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Old 12-21-2011, 05:55 AM   #1
Raquelle
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Default Cancer Genomics Advice

Dear All,

I am a bit of a novice when it come to bioinformatics so please do no condemn my current ignorance. I am a first year PhD student currently researching human papillomavirus (HPV). I am interested in viral integration and how this leads to cancer. It has been suggested to me that the Cancer Genome Project and the Cancer Genome Atlas my be of interest to me. What I wish to do (although I am aware it may not be possible) is to access the currently sequenced cancer genomes and search them for integrated HPV. As the virus integrated randomly I would have to access and search the whole genome.
As I stated before I am a novice and I am not sure if what I am trying to achieve is even possible and I don't work with an bioinformaticians that I can call on. Therefore I was wondering if anyone reading this could give me some advice to firstly if this is possible and secondly how I could best achieve this.

Many thanks

Raquelle
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Old 12-21-2011, 08:35 AM   #2
henry.wood
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I'm an author on a paper which is coming out sometime in January where we have looked for HPV sequence in cancer genomes. You don't need that many reads to detect the virus. 1 million reads per tumour will spot most HPV infections. If you want to look at integration sites then you will need a lot more reads. If you want to search through the databases then you will definitely need to either learn a bit of bioinformatics or find someone to do it for you. You will need reads which haven't yet been aligned and then align to a composite genome of either lots of different viral genomes (this will be quicker), or a mixture of human chromosomes and viral genomes (this will give you better data and allow you to look for integration sites).
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Old 12-21-2011, 09:17 AM   #3
rskr
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FYI Usually the generalized noob type questions get discussed in the General forum, and more specific questions are reserved for Bioinformatics.
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Old 12-21-2011, 12:21 PM   #4
adaptivegenome
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Thread moved to "General". Thanks rskr.
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Old 12-21-2011, 01:51 PM   #5
Richard Finney
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Default viral sequences in genomes

Yep. They there. So are bacterial genes. They're pretty easy to find. Just run your unmatched reads against viral and bacterial sequences. Some questions might not be answered: Where did that adenovirus come from? Did someone in the lab sneeze? Does our donor need a zinc pill and cup of hot tea? Why are plant specific virae showing up? (someone left the window open?)

For your quest, easiest thing might be pick 35% of "left" side of read, 35% of "right" side of read. If one 35% matches a unique human location and no virus and if other side matches a virus but not human, you've got some good evidence. The more evidence, the better your case. Verify with another sequencing technology and on other samples and things are looking good.

If you want to check the TCGA data, please have your professor apply for TCGA access now! It takes a while. Only then will you be allowed to gaze up the As, the Cs, the Ts and the Gs. Buy some hard disks, too.

Last edited by Richard Finney; 12-21-2011 at 01:53 PM.
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Old 12-21-2011, 05:27 PM   #6
hajime
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I suggest you can google and browse the following websites:
(1) Oncomine
(2) UCSC genome browser
(3) UCSC Cancer genome browser
(4) TCGA, including ICGC (International Cancer Genome Consortium)

(1) and (3) did great analyses with sequence data stored at TCGA. I hope them can help you to find your way for study.

Best wishes,
Yi
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Old 12-22-2011, 03:06 AM   #7
Raquelle
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Thanks for your replies...really appreciate the advice. Off on Holiday today so you I'll definitely have a look through the websites that have been suggested over the break.
Raquelle
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Old 12-22-2011, 05:53 AM   #8
marcowanger
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Quote:
Originally Posted by Raquelle View Post
Thanks for your replies...really appreciate the advice. Off on Holiday today so you I'll definitely have a look through the websites that have been suggested over the break.
Raquelle
As an additional info, my experience showed that to detect integration site, 1 single lane of HiSeq2000 is NOT enough.
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Old 11-22-2014, 04:09 AM   #9
GenePool
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Here are a few threads on a tool we've put together to help explore cancer genomics data, particularly The Cancer Genome Atlas:

http://seqanswers.com/forums/showthread.php?t=42471
http://seqanswers.com/forums/showthread.php?t=48485

Good luck!

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GenePool is making genomics data management, analysis, and sharing easier!
Products @ www.stationxinc.com

Last edited by GenePool; 11-23-2014 at 09:26 PM.
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