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Genomic profiling of childhood tumor patient-derived xenograft models to enable rational clinical trial design

https://doi.org/10.1101/566455
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/gcc.22101openalex-snapshot
Gain of 1q is a marker of poor prognosis in Wilms' tumors
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The pediatric preclinical testing program: Description of models and early testing results
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Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma
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Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations
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Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas
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Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
inferredcites →https://doi.org/10.1016/j.juro.2012.09.009openalex-snapshot
Loss of Heterozygosity Analysis at Different Chromosome Regions in Wilms Tumor Confirms 1p Allelic Loss as a Marker of Worse Prognosis: A Study from the Italian Association of Pediatric Hematology and Oncology
inferredcites →https://doi.org/10.1038/modpathol.2014.139openalex-snapshot
BCOR–CCNB3 fusions are frequent in undifferentiated sarcomas of male children
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The genetic basis of early T-cell precursor acute lymphoblastic leukaemia
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Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes
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Mutational heterogeneity in cancer and the search for new cancer-associated genes
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Signatures of mutational processes in human cancer
inferredcites →https://doi.org/10.1038/nature19057openalex-snapshot
Analysis of protein-coding genetic variation in 60,706 humans
inferredcites →https://doi.org/10.1038/nature22973openalex-snapshot
The whole-genome landscape of medulloblastoma subtypes
inferredcites →https://doi.org/10.1038/nature25795openalex-snapshot
Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours
inferredcites →https://doi.org/10.1038/nbt.1619openalex-snapshot
Analyzing 'omics data using hierarchical models
inferredcites →https://doi.org/10.1038/ncomms15936openalex-snapshot
Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma
inferredcites →https://doi.org/10.1038/ncomms7604openalex-snapshot
Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia
inferredcites →https://doi.org/10.1038/ng.2529openalex-snapshot
The genetic landscape of high-risk neuroblastoma
inferredcites →https://doi.org/10.1038/ng.2764openalex-snapshot
The Cancer Genome Atlas Pan-Cancer analysis project
inferredcites →https://doi.org/10.1038/ng.3333openalex-snapshot
Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations
inferredcites →https://doi.org/10.1038/ng.3349openalex-snapshot
Mutational dynamics between primary and relapse neuroblastomas
inferredcites →https://doi.org/10.1038/ng.3444openalex-snapshot
Genomic profiling of Sézary syndrome identifies alterations of key T cell signaling and differentiation genes
inferredcites →https://doi.org/10.1038/ng.3909openalex-snapshot
The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia
inferredcites →https://doi.org/10.1038/nmeth1005-731openalex-snapshot
The External RNA Controls Consortium: a progress report
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Author Correction: The landscape of genomic alterations across childhood cancers
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot
Fast and accurate long-read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/nar/gkx850openalex-snapshot
TissGDB: tissue-specific gene database in cancer
inferredcites →https://doi.org/10.1093/neuonc/nop056openalex-snapshot
A clinically relevant orthotopic xenograft model of ependymoma that maintains the genomic signature of the primary tumor and preserves cancer stem cells in vivo
inferredcites →https://doi.org/10.1101/333617openalex-snapshot
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
inferredcites →https://doi.org/10.1101/gr.096388.109openalex-snapshot
A SNP discovery method to assess variant allele probability from next-generation resequencing data
inferredcites →https://doi.org/10.1101/gr.239244.118openalex-snapshot
Maftools: efficient and comprehensive analysis of somatic variants in cancer
inferredcites →https://doi.org/10.1158/0008-5472.can-06-0610openalex-snapshot
Credentialing Preclinical Pediatric Xenograft Models Using Gene Expression and Tissue Microarray Analysis
inferredcites →https://doi.org/10.1158/0008-5472.can-17-0580openalex-snapshot
TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal
inferredcites →https://doi.org/10.1158/1535-7163.targ-17-lb-b16openalex-snapshot
Abstract LB-B16: The AKR1C3-Activated Prodrug OBI-3424 Exerts Profound In Vivo Efficacy Against Preclinical Models of T-Cell Acute Lymphoblastic Leukemia (T-ALL); a Pediatric Preclinical Testing Consortium Study
inferredcites →https://doi.org/10.1158/1538-7445.am2018-lb-136openalex-snapshot
Abstract LB-136: Pediatric Preclinical Testing Consortium evaluation of a DLL3-targeted antibody drug conjugate rovalpituzumab tesirine, in neuroblastoma
inferredcites →https://doi.org/10.1158/2159-8290.cd-13-0639openalex-snapshot
Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors
inferredcites →https://doi.org/10.1158/2159-8290.cd-14-0622openalex-snapshot
Genomic Landscape of Ewing Sarcoma Defines an Aggressive Subtype with Co-Association of STAG2 and TP53 Mutations
inferredcites →https://doi.org/10.1182/blood-2003-08-2911openalex-snapshot
Characterization of childhood acute lymphoblastic leukemia xenograft models for the preclinical evaluation of new therapies
inferredcites →https://doi.org/10.1182/blood.v99.11.4100openalex-snapshot
The nonobese diabetic/severe combined immunodeficient (NOD/SCID) mouse model of childhood acute lymphoblastic leukemia reveals intrinsic differences in biologic characteristics at diagnosis and relapse
inferredcites →https://doi.org/10.1186/1471-2105-13-8openalex-snapshot
An integrative variant analysis suite for whole exome next-generation sequencing data
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Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline
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TiGER: A database for tissue-specific gene expression and regulation
inferredcites →https://doi.org/10.1186/1472-6750-11-124openalex-snapshot
Real-time PCR-based assay to quantify the relative amount of human and mouse tissue present in tumor xenografts
inferredcites →https://doi.org/10.1186/gb-2011-12-7-r68openalex-snapshot
Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities
inferredcites →https://doi.org/10.1186/s12864-017-3519-7openalex-snapshot
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma
inferredcites →https://doi.org/10.1198/004017005000000661openalex-snapshot
Multilevel (Hierarchical) Modeling: What It Can and Cannot Do
inferredcites →https://doi.org/10.1200/jco.2013.54.0674openalex-snapshot
Emergence of New ALK Mutations at Relapse of Neuroblastoma
inferredcites →https://doi.org/10.1371/journal.pgen.1006501openalex-snapshot
Enrichment of Targetable Mutations in the Relapsed Neuroblastoma Genome
inferredcites →https://doi.org/10.1371/journal.pone.0072182openalex-snapshot
Breakpoint Features of Genomic Rearrangements in Neuroblastoma with Unbalanced Translocations and Chromothripsis
inferredcites →https://doi.org/10.18632/oncotarget.11125openalex-snapshot
A single nucleotide polymorphism genotyping platform for the authentication of patient derived xenografts
inferredcites →https://doi.org/10.18632/oncotarget.20191openalex-snapshot
Loss of heterozygosity on chromosome 16q increases relapse risk in Wilms’ tumor: a meta-analysis
inferredcites →https://doi.org/10.18632/oncotarget.3115openalex-snapshot
TP53 intron 1 hotspot rearrangements are specific to sporadic osteosarcoma and can cause Li-Fraumeni syndrome
inferredcites →https://doi.org/10.18632/oncotarget.468openalex-snapshot
Stratification of Wilms tumor by genetic and epigenetic analysis
inferredcites →https://doi.org/10.18632/oncotarget.6567openalex-snapshot
Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations
inferredcites →https://doi.org/10.18637/jss.v076.i01openalex-snapshot
Stan : A Probabilistic Programming Language

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/pbc.30398openalex-snapshot
In vivo activity of the dual PI3Kδ and PI3Kγ inhibitor duvelisib against pediatric acute lymphoblastic leukemia xenografts
inferred← citeshttps://doi.org/10.1038/s41390-025-03847-yopenalex-snapshot
Opportunities in the translational pipeline for pediatric brain cancer therapies
inferred← citeshttps://doi.org/10.1038/s41416-024-02724-5openalex-snapshot
CD57 defines a novel cancer stem cell that drive invasion of diffuse pediatric-type high grade gliomas
inferred← citeshttps://doi.org/10.1038/s41467-024-51337-2openalex-snapshot
CAR T-cell-mediated delivery of bispecific innate immune cell engagers for neuroblastoma
inferred← citeshttps://doi.org/10.1038/s41571-021-00519-8openalex-snapshot
Advancing therapy for osteosarcoma
inferred← citeshttps://doi.org/10.1038/s41586-023-06706-0openalex-snapshot
Targeting of intracellular oncoproteins with peptide-centric CARs
inferred← citeshttps://doi.org/10.1038/s41598-024-69382-8openalex-snapshot
Whole genome and reverse protein phase array landscapes of patient derived osteosarcoma xenograft models
inferred← citeshttps://doi.org/10.1038/s43018-022-00474-yopenalex-snapshot
The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations
inferred← citeshttps://doi.org/10.1093/neuonc/noaf012openalex-snapshot
Lineage dependence of the neuroblastoma surfaceome defines tumor cell state-dependent and -independent immunotherapeutic targets
inferred← citeshttps://doi.org/10.1158/0008-5472.22424632openalex-snapshot
Supplementary Data from Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma
inferred← citeshttps://doi.org/10.1158/0008-5472.22426861openalex-snapshot
Supplementary Data from A Very Long-Acting PARP Inhibitor Suppresses Cancer Cell Growth in DNA Repair-Deficient Tumor Models
inferred← citeshttps://doi.org/10.1158/0008-5472.22431532openalex-snapshot
Supplementary Figure from M6A RNA Methylation Regulates Histone Ubiquitination to Support Cancer Growth and Progression
inferred← citeshttps://doi.org/10.1158/1078-0432.c.6530664openalex-snapshot
Data from Dual Targeting of Chromatin Stability By The Curaxin CBL0137 and Histone Deacetylase Inhibitor Panobinostat Shows Significant Preclinical Efficacy in Neuroblastoma
inferred← citeshttps://doi.org/10.1158/1078-0432.c.7077821openalex-snapshot
Data from Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach
inferred← citeshttps://doi.org/10.1158/1078-0432.c.7077821.v1openalex-snapshot
Data from Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach
inferred← citeshttps://doi.org/10.1158/2159-8290.22541898openalex-snapshot
Supplementary Figure from Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer
inferred← citeshttps://doi.org/10.12703/r/10-11openalex-snapshot
Xenograft models for pediatric cancer therapies
inferred← citeshttps://doi.org/10.20517/cdr.2021.112openalex-snapshot
Approaches to identifying drug resistance mechanisms to clinically relevant treatments in childhood rhabdomyosarcoma
inferred← citeshttps://doi.org/10.3390/cancers15215269openalex-snapshot
Rhabdomyosarcoma: Current Therapy, Challenges, and Future Approaches to Treatment Strategies
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