory of you and me.

It can be anything you want - good or bad - BUT IT HAS TO BE FAKE.

When you're finished, post this little paragraph on your blog and be surprised (or mortified) about what people DON'T ACTUALLY remember about you.

In other news, I have essentially gotten all my data for my dissertation, and my advisor says that "in theory, in two weeks time, I should have written the whole thing". So yeah, basically all during my spring break at home, I'll be writing (if I can motivate myself, that is!) I still have 2 weeks after that to finalize, etc, but it's nice to finally have a deadline, of sorts.

-AMiB

SNP SNP

So I had another meeting with my dissertation adviser today, and I think we've changed my project completely. It's ok though, because this one doesn't go completely over my head like the last one.

From what I understand, I'm meant to analyze patterns in 4 biopsies of breast cancers, look for DNA amplicons, and try and match them to known gene transcription regions in the human genome. For example, on chromosome 17, there is a large area of DNA amplification on the "q" segment (lol don't I sound fancy - I barely even understand what I'm saying!), and when you match that to the human genome, you see that this is the are in which the HERB B2 binding site is. This is the major site of action of the relatively new anti-breast cancer drug, herceptin. So basically I'm supposed to spend the next few days or so looking at different amplification regions, and looking for patterns of areas of genomic transcription. Or something like that. Maybe I've completely misunderstood, or am just spewing complete BS to look smart.

Probably that last one. lol.

-AMiB

Dissertations

So it looks like I'll be doing some type of research about p53 transcription factor binding sites for my dissertation. If that went over your head when you read it, don't worry - it went straight over mine too, especially when my advisor was trying to explain it to me. All I know is that p53 is a protein that regulates the cell cycle, and it's very important in cancer.

From what I understand about the project, which he said was origianlly supposed to be a PhD project for a Bioinformatics PhD (WTF?!), he wants me to use some random online genome browsers etc to search for p53 transcription factor binding sites, and find all the ones that have to do with cancer. Or something like that. I'm still not completely sure yet. We'll see how that goes lol.

In other news, the Deans of the Manchester Hospitals are coming for their annual visit next Wednesday, if I have time/remember, maybe I'll make a post about how it went. I tend to neglect this blog, even when I don't have a lot of stuff to do. However with this new, semi-empty schedule of this semester, I've had to schedule my own life (Outlook(r) runs my life!) and I tend to leave out things like "blogging" and "relaxing" times lol.

Also, USMLE revision has slowly begun. Some colleagues and I have set up a small weekly study group, and while our first meeting was somewhat of a bust, I think it should get better. Hopefully I (and everyone else) will actually do the work before the session this time.

On the fitness front, I am trying to use this open schedule to my advantage. I wrote a 3-day workout plan for me and my 2 gym buddies, and it's pretty hardcore, if I do say so myself. I've also started taking some new supplements (including a ridiculous 11-tablet multivitamin that turns your piss bright yellow [but don't worry, those are just the B-vitamins]), but I won't really talk about them on here until they work (or not). I am also going on morning walk-jog intervals (I hate calling them runs/jogs because a majority of the time is spent walking, with intermittent jogging) with one of my gym buddies (the other won't wake up that early). All this combined with a 1300-calorie-a-day deficit is keeping me on track with my new short-term weight/body fat loss goals.

So, while I realize this is quite the random post about everything, I'll summarize by saying everything, all in all, seems to be going quite well (and of course the moment I post this something will go horribly wrong).

Until next time,

-AMiB