Cancer Genomics Advice

Raquelle · 12-21-2011, 05:55 AM

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

henry.wood · 12-21-2011, 08:35 AM

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).

rskr · 12-21-2011, 09:17 AM

FYI Usually the generalized noob type questions get discussed in the General forum, and more specific questions are reserved for Bioinformatics.

adaptivegenome · 12-21-2011, 12:21 PM

Thread moved to "General". Thanks rskr.

Richard Finney · 12-21-2011, 01:51 PM

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.

hajime · 12-21-2011, 05:27 PM

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

Raquelle · 12-22-2011, 03:06 AM

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

marcowanger · 12-22-2011, 05:53 AM

Quote:

Originally Posted by Raquelle

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.

GenePool · 11-22-2014, 04:09 AM

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!

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

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12-21-2011, 05:55 AM	#1
Raquelle Junior Member Location: Wales Join Date: Dec 2011 Posts: 2	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

12-21-2011, 01:51 PM	#5
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	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.

12-21-2011, 05:27 PM	#6
hajime Member Location: Taipei, Taiwan Join Date: Mar 2011 Posts: 14	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 __________________ Yi John Huang (PhD student) 886-3-2118800 ext. 3731 Graduate Institute of Biomedical Science, Chang Gung University

11-22-2014, 04:09 AM	#9
GenePool Registered Vendor Location: San Francisco, CA Join Date: Mar 2014 Posts: 18	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! ------------------------------ 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.

12-21-2011, 08:35 AM	#2
henry.wood Member Location: Leeds, UK Join Date: Apr 2010 Posts: 63	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).

12-21-2011, 09:17 AM	#3
rskr Senior Member Location: Santa Fe, NM Join Date: Oct 2010 Posts: 250	FYI Usually the generalized noob type questions get discussed in the General forum, and more specific questions are reserved for Bioinformatics.

12-21-2011, 12:21 PM	#4
adaptivegenome Super Moderator Location: US Join Date: Nov 2009 Posts: 437	Thread moved to "General". Thanks rskr.

12-22-2011, 03:06 AM	#7
Raquelle Junior Member Location: Wales Join Date: Dec 2011 Posts: 2	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