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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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Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma -- CA209-009

Immune checkpoint inhibitors targeting the PD-1 pathway have transformed the management of many advanced malignancies, including clear cell renal cell carcinoma (ccRCC), but the drivers and resistors of PD-1 response remain incompletely elucidated. Here, we analyzed 592 tumors collected from advanced ccRCC patients enrolled in prospective clinical trials of treatment with PD-1 blockade (or mTOR inhibition as control arm) by whole-exome and RNA-sequencing, integrated with immunofluorescence analysis, to define the somatic alteration landscape of late-stage ccRCC and to uncover the immunogenomic determinants of therapeutic response. While conventional genomic markers (tumor mutation burden, neoantigen load) and degree of CD8+ T cell infiltration were not associated with clinical response, we discovered numerous chromosomal alterations in advanced ccRCC associated with response or resistance to PD-1 blockade. These advanced tumors were highly CD8+ T cell infiltrated, with only 22% and 5% with an immune desert and immune excluded phenotype, respectively. Our analysis revealed that CD8+ infiltrated tumors are depleted of favorable PBRM1 mutations and are enriched for unfavorable chromosomal losses of 9p21.3 when compared to non-infiltrated tumors. These data demonstrate how the interplay of somatic alterations and immunophenotypes impacts therapeutic efficacy.

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DUO:0000007
version: 2019-01-07

disease specific research

This data use permission indicates that use is allowed provided it is related to the specified disease.

ModifiersMONDO:0005086 MONDO:0005005 MONDO:0004992 MONDO:0005206 MONDO:0002367

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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
EGAS00001004290 Other

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
EGAF00003476791 fastq.gz 2.1 GB Report
EGAF00003476792 fastq.gz 2.1 GB Report
EGAF00003476793 fastq.gz 1.1 GB Report
EGAF00003476794 fastq.gz 1.1 GB Report
EGAF00003476795 fastq.gz 1.2 GB Report
EGAF00003476796 fastq.gz 1.1 GB Report
EGAF00003477353 fastq.gz 3.9 GB Report
EGAF00003477354 fastq.gz 4.1 GB Report
EGAF00003477355 fastq.gz 8.4 GB Report
EGAF00003477356 fastq.gz 10.0 GB Report
EGAF00003477357 fastq.gz 3.1 GB Report
EGAF00003477358 fastq.gz 3.6 GB Report
EGAF00003477359 fastq.gz 3.9 GB Report
EGAF00003477360 fastq.gz 4.2 GB Report
EGAF00003477361 fastq.gz 6.7 GB Report
EGAF00003477362 fastq.gz 7.6 GB Report
EGAF00003477363 fastq.gz 6.9 GB Report
EGAF00003477364 fastq.gz 7.4 GB Report
EGAF00003477365 fastq.gz 10.1 GB Report
EGAF00003477366 fastq.gz 11.1 GB Report
EGAF00003477367 fastq.gz 3.8 GB Report
EGAF00003477368 fastq.gz 4.1 GB Report
EGAF00003477369 fastq.gz 7.0 GB Report
EGAF00003477370 fastq.gz 8.1 GB Report
EGAF00003477371 fastq.gz 14.1 GB Report
EGAF00003477372 fastq.gz 16.4 GB Report
EGAF00003477373 fastq.gz 7.7 GB Report
EGAF00003477374 fastq.gz 8.4 GB Report
EGAF00003477375 fastq.gz 3.1 GB Report
EGAF00003477376 fastq.gz 3.4 GB Report
EGAF00003477377 fastq.gz 6.2 GB Report
EGAF00003477378 fastq.gz 7.0 GB Report
EGAF00003477379 fastq.gz 6.9 GB Report
EGAF00003477380 fastq.gz 7.7 GB Report
EGAF00003477381 fastq.gz 3.4 GB Report
EGAF00003477382 fastq.gz 3.7 GB Report
EGAF00003477383 fastq.gz 2.9 GB Report
EGAF00003477384 fastq.gz 3.4 GB Report
EGAF00003477385 fastq.gz 9.6 GB Report
EGAF00003477386 fastq.gz 10.1 GB Report
EGAF00003477387 fastq.gz 3.8 GB Report
EGAF00003477388 fastq.gz 4.2 GB Report
EGAF00003477389 fastq.gz 3.9 GB Report
EGAF00003477390 fastq.gz 4.1 GB Report
EGAF00003477391 fastq.gz 3.3 GB Report
EGAF00003477392 fastq.gz 3.5 GB Report
EGAF00003477393 fastq.gz 3.3 GB Report
EGAF00003477394 fastq.gz 3.6 GB Report
EGAF00003477395 fastq.gz 22.5 GB Report
EGAF00003477396 fastq.gz 25.4 GB Report
EGAF00003477397 fastq.gz 3.6 GB Report
EGAF00003477398 fastq.gz 3.9 GB Report
EGAF00003477399 fastq.gz 7.1 GB Report
EGAF00003477400 fastq.gz 8.4 GB Report
EGAF00003477401 fastq.gz 5.6 GB Report
EGAF00003477402 fastq.gz 6.5 GB Report
EGAF00003477403 fastq.gz 8.0 GB Report
EGAF00003477404 fastq.gz 8.5 GB Report
EGAF00003477405 fastq.gz 3.3 GB Report
EGAF00003477406 fastq.gz 3.5 GB Report
EGAF00003477407 fastq.gz 14.1 GB Report
EGAF00003477408 fastq.gz 14.6 GB Report
62 Files (401.3 GB)