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Genomic rearrangements involving programmed death ligands are recurrent in primary mediastinal large B-cell lymphoma.
The pathogenesis of primary mediastinal large B-cell lymphoma (PMBCL) is incompletely understood. Recently, specific genotypic and phenotypic features have been linked to tumor cell immune escapeExpand
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Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer
We performed phylogenetic analysis of high-grade serous ovarian cancers (68 samples from seven patients), identifying constituent clones and quantifying their relative abundances at multipleExpand
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Clonal genotype and population structure inference from single-cell tumor sequencing
Single-cell DNA sequencing has great potential to reveal the clonal genotypes and population structure of human cancers. However, single-cell data suffer from missing values and biased allelic countsExpand
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Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling
TLDR
We present CellAssign, a probabilistic model that leverages prior knowledge of cell-type marker genes to annotate single-cell RNA sequencing data into predefined or de novo cell types. Expand
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Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer
BackgroundGenomic analyses of hundreds of prostate tumors have defined a diverse landscape of mutations and genome rearrangements, but the transcriptomic effect of this complexity is less wellExpand
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Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study
Background Follicular lymphoma (FL) is an indolent, yet incurable B cell malignancy. A subset of patients experience an increased mortality rate driven by two distinct clinical end points:Expand
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Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer
Next‐generation sequencing is making sequence‐based molecular pathology and personalized oncology viable. We selected an individual initially diagnosed with conventional but aggressive prostateExpand
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clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers
Measuring gene expression of tumor clones at single-cell resolution links functional consequences to somatic alterations. Without scalable methods to simultaneously assay DNA and RNA from the sameExpand
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Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer
High-grade serous ovarian cancer (HGSC) exhibits extensive malignant clonal diversity with widespread but non-random patterns of disease dissemination. We investigated whether local immuneExpand
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Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires
Essential features of cancer tissue cellular heterogeneity such as negatively selected genome topologies, sub-clonal mutation patterns and genome replication states can only effectively be studied byExpand
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