Cancer Genomics using Illumina GA

[apratap]

Hi All

We recently have run cancer samples on Illumina. As this is our first such run, I wanted to know the tools out there to process/analyze the cancer NGS data.

We want to compare the data from the cancerous and non-cancerous cell lines and also would be nice to show some differences in genotype and/or expression levels.

Any paper/software that you could point me to will help.

Thanks,
-Abhi

[nilshomer]

Hi All

We recently have run cancer samples on Illumina. As this is our first such run, I wanted to know the tools out there to process/analyze the cancer NGS data.

We want to compare the data from the cancerous and non-cancerous cell lines and also would be nice to show some differences in genotype and/or expression levels.

Any paper/software that you could point me to will help.

Thanks,
-Abhi

We have done the same thing in our lab (tumor/normal whole-genome resequencing). A list of NGS software can be found in this post. We use BFAST to align the reads to the human reference (admittedly I am the author). We convert the alignments to the SAM format, and use the built in SAMtools for variant calling (SNPs and indels within the reads) or pileup (for coverage counting). For structural variation (inversions, large-scale inter-chromosomal/intra-chromosomal translocations, large insertions and deletions) we have our own in-house tools. Hope this helps!

[apratap]

Thanks for a quick revert. It is nice to know about BFAST. I will do some testing and see how it works. I have heard about the SAM format and SAMTools but have not used them till now. Guess it is time I try them. Also just wondering if there are are tools/scripts to convert the Eland (export) format to SAM format. It is one of the obvious alignment software we use.

Thanks,
-Abhi

[apratap]

I forgot to ask but I was not able to find a lot on Structural Variation. May be it is under active development. Any specific tools or papers any one would like to recommend ??

Thanks,
-Abhi

[nilshomer]

I forgot to ask but I was not able to find a lot on Structural Variation. May be it is under active development. Any specific tools or papers any one would like to recommend ??

Thanks,
-Abhi

There should be an eland2sam tool out there (either in the samtools "misc" directory, or ask Illumina). If you have a bioinformatician handy, I am sure they can make one pretty easily.

As for papers, I would look at the "whole-genome resequencing" papers (not a complete list):

• SEQUENCE AND STRUCTURAL VARIATION IN A HUMAN GENOME UNCOVERED BY SHORT-READ, MASSIVELY PARALLEL LIGATION SEQUENCING USING TWO BASE ENCODING
• Accurate whole human genome sequencing using reversible terminator chemistry
• DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome
• The diploid genome sequence of an Asian individual
• The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group
• "The cancer genome" (nature review)
• "Venter genome paper"
• "Watson" genome paper
• ...

For structural variation, there are some tools [not complete]:

• PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
• Transcriptome sequencing to detect gene fusions in cancer
• Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
• Pindel: a pattern growth approach to detect break points of large
  deletions and medium sized insertions from paired-end short
  reads
• ...

I hope I don't offend anyone left out above.

So I have done a bit of the literary review for you there already. A full discussion of other specific tools is probably better for other specific threads.

[apratap]

Many Thanks for the pointers Nils. It is enough to get me started.

-A

[krobison]

WU genome center has a list of Cancer Genomics tools which includes some tools for structural variation

http://genome.wustl.edu/tools/cancer-genomics

also, there is MoDIL for finding short indels in libraries

http://www.nature.com/doifinder/10.1038/nmeth.f.256