On Fri, Apr 15, 2011 at 7:19 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 04/15/2011 06:05 AM, Vincent Carey wrote:
>
>> I will comment on my limited view and progress.  I need to work from
>> an exemplar.  I committed cheung2010 in the experimental data archive
>> (devel only).  This relates to PMID 20856902, genetics of expression
>> in immortalized B cells.
>>
>> There are 147 individuals with hapmap phase 3 genotypes and hgfocus
>> arrays (:-( but about 45 have RNA-seq data in GEO.  fastq is available
>> with the SRAtools fastq-dump and you can get the sra data reasonably
>> quickly using ascp.  I will eventually make a sample from their
>> RNA-seq data available in this package to look at SNP-driven
>> allele-specific expression and other aspects of SNP-dependent
>> expression regulation.
>>
>> Probably there is DNA-seq data out there on these coriell cell lines
>> but for the moment I will be looking at the chip-based SNPs and
>> imputation on those.  Better representations for 8 million SNP per
>> sample would probably come in handy, but breaking them up by
>> chromosome in SnpMatrix instances is OK so far.  I think we have to
>> recognize that in any of these paradigms discrete calls are often not
>> going to cut it, and uncertainty representations will be important.
>>
>> VCF representations of indels in 1000 genomes are available, but I
>> don't know that we have good tools for importing and modeling those.
>> Another exemplar that should be considered.
>>
>> On Fri, Apr 15, 2011 at 7:16 AM, Michael Lawrence
>> <lawrence.michael@gene.com>  wrote:
>>
>>> Hi guys,
>>>
>>> Congrats on the release. For this next one, one focus, in my opinion,
>>> should
>>> be on analyzing variants in the context of sequencing data. This includes
>>> infrastructure for things like calling variants (in DNA and RNA), as well
>>> as
>>> determining their effects (e.g., coding and splicing changes). It would
>>> be
>>> good if we could come up with a plan. If we had one, we could commit some
>>> resources here to the problem.
>>>
>>> Is anyone willing to help out on this? What do you guys think?
>>>
>>
> We could certainly play a role in annotation of variants and support for
> interfacing with established 3rd party formats. Obviously also the
> representation of variants that overlap with IRanges / Biostrings
> infrastructure. Martin
>
>

Great, this is in line with what I was thinking. We need a way to formally
represent sets of variants, as well as transcripts and proteins (i.e.,
something based on a GRange[List]). Then we can map between coordinate
systems and request the consequences of mutations. I was looking at the
Ensembl variations Perl API;  it might be good for inspiration.

Is there somewhere like a wiki where we could start hashing this out?

Michael


>
>
>>> Thanks,
>>> Michael
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>

	[[alternative HTML version deleted]]

