Dear All: I would like to know if there are techniques to minimize the perturbation caused by tissue contamination, for example, normal lung tissue contamination on a breast metastasis. What is the best strategy to deal with this problem? I think this should be dealt with at the "low" level normalization process, please help. Best regards Hao Liu, Ph. D

Hao Liu wrote: > > I would like to know if there are techniques to minimize the perturbation > caused by tissue contamination, for example, normal lung tissue > contamination on a breast metastasis. What is the best strategy to deal > with this problem? > > I think this should be dealt with at the "low" level normalization > process, please help. I think it should be dealt with at the level of tissue extraction, i.e. use microdissection. Best wishes Wolfgang -- ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber

> I would like to know if there are techniques to minimize the perturbation > caused by tissue contamination, for example, normal lung tissue > contamination on a breast metastasis. What is the best strategy to deal > with this problem? I suppose that experimentalists did their best when performing the biopsy, and that you have to deal with the mix of tissues the best you can. I remember seeing a talk at ISMB addressing the issue: http://bioinformatics.oupjournals.org/cgi/content/abstract/17/suppl_1/ S279 (although I did not have the opportunity to dig the method or use it) Hopin' it helps, L.

Hi Hao, In our lab we resort to the viewpoint that any contaminated stromal or myeloid tissue is usually close enough to the tissue of interest that it is in interaction with it. You would probably also find changes in gene expression in these celltypes compared to unaffected stromal tissue. Only in situ methods will tell you in which tissue type the change has taken place. Jan > -----Original Message----- > From: Hao Liu [mailto:liuha@umdnj.edu] > Sent: dinsdag 4 mei 2004 06:25 > To: Wolfgang Huber > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] tissue contamination problem in microarray > > > hi! Wolfgang: > > I actually talked with some very good pathologists, according to them > even microdissected sample (cancer tissue) could have around 20% > contamination from surrounding tissue. > > Your answer to my question makes me wonder if I heard is true, can > someone help to clarify this issue? Thanks > > Best > Hao > > On Mon, 3 May 2004, Wolfgang Huber wrote: > > > > > > > Hao Liu wrote: > > > > > > I would like to know if there are techniques to minimize > the perturbation > > > caused by tissue contamination, for example, normal lung tissue > > > contamination on a breast metastasis. What is the best > strategy to deal > > > with this problem? > > > > > > I think this should be dealt with at the "low" level normalization > > > process, please help. > > > > I think it should be dealt with at the level of tissue > extraction, i.e. > > use microdissection. > > > > Best wishes > > Wolfgang > > > > -- > > ------------------------------------- > > Wolfgang Huber > > Division of Molecular Genome Analysis > > German Cancer Research Center > > Heidelberg, Germany > > Phone: +49 6221 424709 > > Fax: +49 6221 42524709 > > Http: www.dkfz.de/abt0840/whuber > > ------------------------------------- > > > > Best regards > > Hao Liu, Ph. D > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >