Welch et al., TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes, NEJM 2016

rmadupuri commented 6 years ago

Please keep this checklist for curation of a new study.

[x] create a issue on datahub before curating a study (one issue per study) and copy this checklist to the issue tracker
[x] List information of the dataset/paper in the issue, e.g. pmid, paper link, suppl file link
[x] 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
[x] Push to triage portal
[ ] Import into msk and public portal database
[ ] Update cBioPortal news

yichaoS commented 5 years ago

PMID: 27959731

[x] Does study name and study ID follow our convention? e.g. Tumor_Type (Institue, Journal Year); brca_mskcc_2015
[x] Is study meta data complete? e.g. pmid, group of PUBLIC
[x] Were all samples profiled with WES/WGS? If not, is gene panel file curated?
[x] Are oncotree codes of all samples curated; Cancer Type and Cancer Type Detailed needs to be added in addition to Oncotree Code
[x] Clinical sample and patient data with meta files
[x] Mutations data with meta files
[x] MAF is based on hg19
[x] MAF with 2 isoforms: uniprot and mskcc
[ ] CNA data with meta files
[ ] CNA segment data with meta files
[ ] Expression data including z-scores with meta files
[x] Case-lists for all profiles
[x] Passes Validation
[ ] Manual checking (Niki or JJ): Triage Portal

Supplemental curated:

Clinical file (provided by email from author)
Gene panel (provided by paper and email from author)
Maf (all somatic, provided by email from author; RMP, Exome and AmpliSeq; 100% non-failed; day0)

Issues:

Patients listed below are sequenced by both Exome/RMG or AmpliSeq (on day 0); tho in clinical files each sample is only assigned one sequencing method

(for example 1002 in supplemental is said to be sequenced by both AmpliSeq and Exome on day 0 and both Ampliseq and Exome MAF has 1002, yet in clinical file, 1002 is only said to be sequenced by Exome)

Complete list of samples with this issue: 1002 1004 1010 1011 1013 1014 1017 1019 1023 1035 1036 1037 1041 1047 1048 1049 1058 1062

Extra 14 patients given from the author email (are they normals?) In clinical file we got extra 14 patients that were not mentioned in the paper, yet in other genomic files provided.

1110 1103 1083 1109 1102 1099 1105 1087 1033 1108 1086 1104 1100 1097

Combined MAF doesn't have mutations for all sequenced samples. manually adjusted the seq case list
Add attributes to CDD

Testing Instance: http://triage.cbioportal.mskcc.org/study?id=mnm_washu_2016#summary

yichaoS commented 5 years ago

Re-pasted @rmadupuri comments: Hi @yichaoShttps://github.com/yichaoS, here's the first review of the study:

[x] 1. Convert OVERALL_SURVIVAL_DAYS to OS_MONTHS?
[x] 2. Can EXPIRED Yes, No be changed to OS_STATUS DECEASED, ALIVE? (Not sure if that’s right)
[x] 3. Include SOMATIC_STATUS attribute in clinical file and normal status in study description?
[ ] 4. (minor thing) 5 rows in the maf missed annotation.
[x] 5. Can enhanced exome sequencing be removed/replaced with NA in gene_matrix since there's no explicit panel?
[x] 6. for samples sequenced by multiple gene panels, separate them.
[ ] 7. extra 10 samples in the sheets author sent

I didn't find other issues but have the same question from your comment above (point 1) (@ritikakundrahttps://github.com/ritikakundra) Thanks!

yichaoS commented 5 years ago

@ramya I'm not sure about EXPIRED either. Keeping it as it is for now.

ritikakundra commented 5 years ago

@yichaoS I think Expired will mean Deceased

yichaoS commented 5 years ago

@ritikakundra @rmadupuri I re-annotated the MAFs and strangely those 5 are still not annotated, and it happened that they all lack values in the consequences columns. Would that be the reason?

ritikakundra commented 5 years ago

Can you try some on GN browser link to see if they are not suppose to get annotated.

From: Yichao Sun notifications@github.com Sent: Thursday, May 16, 2019 4:12:08 PM To: cBioPortal/datahub Cc: Kundra, Ritika/Sloan Kettering Institute; Mention Subject: [EXTERNAL] Re: [cBioPortal/datahub] Welch et al., TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes, NEJM 2016 (#337)

@ritikakundrahttps://github.com/ritikakundra @rmadupurihttps://github.com/rmadupuri I re-annotated the MAFs and strangely those 5 are still not annotated, and it happened that they all lack values in the consequences columns. Would that be the reason?

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yichaoS commented 5 years ago

@ritika I tried that. All 5's results was saying this is introgenetic_variant in consequence, and the protein change is empty. I manually filled the consequence in, but the annotation remains empty.

ritikakundra commented 5 years ago

Are you saying 5 records or 5'?

Cos 5' wont get annotated

From: Yichao Sun notifications@github.com Sent: Friday, May 17, 2019 1:22:56 PM To: cBioPortal/datahub Cc: Kundra, Ritika/Sloan Kettering Institute; Mention Subject: [EXTERNAL] Re: [cBioPortal/datahub] Welch et al., TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes, NEJM 2016 (#337)

@ritikahttps://github.com/ritika I tried that. All 5's results was saying this is introgenetic_variant in consequence, and the protein change is empty. I manually filled the consequence in, but the annotation remains empty.

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yichaoS commented 5 years ago

@ritikakundra No No. I meant "all five records's"

ritikakundra commented 5 years ago

Then if they are intronic then its fine if they are not, right?

From: Yichao Sun notifications@github.com Sent: Friday, May 17, 2019 1:32:27 PM To: cBioPortal/datahub Cc: Kundra, Ritika/Sloan Kettering Institute; Mention Subject: [EXTERNAL] Re: [cBioPortal/datahub] Welch et al., TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes, NEJM 2016 (#337)

No No. I meant "all five records's"

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yichaoS commented 5 years ago

@ritikakundra I thought so too. So I guess the MAF is fine now?

ritikakundra commented 5 years ago

Curated study:https://www.cbioportal.org/study/summary?id=mnm_washu_2016

cBioPortal / datahub

Welch et al., TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes, NEJM 2016 #337