hg38 for segmentation

[Anish Bhaswanth]

Hi,

Our group is trying to use cBioPortal for one of our cancer projects. We have Mutation, CNV, RNA-Seq and Methylation data.

For CNV, we would like to make use of .seg file for visualization. But, we noticed it allows only hg19 coordinates and we have our data analyzed on the hg38 reference genome.

Is there a workaround for this? Liftover is not an option because all the remaining analysis was performed on hg38, so it would not be pragmatic to convert all data to hg19.

If not, can you tell us when there might be an update for hg38 input?

Thank you,

Anish.

[Benjamin Gross]

Hi Anish,

I do see our Segmented Data documentation says we only support hg19 (https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#segmented-data), but I don’t believe this is correct.  We have support now for multiple reference genomes across studies (not within a single study), so I think you should be ok.  Having said that, I’m not sure if there is something inherit in our embedded IGV viewer for a particular reference genome?  Ino do you know?

Best,

Benjamin

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[Anish Bhaswanth]

Hi Benjamin,

Thanks for getting back to me. 

We did try executing the portal with hg38 genome, but it threw us an error saying that it wasn’t expecting coordinates in chromosomes beyond the range of what you would expect in hg19.

Is there a version of cbioportal from which hg38 is accepted?

Thanks,

Anish.

[de Bruijn, Ino/Sloan Kettering Institute]

Hi Anish,

 

Thanks for reaching out!

 

We are extending the hg38 support in cBioPortal, but haven’t been using it much ourselves yet in production. There are a few groups that have successfully imported hg38 based studies

 

That being said, I don’t know of anyone trying to load hg38 segmentation files yet. It sounds to me like the error might be coming from the IGVjs viewer? Could you share a full error trace or the exact error that is being outputted?

 

If I look at the code it does seem like we try to use the reference genome specified in the queried study:

 

https://github.com/cBioPortal/cbioportal-frontend/blob/177e3de3d74393e0787d3a158830d976eceb030c/src/pages/studyView/tabs/CNSegments.tsx#L95-L100

 

But it’s possible that something goes wrong when passing on these study properties to the IGV viewer.

 

For the meta_study.txt file did you set reference_genome to hg38?

 

https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#meta-file

 

We might be able to help debug if it’s possible for you to send over the study data privately

 

Best wishes,

Ino

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[Sjoerd van Hagen]

Hi Anish,

You do have to set up cBioPortal to support both genome builds, including setting up two instances of genome nexus. The chromosome lengths are pulled from genome nexus so I guess that is where the issue is.

Best,

Sjoerd.

---

Sjoerd van Hagen

Team Lead cBioPortal & Open Targets

E sjo...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

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[de Bruijn, Ino/Sloan Kettering Institute]

Thanks Sjoerd –

 

Note that we do provide a live version of hg38 of genome nexus (https://grch38.genomenexus.org), which will be used by default. Similarly, for hg19 studies the default settings will use https://www.genomenexus.org . Therefore it’s not necessary to set up the multiple instances of genome nexus

 

Best wishes,

Ino

 

From: Sjoerd van Hagen <sjo...@thehyve.nl>
Date: Tuesday, March 9, 2021 at 10:07 AM
To: Anish Bhaswanth <ani...@gmail.com>
Cc: Benjamin Gross <benjami...@gmail.com>, "cbiop...@googlegroups.com" <cbiop...@googlegroups.com>, "sanderr...@thehyve.nl" <sanderr...@thehyve.nl>, "Sumer, Selcuk O./Sloan Kettering Institute" <sum...@mskcc.org>, "Li, Xiang/Sloan Kettering Institute" <li...@mskcc.org>, "de Bruijn, Ino/Sloan Kettering Institute" <debr...@mskcc.org>
Subject: [EXTERNAL] Re: Re: [cbioportal] hg38 for segmentation

 

Hi Anish,

 

You do have to set up cBioPortal to support both genome builds, including setting up two instances of genome nexus. The chromosome lengths are pulled from genome nexus so I guess that is where the issue is.

 

Best,

 

Sjoerd.

 

---

 

Sjoerd van Hagen

Team Lead cBioPortal & Open Targets

 

E sjo...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

 

    

 

[Anish Bhaswanth]

Hi All,

Thanks for all the suggestions. 

I will first add the hg38 reference genome option to meta_study.txt and re-run the code. Hopefully it works.

Will update you on the results.

Best,

Anish.

[Anish Bhaswanth]

Hi Everyone,

We did try adding the hg38 genome to meta_study.txt file. We still received the following errors:

I’m getting these error

 

ERROR: brca_aurora_cr_igv_hg38.seg: lines [18, 19, 873, (322 more)]: columns [4, 3]: Genomic position beyond end of chromosome (chr20:0-63025520); values encountered: ['64288000', '64291001', '6433                                                                 4000', '(120 more)']

ERROR: brca_aurora_cr_igv_hg38.seg: lines [63, 774, 1156, (232 more)]: columns [4, 3]: Genomic position beyond end of chromosome (chrX:0-155270560); values encountered: ['156031000', '155560000', '                                                                 155560001', '(26 more)']

ERROR: brca_aurora_cr_igv_hg38.seg: lines [69, 780, 1162, (192 more)]: column 2: Unknown chromosome, must be one of (1|2|3|4|5|6|7|X|8|9|10|11|12|13|14|15|16|17|18|20|Y|19|22|21|23|24); value encou                                                                 ntered: 'M'

ERROR: brca_aurora_cr_igv_hg38.seg: lines [90, 654, 1018, (197 more)]: columns [4, 3]: Genomic position beyond end of chromosome (chr7:0-159138663); values encountered: ['159336000', '159208000', '                                                                 159208001', '(8 more)']

ERROR: brca_aurora_cr_igv_hg38.seg: lines [97, 98, 99, (228 more)]: columns [4, 3]: Genomic position beyond end of chromosome (chr3:0-198022430); values encountered: ['198116000', '198116001', '198                                                                 123000', '(30 more)']

ERROR: brca_aurora_cr_igv_hg38.seg: lines [147, 148, 149, (333 more)]: columns [4, 3]: Genomic position beyond end of chromosome (chr5:0-180915260); values encountered: ['180949000', '180949001', '                                                                 180954000', '(60 more)']

ERROR: brca_aurora_cr_igv_hg38.seg: lines [302, 724, 1048, (192 more)]: column 4: Genomic position beyond end of chromosome (chr11:0-135006516); value encountered: '135076000'

ERROR: brca_aurora_cr_igv_hg38.seg: lines [318, 848, 1116, (296 more)]: columns [4, 3]: Genomic position beyond end of chromosome (chr17:0-81195210); values encountered: ['83235000', '82092000', '8                                                                 2092001', '(140 more)']

ERROR: brca_aurora_cr_igv_hg38.seg: lines [325, 326, 849, (290 more)]: columns [4, 3]: Genomic position beyond end of chromosome (chr18:0-78077248); values encountered: ['79289000', '79289001', '80                                                                 264000', '(123 more)']

Thanks,

Anish.

[Ram RS]

Sorry to necro this post, but I'm in the exact situation as Anish - all my omics analyses use hg38, and they're all accepted by cBio except for CNV seg, which can only do hg19. Like Anish said, it is not practical to lift over all omics to hg19. Do we have any timeline on when cBio plans to add hg38 support across the bard?