Metadata record for the manuscript: A genomic mutation signature predicts the clinical outcomes of immunotherapy and characterizes immunophenotypes in gastrointestinal cancer
Creators: name: Jiao, Xi
name: Wei, Xin
name: Li, Shuang
name: Liu, Chang
name: Chen, Huan
name: Gong, Jifang
name: Li, Jian
name: Zhang, Xiaotian
name: Wang, Xicheng
name: Peng, Zhi
name: Qi, Changsong
name: Wang, Zhenghang
name: Wang, Yujiao
name: Wang, Yanni
name: Zhuo, Na
name: Zhang, Henghui,
name: Lu, Zhihao
name: Shen, Lin
Publisher: name: figshare
Year: 2021
Subjects: Biological Sciences not elsewhere classified
Cancer
Biomarkers
Oncology and Carcinogenesis not elsewhere classified

description: <b>Summary</b><br>

This
metadata record provides details of the data supporting the claims of the
related manuscript: “A genomic mutation signature predicts
the clinical outcomes of immunotherapy and characterizes immunophenotypes in
gastrointestinal cancer”.

The
related study analysed the genomic profiles of 227 immunotherapeutic
gastrointestinal cancer patients treated with immunotherapy from the Memorial
Sloan Kettering (MSK) Cancer Center cohort in order to investigate the association
between genetic variations and immunotherapy benefit.

 

Type of data:
genomic profile analysis 

Subject of
data: <i>Homo sapiens</i>

Sample size:
227

Population
characteristics: immunotherapeutic gastrointestinal cancer patients treated
with immunotherapy

Recruitment:
This study was done retrospectively and no patients were directly recruited
prospectively.

 

<b>Data
access</b>

The datasets
of the MSK-GI, Janjigian &amp; Pender, PUCH and TCGA cohort generated and
analysed during the current study have been deposited at https://doi.org/10.6084/m9.figshare.14174807.v2 and https://doi.org/10.6084/m9.figshare.14174828 in the files ‘MSK-GI_JP_PUCH_clinical_info_with_GIPS.xlsx’ and ‘TCGA_clinical_info_with_GIPS_and_immune_signatures(2).xlsx’, respectively.

 

The
genomic and clinical data of the MSK-GI cohort, Janjigian &amp; Pender and PUCH
cohorts are openly available and were downloaded from the following places: http://www.cbioportal.org/study?id=tmb_mskcc_2018, https://www.cbioportal.org/study/summary?id=egc_msk_2017, http://clincancerres.aacrjournals.org/content/27/1/202.article-info, https://www.bcgsc.ca/downloads/immunoPOG/ and https://doi.org/10.6084/m9.figshare.14168879.

 

The DNA-seq and RNA-seq
data of the TGCA data used in Supplementary Figure 7 can be downloaded from https://gdc.cancer.gov/about-data/publications/pancanatlas
in files ‘EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv’ and ‘mc3.v0.2.8.PUBLIC.maf.gz’.

 

A
comprehensive list of all data underlying the related article is openly
available with this <i>figshare </i>record
in the file ‘Jiao_et_al_2021_data_underlying_article_list.xlsx’.

 

<b>Corresponding author(s) for this study</b>

Prof.
Zhihao Lu, Department of Gastrointestinal Oncology, Key Laboratory of
Carcinogenesis and Translational Research (Ministry of Education), Peking
University Cancer Hospital &amp; Institute, Fu-Cheng Road 52, Hai-Dian District,
Beijing 100142, China. Tel: +86-10-88196561; Email: zhihaolupku@bjmu.edu.cn

Prof.
Lin Shen, Department of Gastrointestinal Oncology, Key Laboratory of
Carcinogenesis and Translational Research (Ministry of Education), Peking
University Cancer Hospital &amp; Institute, Fu-Cheng Road 52, Hai-Dian District,
Beijing 100142, China. Tel: +86-10-88196561; Email: shenlin@bjmu.edu.cn.

<br>
<b>Study approval </b>

This
study was approved by the Institutional Review Board at the Peking University
Cancer Hospital (2020MS01) and conducted under the Declaration of Helsinki. For
the three publicly available cohorts, institutional review board approvals at
Memorial Sloan Kettering Cancer Center and the University of British Columbia
BC Cancer Research were also obtained.