[HTML][HTML] Oncogenic signaling pathways in the cancer genome atlas
Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and
cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-…
cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-…
The immune landscape of cancer
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising
33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we …
33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we …
[HTML][HTML] An integrated TCGA pan-cancer clinical data resource to drive high-quality survival outcome analytics
…, P Sipahimalani, A Tam, N Thiessen, K Tse, T Wong… - Cell, 2018 - cell.com
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic
annotation data along with multi-platform molecular profiles of more than 11,000 human tumors …
annotation data along with multi-platform molecular profiles of more than 11,000 human tumors …
[HTML][HTML] Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer
…, P Sipahimalani, A Tam, N Thiessen, K Tse, T Wong… - Cell, 2018 - cell.com
We conducted comprehensive integrative molecular analyses of the complete set of tumors
in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and …
in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and …
[HTML][HTML] Comprehensive characterization of cancer driver genes and mutations
Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced
algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on …
algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on …
[HTML][HTML] Machine learning identifies stemness features associated with oncogenic dedifferentiation
…, P Sipahimalani, A Tam, N Thiessen, K Tse, T Wong… - Cell, 2018 - cell.com
Cancer progression involves the gradual loss of a differentiated phenotype and acquisition
of progenitor and stem-cell-like features. Here, we provide novel stemness indices for …
of progenitor and stem-cell-like features. Here, we provide novel stemness indices for …
[HTML][HTML] Genomic and functional approaches to understanding cancer aneuploidy
…, P Sipahimalani, A Tam, N Thiessen, K Tse, T Wong… - Cancer cell, 2018 - cell.com
Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal
characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, …
characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, …
[HTML][HTML] Genomic and molecular landscape of DNA damage repair deficiency across the cancer genome atlas
DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic
response. We systematically analyzed somatic alterations to provide a comprehensive view of …
response. We systematically analyzed somatic alterations to provide a comprehensive view of …
[HTML][HTML] Spatial organization and molecular correlation of tumor-infiltrating lymphocytes using deep learning on pathology images
…, P Sipahimalani, A Tam, N Thiessen, K Tse, T Wong… - Cell reports, 2018 - cell.com
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained
images of TCGA samples remain underutilized. To highlight this resource, we present …
images of TCGA samples remain underutilized. To highlight this resource, we present …
The cancer genome atlas comprehensive molecular characterization of renal cell carcinoma
Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers
with different genetic drivers, clinical courses, and therapeutic responses. The current …
with different genetic drivers, clinical courses, and therapeutic responses. The current …