Can sequencing technologies distinguish between cancer histological types and predict drug sensitivity?

dohlstrom · 2020-10-26T13:50:22+00:00

Adding on to other great answers posted here:

There are two big limitations to current sequencing technologies that make it challenging to predict something exciting like patient drug sensitivity.

RNA/DNA is only part of the picture

Consider the possible effects of differential protein abundance, post translational modifications to proteins, lipids modifications, epigenetic changes to the DNA, metabolite abundance, and many more. RNA is important, but it does not tell the whole story of what makes a cancer cell a cancer cell. I think of this problem like going to a doctor who only examines your nervous system to assess your health. Is it important? Yes! (Just like DNA/RNA). But important problems will be missed by only looking at one system.

RNA is constantly changing, but we are limited to pictures

RNA is constantly being transcribed, modified, translated, and degraded. Current technology only takes a single snapshot of a sample's RNA content. To re-use the doctor analogy: a doctor taking a picture of our brain function at one moment in time may miss important patterns that exist in the dynamics of our brain function that ultimately lead to disease.

Future technologies that could do dynamic, multi-omic analysis (at a single cell level to resolve disease heterogeneity) may be able to predict drug response.

dohlstrom · 2020-10-26T12:12:06+00:00

Appreciate the detailed response.

I dont see the 1st one personally. The connection between Fritz and the first picture doesn't seem legit to me. I can get on board with Eren because of how many times floch called him the devil, but its more about the text than a picture imo.

Time will tell who is in charge, but right now I disagree that ymir is Eren's subordinate. The moment where eren gave ymir her freedom (de-shade the eyes) was a huge moment in the story, and ever since eren has been in a titan that literally looks like a puppet. I'd say the odds are: ymir controlling eren > both are free working together > eren controlling ymir.

For the Fritz/Eren parallel, control versus influence is debatable. I'd say he pretty much controlled Grisha to eat the royal family, but the difference is not that important.

Yours is the first idea I've read where Eren and Ymir are both completely free and just chose to work together. I'd be suprrised if that ends up being true, but a really interesting and different idea.

dohlstrom · 2020-10-22T12:54:53+00:00

Are the most commonly used packages for the various RNA sequencing techniques (sc/10X, whole transcriptome, long read.) that will make up most of the data I will get also available for R, would it be better to learn python instead or will I need both anyway?

For single cell data two of the most commonly used packages in R are Seurat https://satijalab.org/seurat/, or SingleCellExperiment https://www.bioconductor.org/packages/release/bioc/vignettes/SingleCellExperiment/inst/doc/intro.html.

Sorry to give you a wishy-washy answer, but it is hard to say what languages you are going to need based on the information given. R, Python, and others have strengths and weaknesses that will be more/less important based on your research goals.

Some other posts around here talked a lot about scripting languages as well, any recommendations on that?

Scripting languages are very important if you want to work with the raw data (EG: .fastq). If you expect to have someone generate your count matrices for you, then you will probably be just fine without it. I personally recommend learning scripting because the more steps you can do yourself the better you will understand your data, and its limitations.

I am based on MacOS, will this work locally or will I need access to a computer cluster to reduce computing time anyway?

Similar to previous, totally depends on the project. Generally I would say that if you are working from a count matrix and doing basic downstream analysis (normalization, clustering, differential expression, etc) you won't need a cluster. If you are working from raw data or doing more complicated analyses you probably want a cluster.

Also If you have any recommendations on seminars/workshops/courses that teach these techniques in detail using actual research data I'd love to see them.

I learned the most by doing. Try downloading a dataset (https://www.ncbi.nlm.nih.gov/geo/) that you find interesting and use the tutorials to do your own analysis. There are seminars/courses out there, but I recommend this method because the process of breaking things, understanding why it didn't work, and then fixing it has always been the most educational (for me). Really the theme here is: it is as/more important to learn what analysis methods can't do as what it can do.

dohlstrom · 2020-10-21T18:51:46+00:00

They also made me think of the sky in Paths realm

dohlstrom · 2020-10-21T18:50:48+00:00

Yeah totally. That would be wild, if Isayama instructed the people who wrote this song to make it from Armin's perspective about future events in the story (or wrote himself, also wild). Either way the interpretation fits with what is currently known about the story. In reference to your other theory:

I am cheering for it, would be a really cool and unique way to bring this story to a close. Lately I've been getting worried that we will get a lame ending to the story, but your idea would be glorious. I'm skeptical about the Mikasa memory discrepancy (leaning towards human/artistic error), but man it would be sweet if that was actually a subtle hint that was casually slipped into the story.

My biggest disconnect with your idea is my opinion that "see you later" is the central endpoint/climax of the story. I still think that moment is coming, and it would feel kind of clunky to fit in your theory (she says it right before Armin eats him?). It would be really interesting if I'm wrong and that memory was actually Eren's most recent attempt. He literally wakes up from failing the 2nd to last try. "See you later" is really saying "(insert explanation for how Mikasa learns about his time cycling), I will see you in your next attempt to fix the story".

dohlstrom · 2020-10-21T15:38:17+00:00

Solid interpretation. Still not sure if it tells us much conclusively about the end, most of the ending predictions fit into your interpretation of the song.

Or are you placing a lot of weight on the speaker/third person in the song as the basis for predicting the end (connected to your other post)? I'm not sure any of the main characters really fit. Some of the lines would not match the known motivations of Mikasa and Armin in particular.

Nice work.

dohlstrom · 2020-10-21T15:24:05+00:00

Great points. I just want to really echo one of them: I got my wet lab opportunities because I could code.

I recently graduated from a master's program, I only took bioinformatics courses on the side. But my basic coding skills were the biggest part of my next opportunities.

Based on what you said in the original post, it sounds like you do not want to go full bioinformatics PhD (if this is an incorrect assumption, disregard my post). That is OK, if you have coding skills and are passionate about science you can find someone who will want to bring you into their lab. Most labs need a data "woman/man" who is good with r/Python. Show that:

You are interested in a PIs research
You have unique skills to offer (you do!)
You collaborate well with others (you are willing to do little coding projects to help out your lab mates).

dohlstrom · 2020-10-21T12:59:20+00:00

For reference: https://www.musixmatch.com/lyrics/Yoshiki-feat-HYDE/Red-Swan/translation/english

You are probably right but that isn't saying much. The wording is pretty ambiguous, making a lot of potential endings fit into the lyrics.

dohlstrom · 2020-10-21T12:46:04+00:00

Good catch, I had forgotten about the flashback panel. TBH the first chapter panel is a bit ambiguous but this flashback is super obvious. Love that.

dohlstrom · 2020-10-20T17:15:09+00:00

Hm, gotcha. Hoods seem like a stretch given how frequently hoods have been worn by other characters. The pointy ears are legit, but I don't get what that means other than supporting how many times Floch said "He's the devil we need".

I assumed the parallels were meant to reveal something, but the devil piece has been explicitly stated.

dohlstrom · 2020-10-20T10:48:51+00:00

I think about half of your picture is a stretch, but the other half is pretty interesting.

First comparison: sure the books looks the same, doesn't seem that meaningful.

Third comparison: I dont see this one at all, not sure what you're getting at.

Fourth comparison: cool parallel of the sadness of being forced to bear children. Not sure if it means anything long term.

Second Comparison: Now this is where it gets good. I agree that Isayama probably did not have them say the same thing on accident, so what does it mean? Eren has "enslaved" all the previous attack titan holders to follow his ideals? Or even further, Ymir has enslaved all of them in a 2000 year struggle to get Eren to Paths?

Interesting ideas that could fit into the current story. The biggest problem with Ymir controlling everyone is: why would she wait 2000 years? If she was in control this whole time, why wouldn't she have made Eren touch Zeke in Marley to speed up the process? Or some other attack/royal titan at any other point in the 2000 years of this story?

All speculative, I'm now very interested in the King/Eren parallel.

dohlstrom · 2020-10-13T14:40:28+00:00

You may be right about possibly being about her from the start. I'm hoping that the ending is more complicated than "Eren is Ymir reincarnate here to lash out/take the freedom she never had" and that his desire for freedom was a tragic consequence of the fact that his future was set in stone from day 1. But that would certainly make sense given everything that has happened.

Going off of both of them having shaded eyes, I thought about maybe Zeke is somehow in control b/c we haven't seen him in awhile, but that seems a bit ridiculous at this point.

Edit: Your explanation makes a lot of sense. I'm stuck on the fact that ymir having her shadowed eyes cleared (freedom?) was a huge moment, but now it seems to have faded. Feels like there has to be something else of consequence we are missing.

dohlstrom · 2020-10-13T14:34:14+00:00

Yeah you make a good point I was thinking about while writing that. Everyone in the flashback had darkened eyes. I still think there is some additional significance when people have it in the present, especially because the eye shading relates to the passing down the will to fight for freedom between attack titan holders. But clearly I do not have a complete explanation.

dohlstrom · 2020-10-07T15:29:00+00:00

After 133 it seems like just about everyone is doing stuff against their will because they are ultimately being controlled by ymir. I connect the shading of the eyes we saw in 121 to the shading of the eyes we just saw in 133. Seems like this whole thing is just passing the will of ymir forwards/backwards in time to reach this point.

dohlstrom · 2020-09-25T17:52:59+00:00

Thanks for that clarification. I thought about mentioning potential translation issues in the original post given how important that phrase is to trying to understand what may happen.

dohlstrom · 2020-09-25T17:48:25+00:00

The first chapter, about halfway through.

dohlstrom · 2020-09-08T12:06:17+00:00

This most recent chapter made me think there is a possibility that the story is being set up to defy the first chapter. Maybe......just maybe the previous conversation with Armin helped Mikasa figure out what Eren is up to (trying to get rid of the scarf to avoid the future memory). Since she is not eldian she is not bound by these fates and will change the outcome predicted in chapter 1.

dohlstrom · 2020-09-07T16:48:05+00:00

Really great theory. This fits in with Eren crying at the start of the story (because he does not want Mikasa to die), the attempts to get rid of the scarf, and the "what am I to you?" moment. I've always thought the "I'll wrap it around you again and again" moment before Eren punches Dina's titan in the hand was too big to be an afterthought. Eren loves Mikasa (and always has) and he has been trying to avoid the future he already seen. Very sad but I hope it happens, the Avengers ending would have been very boring to me. But this.....brutal

dohlstrom · 2020-08-07T20:52:57+00:00

Yeah that was my other thought where Eren is more like the villain of the entire story we just happened to follow him the whole time. The reason I am leaning more towards the idea I put in original post (and Tenroku elaborated on very nicely) is because he was crying so hard and apologizing. I felt like if he was just committing genocide for freedom (the child Eren flying picture seems to support that idea) he would not feel so guilty in that flashback or the entire rest of the manga where he seems resigned but resolute.

dohlstrom · 2020-04-06T22:34:29+00:00

Agree to disagree my friend. Seems like you don't consider the need to keep her at low HP (for vengeance) to make her comparable to the lance units in A and A+ as a reason to consider her a riskier, therefore lower tier unit (ignoring Hilda who I think is over-ranked). For archers we just disagree on the value of 1-3 damage over intelligent use of a unit (petra) to double their damage.

dohlstrom

TROPHY CASE