Immune DNA signature of T-cell infiltration in breast tumor exomes
Author
dc.contributor.author
Levy, Eric
Author
dc.contributor.author
Marty, Rachel
Author
dc.contributor.author
Gárate Calderón, Valentina
Author
dc.contributor.author
Woo, Brian
Author
dc.contributor.author
Dow, Michelle
Author
dc.contributor.author
Armisen Yáñez, Ricardo
Author
dc.contributor.author
Carter, Hannah
Author
dc.contributor.author
Harismendy, Olivier
Admission date
dc.date.accessioned
2016-12-19T15:33:35Z
Available date
dc.date.available
2016-12-19T15:33:35Z
Publication date
dc.date.issued
2016
Cita de ítem
dc.identifier.citation
Scientific Reports Volumen: 6 Número de artículo: 30064 Jul 2016
es_ES
Identifier
dc.identifier.other
10.1038/srep30064
Identifier
dc.identifier.uri
https://repositorio.uchile.cl/handle/2250/141954
Abstract
dc.description.abstract
Tumor infiltrating lymphocytes (TILs) have been associated with favorable prognosis in multiple tumor types. The Cancer Genome Atlas (TCGA) represents the largest collection of cancer molecular data, but lacks detailed information about the immune environment. Here, we show that exome reads mapping to the complementarity-determining-region 3 (CDR3) of mature T-cell receptor beta (TCRB) can be used as an immune DNA (iDNA) signature. Specifically, we propose a method to identify CDR3 reads in a breast tumor exome and validate it using deep TCRB sequencing. In 1,078 TCGA breast cancer exomes, the fraction of CDR3 reads was associated with TILs fraction, tumor purity, adaptive immunity gene expression signatures and improved survival in Her2+ patients. Only 2/839 TCRB clonotypes were shared between patients and none associated with a specific HLA allele or somatic driver mutations. The iDNA biomarker enriches the comprehensive dataset collected through TCGA, revealing associations with other molecular features and clinical outcomes.