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Article
Open AccessA first-in-human phase 1/2 study of FGF401 and combination of FGF401 with spartalizumab in patients with hepatocellular carcinoma or biomarker-selected solid tumors
Deregulation of FGF19-FGFR4 signaling is found in several cancers, including hepatocellular carcinoma (HCC), nominating it for therapeutic targeting. FGF401 is a potent, selective FGFR4 inhibitor with antitumo...
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Article
Open AccessTGFβ-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts
Despite the increasing interest in targeting stromal elements of the tumor microenvironment, we still face tremendous challenges in develo** adequate therapeutics to modify the tumor stromal landscape. A maj...
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Article
Open AccessAuthor Correction: Characterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features
The original version of this Article contained an error in the author affiliations. The affiliation of Kevin P. White with Tempus Labs, Inc. Chicago, IL, USA was inadvertently omitted. This has now been correc...
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Article
Open AccessCharacterization of Nigerian breast cancer reveals prevalent homologous recombination deficiency and aggressive molecular features
Racial/ethnic disparities in breast cancer mortality continue to widen but genomic studies rarely interrogate breast cancer in diverse populations. Through genome, exome, and RNA sequencing, we examined the mo...
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Article
Genetic mechanisms of target antigen loss in CAR19 therapy of acute lymphoblastic leukemia
We identified genetic mutations in CD19 and loss of heterozygosity at the time of CD19– relapse to chimeric antigen receptor (CAR) therapy. The mutations are present in the vast majority of resistant tumor cells ...
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Article
Open AccessPureCN: copy number calling and SNV classification using targeted short read sequencing
Matched sequencing of both tumor and normal tissue is routinely used to classify variants of uncertain significance (VUS) into somatic vs. germline. However, assays used in molecular diagnostics focus on known...
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Protocol
Meta-Analysis in Gene Expression Studies
This chapter introduces methods to synthesize experimental results from independent high-throughput genomic experiments, with a focus on adaptation of traditional methods from systematic review of clinical tri...
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Article
Open AccessDNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors
To date, there have been no reports characterizing the genome-wide somatic DNA chromosomal copy-number alteration landscape in metastatic urothelial carcinoma. We sought to characterize the DNA copy-number pro...
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Article
Open AccessESTs and EST-linked polymorphisms for genetic map** and phylogenetic reconstruction in the guppy, Poecilia reticulata
The guppy, Poecilia reticulata, is a well-known model organism for studying inheritance and variation of male ornamental traits as well as adaptation to different river habitats. However, genomic resources for st...
