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Old 12-14-2015, 11:44 AM   #1
papori
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Default CNV from TCGA level 3

Hi all!
I am looking for CNV public profiles for the TCGA data to use as a reference.
Do you know if there are TCGA level 3 copy number profiles that available for more than GBM, OV and LUSC?

For example: BRCA, COAD, HNSC etc.

i found here that only these are availble..
https://tcga-data.nci.nih.gov/tcga/tcgaDataType.jsp

Thanks,
Pap
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Old 12-14-2015, 12:53 PM   #2
Richard Finney
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There are many snp6 copy number level 3 files for many TCGA diseases.
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Old 12-14-2015, 12:58 PM   #3
papori
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Quote:
Originally Posted by Richard Finney View Post
There are many snp6 copy number level 3 files for many TCGA diseases.
Thanks! but i need the Copy number alterations for aggregated/segmented regions, per sample, and not the SNP data..
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Old 12-14-2015, 01:28 PM   #4
Richard Finney
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Copy number can be guestimated from SNP6 data.

See this post ...
https://www.biostars.org/p/112310/

Example file from
http://tcga-data.nci.nih.gov///tcgaf...v_hg19.seg.txt

It looks like this ...
Sample Chromosome Start End Num_Probes Segment_Mean
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 1 3218610 59982831 30896 0.005
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 1 59983689 59983731 2-1.8298
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 1 59987818 247813706 97244 4e-04
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 2 484222 85332445 48655 0.0055
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 2 85332460 85333406 2-1.9034
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 2 85333976 242476062 81598 0.0048
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 3 2212571 197538677 105526 3e-04
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 4 1053934 188762240 101844 6e-04
AQUAE_p_TCGA_112_304_b2_N_GenomeWideSNP_6_A04_1348246 5 914233 41791600 24110 0.0018
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Old 12-15-2015, 03:29 AM   #5
papori
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Hi! great! i think...

What i understand from this format is that if the "Segment_Mean" negative, there is assuming for "loss", and if its possitive assuming for "gain".
If i will (2^Segment_Mean)*2 i will get the actual CN.

Am i right?

BTW, what is the difference between the *hg19.seg.txt file and *nocnv_hg19.seg.txt file?
i can see the "no" in the name, but both looks like CN files......

Thanks!!
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