TRACERx - McGranahan et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science. 2016.

cBioPortal / datahub

A centralized location for storing curated data from cBioPortal

168 stars 119 forks source link

TRACERx - McGranahan et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science. 2016. #733

Closed jjgao closed 7 months ago

jjgao commented 5 years ago

https://www.ncbi.nlm.nih.gov/pubmed/26940869

[ ] create a issue on datahub before curating a study (one issue per study) and copy this checklist to the issue tracker
[ ] List information of the dataset/paper in the issue, e.g. pmid, paper link, suppl file link
[ ] Document the curation process, e.g. how and by whom the data was transformed
[ ] Follow the data checklist
[ ] Create a pull request to datahub once the data is curated
[ ] Push to triage portal
[ ] Import into msk and public portal database
[ ] Update cBioPortal news

yichaoS commented 4 years ago

@jjgao: @sbabyanusha presented this paper at our journal club yesterday and she identified that there's no MAF provided along with publication.

jjgao commented 4 years ago

@yichaoS @sbabyanusha @ritikakundra can we try to contact the author?

yichaoS commented 4 years ago

@jjgao We were about to email the author, then noticed that, seems like the paper is using the same 34 patient set (@sbabyanusha doubled checked the list in clinical supplemental) and re-using sequencing data for analysis from a previous published study: https://science.sciencemag.org/content/348/6230/124. The other paper seems to have the complete sequencing data with coordinates&allele. We will try to curate this study (not the ref study) then in next (or soon) scrum. @ritikakundra @sbabyanusha @rmadupuri

yichaoS commented 4 years ago

@jjgao me and @sbabyanusha took another closer look at the study, and realized there are 4 parts of the cohort

Discovery cohort:
- 7 patients: mutation data is in European Genome-phenome Archive. (ref 8, 9)
Validation cohorts:
- 34 patients: already in nsclc_mskcc_2015 (ref 2)
- 64 patients: skcm_mskcc_2014 (ref 4)
- 110 patients: skcm_dfci_2015 (ref 17)

We're going to email the author to ask for the MAF of the 7 patients.

jjgao commented 4 years ago

Thanks @yichaoS @BabyASatravada . I didn't realize they only have 7 new patients. In that case, I should deprioritize this one if it's hard to get the data.

yichaoS commented 4 years ago

Emailed the author for the MAF of the 7 primary NSCLC patients.

stale[bot] commented 3 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

jjgao commented 3 years ago

Sicne it's only 7 patients, maybe we should just close this ticket, esp if the author hasn't responded..

yichaoS commented 3 years ago

Replied by Charles Swanton (charles.swanton@crick.ac.uk) on 8/25/2020:

I am sure we can provide this information asap
Nicky(nicholas.mcgranahan@crick.ac.uk) and Mariam(m.jamal-hanjani@ucl.ac.uk) are cc’ed who will know where these data are

Followed up on 6/1/2021

stale[bot] commented 2 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

stale[bot] commented 1 year ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

sbabyanusha commented 7 months ago

This issue is being closed as we couldn't get a response from the author.