Identification of neoantigens for individualized therapeutic cancer vaccines
Somatic mutations in cancer cells can generate tumour-specific neoepitopes, which are
recognized by autologous T cells in the host. As neoepitopes are not subject to central …
recognized by autologous T cells in the host. As neoepitopes are not subject to central …
Best practices for variant calling in clinical sequencing
DC Koboldt - Genome Medicine, 2020 - Springer
Next-generation sequencing technologies have enabled a dramatic expansion of clinical
genetic testing both for inherited conditions and diseases such as cancer. Accurate variant …
genetic testing both for inherited conditions and diseases such as cancer. Accurate variant …
Calling somatic SNVs and indels with Mutect2
Mutect2 is a somatic variant caller that uses local assembly and realignment to detect SNVs
and indels. Assembly implies whole haplotypes and read pairs, rather than single bases, as …
and indels. Assembly implies whole haplotypes and read pairs, rather than single bases, as …
Generation of tumor-reactive T cells by co-culture of peripheral blood lymphocytes and tumor organoids
KK Dijkstra, CM Cattaneo, F Weeber, M Chalabi… - Cell, 2018 - cell.com
Cancer immunotherapies have shown substantial clinical activity for a subset of patients with
epithelial cancers. Still, technological platforms to study cancer T-cell interactions for …
epithelial cancers. Still, technological platforms to study cancer T-cell interactions for …
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 …
cancers with different genetic drivers, clinical courses, and therapeutic responses. The …
Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy
CD8+ T cell–dependent killing of cancer cells requires efficient presentation of tumor
antigens by human leukocyte antigen class I (HLA-I) molecules. However, the extent to …
antigens by human leukocyte antigen class I (HLA-I) molecules. However, the extent to …
Nivolumab plus ipilimumab in advanced salivary gland cancer: a phase 2 trial
Salivary gland cancers (SGCs) are rare, aggressive cancers without effective treatments
when metastasized. We conducted a phase 2 trial evaluating nivolumab (nivo, anti-PD-1) …
when metastasized. We conducted a phase 2 trial evaluating nivolumab (nivo, anti-PD-1) …
[HTML][HTML] Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines
Summary The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000
tumor-normal exome pairs across 33 different cancer types, in total> 400 TB of raw data files …
tumor-normal exome pairs across 33 different cancer types, in total> 400 TB of raw data files …
[HTML][HTML] Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the Association for …
Widespread clinical laboratory implementation of next-generation sequencing–based
cancer testing has highlighted the importance and potential benefits of standardizing the …
cancer testing has highlighted the importance and potential benefits of standardizing the …
Comprehensive and integrated genomic characterization of adult soft tissue sarcomas
Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic
diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue …
diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue …