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Takafumi NAKANE

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Nov 16, 2022, 9:14:47 AM11/16/22
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Dear person in charge

My name is Nakane and I am a bioinformatician at the DNA Chip Research Institute.

I need the following data to analyze the intra-tumor heterogeneity, but I cannot find any data on CNA. Is there a file in the dataset that contains this information?

Required Data
・Number of reads matching the reference allele.
・Number of reads matching the alternate allele.
・Major copy number of segment overlapping mutation.
・Minor copy number of segment overlapping mutation.
・Total copy number of segment in healthy tissue.

Thank you in advance.

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○●----------------------------------------------------●○
  DNA Chip Research Inc.
  Takafumi NAKANE
  1-15-1 Kaigan, Suzue Baydium 5F
Minato-ku, Tokyo 105-0022, Japan
  TEL: (+81) 3-5777-1700
  Email: t-na...@dna-chip.co.jp
  URL: https://www.dna-chip.co.jp/en/
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debr...@mskcc.org

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Nov 18, 2022, 6:11:06 PM11/18/22
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Hi Takafumi NAKANE,

 

Thanks for reaching out!

 

We have this in most of the mutation data files:

 

Number of reads matching the reference allele.
Number of reads matching the alternate allele.

 

See e.g.:

 

https://media.githubusercontent.com/media/cBioPortal/datahub/master/public/ov_tcga/data_mutations.txt

 

The columns are:

 

- t_ref_count, t_alt_count, n_ref_count, n_alt_count

 

See also:

 

https://docs.cbioportal.org/file-formats/#mutation-data

 

We don’t have this easily accessible:

 

Major copy number of segment overlapping mutation.
Minor copy number of segment overlapping mutation.
Total copy number of segment in healthy tissue.

 

We do have segmented copy number data. E.g.:

 

https://github.com/cBioPortal/datahub/blob/master/public/ov_tcga/data_cna_hg19.seg

 

and documentation:

 

https://docs.cbioportal.org/file-formats/#segmented-data

 

But this is prolly not exactly what you want. We are working on incorporating the type of information you requested into cBioPortal, but there are no public studies available yet

 

Thanks!

Ino

URL: https://www.dna-chip.co.jp/en/
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