About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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WES Variant Calling Analyses from the CheckMate-9ER Clinical Trial

DNA was extracted from tumor samples and blood samples using the Qiagen DNA FFPE and Qiagen DNA Blood Mini Kit, respectively (Qiagen, Germantown, CA). Whole-exome libraries for tumor and blood DNA samples were prepared using the SureSelectXT v5 Kit (Agilent) following validated standard operating procedures for DNA extracted from tumors and germline control samples. Libraries sequenced using the Illumina HiSeq2500 (Illumina, San Diego, CA) following 2 × 100 paired-end sequencing, targeting a depth of coverage of 100×. Sequence alignment and variant calling were performed using a published WES processing pipeline[Chang H, Sasson A, Srinivasan S, et al. Bioinformatic methods and bridging of assay results for reliable tumor mutational burden assessment in non-small cell lung cancer. Mol Diagn Ther 2019;23:507–20] based on Human Build 37 (GRCh37). A maf file is provided.

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DUO:0000026
version: 2021-02-23

user specific restriction

This data use modifier indicates that use is limited to use by approved users.

DUO:0000027
version: 2021-02-23

project specific restriction

This data use modifier indicates that use is limited to use within an approved project.

Requests for access the BMS accession numbers in EGA a request must be submitted through the “Request Data” button on the EGA website.

Access to this data is restricted. Data access requests must be submitted through the “Request Data” button on the EGA website. Upon receipt of a request, the BMS Data Sharing team will coordinate execution of a Data Access Agreement. Access to the data will be granted only after the agreement has been fully executed. We are committed to providing you with answers to your questions and concerns. Please contact us using the information below, and we will respond to your inquiry as quickly as possible. Technical Support: RDD_DataSpecimenRequests@bms.com

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000001905 Cancer Genomics

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
i
EGAF50000904663 txt 6.7 MB
1 File (6.7 MB)