CNV from TCGA level 3

papori · 12-14-2015, 11:44 AM

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

Richard Finney · 12-14-2015, 12:53 PM

There are many snp6 copy number level 3 files for many TCGA diseases.

papori · 12-14-2015, 12:58 PM

Quote:

Originally Posted by Richard Finney

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..

Richard Finney · 12-14-2015, 01:28 PM

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

papori · 12-15-2015, 03:29 AM

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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12-14-2015, 11:44 AM	#1
papori Senior Member Location: berd Join Date: Dec 2010 Posts: 181	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

12-14-2015, 12:53 PM	#2
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	There are many snp6 copy number level 3 files for many TCGA diseases.

12-14-2015, 01:28 PM	#4
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	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

12-15-2015, 03:29 AM	#5
papori Senior Member Location: berd Join Date: Dec 2010 Posts: 181	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!!