Forum:Presenting "Role of genomics in cancer" to graduate students from different fields.

Question

[Naren]

Hello friends,

I have to present the above topic to graduate mates from areas related to Chemical Biology from our institute. I have to go really deep into the presentation because I will be judged by 3 scientists working on Cancer Biology.

The level of presentation is "Detailed" that means deep discussion on the topic. How to go about this, what topics I shouldn't miss?

Any good papers covering the topic are welcome.

Duration: 20 mins.

Any suggestions?

What I have in mind is

• Basic Bioinformatics on next-gen sequencing
• ChIP Seq
• Cancer Gene Expression Databses and tools etc.

Note: I have Bioinformatics background but no real experience in cancer genomics.

[dariober]

Hi- It's an interesting question but maybe you get better feedback from Biostars if you post a few bullet points of what you have already in mind. Then some of us can help filling the gaps. Also, what do you mean by diverse areas: biology, computer science, or else?

[Naren]

Thanks, edited the post.

[ivivek_ngs]

You need to highlight what areas you have in mind as of now and what kind of chores you need to address and see what people sets as gap fills since the field is huge and one can input a lot of topics, starting from biology, molecular mechanisms, technology advancements, tools developed over years and importance and improvements of genomics over the years and how they address the diagnostics and research and even improved.. So a bit more details will enable us to help you with suitable feedbacks.

Answer 1

[ivivek_ngs]

To start with you can take a look at this review here. Reviews are always good way to start with such broader perspective that you might want to address. Then you can take a look at this paper and here from the TCGA Pan-Cancer project in that you will get to know the different tools being used and also what levels of NGS applications are being used to address queries. Expression data is complex to derive the mutational spectrum or load so probably you might want to see the papers or reviews on WGS and WES and then see how the correlation is derived with expression data. For databases on Variants and Drivers mutations you can take a look at COSMIC and Intogen and OASIS. They are quite descriptive and useful tools. Another excellent resource is cbioportal. I guess for the start these can be good resource to build up a presentation.

Coming to ChIP-Seq in cancers, it will be more useful to capture the epigenomic landscapes that actually mediates the tumor progession and maintenance that can be guided by specfic histone marks or transcription factors. It is a very broad field to address. You can take a look at the encode project but then better to look at different cancers and use of ChIP-Seq for TFs or specific histone marks for epigenetic profiling. I am sure others can highlight much better papers on ChIP-Seq in cancer research. But then you can get databases for Methylation data as well that might be able to address your queries rather than just ChIP-Seq from here.

[DG]

I agree, reading some reviews is the best way to start. You only have 20 minutes so that doesn't really allow you to be both broad and deep. I'm guessing what they want is just some depth (non superficial) and reasonably broad. If you're focusing on genomics in cancer the TCGA and related projects is a great place to start because those projects are redefining how many cancers are subtyped and that directly impacts treatment even outside of the personalized medicine angle.

With things like ChiP-Seq and other technologies I might save those for the end when you typically talk about some other twists on the technology and what it can give you for information. Your depth part is probably going to want to focus on genomics itself, how sequencing works, etc. Particularly because you can talk a bit there about the chemistry involved.

[ivivek_ngs]

Yes infact this is something I missed out on. It would be important to highlight the chemistry involved in the sequencing technology to give a solid foothold of how sequencing work since it is a chemical biology institute. It is a very nice point to highlight @Dan Gaston. But everything should be more of highlights and applications if its a generic overview of the field rather than what your actual research is. Since it might be a graduate student assignment.

Answer 2

[venu]

As you have mentioned students are from chemical biology background, they must have some idea of cancer pathology. So no need to give any deep introduction to cancer in this case (keeping in mind limited duration). Further, I would highlight the following points

• How the raw data is produced (Whole genome or exome etc) ?
• Alignment of raw data to a reference genome (with some intro on reference genome) and why it is needed ?
• How biological variants (if WGS/WES and DEG if it is WTS etc) are detected from alignments ?

And before going to the third point, one must give an idea of Germline and Somatic mutations, why somatic mutations are important in cancers and driver gene mutations. I think it would be more effective if you take one type cancer as an example and explain things around it.

P.S: There might be more effective ways, I've proposed this as I've previously explained in this way to few of my chemical biology colleagues.

[Naren]

I have to go really deep into the presentation because I will be judged by 3 scientists working on Cancer Biology

[DG]

I am assuming from your post that you are a graduate student and this is part of a graduate seminar series or similar? If that is the case the judges will be judging you a) in comparison to other graduate students and b) based on the fact that you are a graduate student whose core expertise is not cancer biology. You only have 20 minutes, which is about half of the time you have for say class lectures or full blown departmental seminars. So you really can't go so deep that you start getting lost in the weeds, you don't have time. The scientists will also be putting a lot of their judging in your ability to present. Time management, flow of your presentation, comfort with the material, etc.

[ivivek_ngs]

It will really depend on what your knowledge abundance its about and in what time you can take a note of all these varied topic to put them in a viable presentation that you will be able to convey. Adding to length and breadth in any field of research to me is not a great choice, just to please the panel. It should be important for you to understand the cancer biology first and the different models that have been proposed till date and then you can jump to how advancements have happened over the years from array technologies and then exponential leap to NGS and its applications dealing with far more complex questions which were not able to be addressed earlier than 8-10 years. Obviously the field is every growing and it has its own caveats but that does not obscure the fact of how revolutionising this field is. 20 minutes might be too less or too stretched depending upon what you address. So touch up stuffs which you really can get hold of in coming days and make presentation accordingly. The panel wants to know if you are fit to work in the field rather than how experienced you are, probably assuming that you are applying for a research position. I am sure since you pointe you have Bioinformatic skills am not going to decipher its attributes but then your previous work should speak of it. Now your real test will be how you sum up the field of NGS and its applications in cancer research that drives the field of research, diagnostics, precision and personalised medicine. I believe presentations of this kind should not be complete as they never are and there is still scope of improvement when one delivers it. You need to show what you have learned from reading the reviews and how you can use it to effective use in future and I think that will be more than enough for you to really be judged well by the panel. I do not think panel expects you to know everything except for the field and its use in cancer research and how you will beef up your skill sets in coming days to join hands in contributing to the field.

P.S.: These are my personal views , one might differ but if its in academic then you are there to learn and implement and then add to scientific community with your contributions. So you should be trained be it self or mentored and that should be also mentioned in your presentations.

Answer 3

[H.Hasani]

• Mutational roles and the associated tools
• Cancer driver genes and the identification tools