Mutation Data Versioning

[grego...@gmail.com]

Hello,

I have noticed that different versions of PanCancer mutation data have been deposited in the browser here: https://genome-cancer.soe.ucsc.edu/proj/site/xena/datapages/?dataset=TCGA.PANCAN.sampleMap/PANCAN_mutation&host=https://tcga.xenahubs.net

The current version is not a complete representation of previous versions. It lacks several columns and several samples that were present in a previous version the last time I accessed the data on 12 June 2015.

Is there a place where data is versioned besides in the JSON metadata (see discussion here: https://groups.google.com/forum/?fromgroups#!msg/ucsc-cancer-genomics-browser/eg6nJOFSefw/ugDDKLIOAwAJ;context-place=forum/ucsc-cancer-genomics-browser)? If not, would you be able to update the mutation data to the more complete format?

Thanks,
Greg

[Jing Zhu]

Hi Greg,

On Wednesday, August 10, 2016 at 1:57:55 PM UTC-7, Gregory Way wrote:

Hello,

I have noticed that different versions of PanCancer mutation data have been deposited in the browser here: https://genome-cancer.soe.ucsc.edu/proj/site/xena/datapages/?dataset=TCGA.PANCAN.sampleMap/PANCAN_mutation&host=https://tcga.xenahubs.net   

 

The current version is not a complete representation of previous versions. It lacks several columns and several samples that were present in a previous version the last time I accessed the data on 12 June 2015. 

 

Yes. These are not from the same release.  However I am surprised by "lacking several columns", could you say how the columns are different? 

Sample number change is not surprising because we periodically update TCGA data. This particular dataset is compiled by the Xena team at UCSC, and in almost all cases, TCGA has multiple version of mutation calls from several sequencing and analysis groups, broad, WashU, BCM, and UCSC, plus there are curated and automated calls, plus there are different sequencing platforms. So we made our internal decision on which dataset to include, and the exact selection has been changed over time, not drastically, but there are changes. The change will effect sample numbers. 

Is there a place where data is versioned besides in the JSON metadata (see discussion here: https://groups.google.com/forum/?fromgroups#!msg/ucsc-cancer-genomics-browser/eg6nJOFSefw/ugDDKLIOAwAJ;context-place=forum/ucsc-cancer-genomics-browser)?

Starting 2016, we store our release data on AWS S3, which means that all versions of data starting 2016 will be on S3. We plan to do so in the future as long as there is resource to sustain it.  .json files are part of the data releases, which will stores the version information.   Our previous data releases are not on S3.  Do you need the previous version that you retrieved in June 12?  We can send to you directly. 

 

If not, would you be able to update the mutation data to the more complete format?

Jing

 

 

Thanks,
Greg

[Gregory Way]

Hi Jing,

Thank you for your prompt response! The columns in the current data version are far fewer than the 12 June 2015 version.

It is clear that columns were merged because several in the older version are redundant. However, there are also several useful columns (e.g. HGVSc, Entrez_Gene_Id, PolyPhen, etc.) that are omitted.

These are the columns in the current version on the browser:

#sample

chr

start

end

reference

alt

gene

efffect

DNA_VAF

RNA_VAF

Amino_Acid_Change

These are the columns in the 12 June 2015 version:

Hugo_Symbol

Entrez_Gene_Id

Center

NCBI_Build

Chromosome

Start_Position

End_Position

Strand

Variant_Classification

Variant_Type

Reference_Allele

Tumor_Seq_Allele1

Tumor_Seq_Allele2

dbSNP_RS

dbSNP_Val_Status

Tumor_Sample_Barcode

Matched_Norm_Sample_Barcode

Match_Norm_Seq_Allele1

Match_Norm_Seq_Allele2

Tumor_Validation_Allele1

Tumor_Validation_Allele2

Match_Norm_Validation_Allele1

Match_Norm_Validation_Allele2

Verification_Status

Validation_Status

Mutation_Status

Sequencing_Phase

Sequence_Source

Validation_Method

Score

BAM_File

Sequencer

Tumor_Sample_UUID

Matched_Norm_Sample_UUID

HGVSc

HGVSp

HGVSp_Short

Transcript_ID

Exon_Number

t_depth

t_ref_count

t_alt_count

n_depth

n_ref_count

n_alt_count

all_effects

Allele

Gene

Feature

Feature_type

Consequence

cDNA_position

CDS_position

Protein_position

Amino_acids

Codons

Existing_variation

ALLELE_NUM

DISTANCE

STRAND

SYMBOL

SYMBOL_SOURCE

HGNC_ID

BIOTYPE

CANONICALCCDS

ENSP

SWISSPROT

TREMBL

UNIPARC RefSeq

SIFT

PolyPhen

EXON

INTRON

DOMAINS

GMAF

AFR_MAF

AMR_MAF

ASN_MAF

EAS_MAF

EUR_MAF

SAS_MAF

AA_MAF

EA_MAF

CLIN_SIG

SOMATIC

PUBMED

MOTIF_NAME

MOTIF_POS

HIGH_INF_POS

MOTIF_SCORE_CHANGE

IMPACT

PICK

VARIANT_CLASS

TSL

HGVS_OFFSET

PHENO

tumor_type

Thanks!

Greg

[Jing Zhu]

Hi Greg,

These columns are from TCGA .maf files for sure. 

We download and process these maf files to derive the xena data file (the ones with far small number of columns) that we provide for downloads.  

I don't think we provided .maf file for download, at least not intentionally.   We do provide a raw data link in our web site dataset detailed page to point to where we get the raw data, under "raw data" line.  However, for TCGA data, the url should only points to a TCGA DCC directory, and you will need to further click through their web site to get to the .maf files.    

Not sure what happened. If you are interested in these type of .maf files. You will need to go to GDC (https://gdc-portal.nci.nih.gov/search/s)  to download from there directly. GDC has replaced DCC this summer. Our future TCGA data release will also base on GDC data.  Also, just a note on reference genome, GDC data is mapped to hg38, not hg19. 

Jing

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