Elaine R. Mardis
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View article: Single cell and spatial transcriptomic profiling of the type 2 diabetic coronary microcirculation and myocardium
Single cell and spatial transcriptomic profiling of the type 2 diabetic coronary microcirculation and myocardium Open
Coronary microvascular disease (CMD) is an early complication of type 2 diabetes (T2D) involving adverse endothelial and smooth muscle function, vascular remodeling, and alterations in mechanics. These culminate in impaired coronary blood …
View article: CTIM-33. PERSONALIZED MULTIVALENT DNA VACCINATION SAFELY INDUCES BROAD NEOANTIGEN-SPECIFIC T CELL RESPONSES IN NEWLY DIAGNOSED MGMT UNMETHYLATED GLIOBLASTOMA IN A CLINICALLY RELEVANT TIME SCALE
CTIM-33. PERSONALIZED MULTIVALENT DNA VACCINATION SAFELY INDUCES BROAD NEOANTIGEN-SPECIFIC T CELL RESPONSES IN NEWLY DIAGNOSED MGMT UNMETHYLATED GLIOBLASTOMA IN A CLINICALLY RELEVANT TIME SCALE Open
Glioblastoma is a highly lethal malignancy with dismal overall survival and near universal recurrence despite maximal multimodal therapy. Patients with unmethylated O6-methylguanine methyltransferase (MGMT) promoters do not derive survival…
View article: TIP-30. Molecularly-guided phase 2 umbrella trial for children and young adults with newly-diagnosed high-grade glioma (HGG) including diffuse intrinsic pontine glioma (DIPG): CONNECT TarGeT (Targeted pediatric HGG therapy) trial in progress
TIP-30. Molecularly-guided phase 2 umbrella trial for children and young adults with newly-diagnosed high-grade glioma (HGG) including diffuse intrinsic pontine glioma (DIPG): CONNECT TarGeT (Targeted pediatric HGG therapy) trial in progress Open
Children and young adults with HGGs have limited treatment options and a dismal prognosis, underscoring the critical need to develop novel, biologically-rational, and minimally toxic therapies for this vulnerable population. Genome-wide di…
View article: IMGP-04. Targetable somatostatin receptor expression assessed by DOTATATE PET imaging in children and young adults with recurrent/progressive high-risk central nervous system (CNS) tumors: Initial screening results from the CONNECT2007 Lutathera Phase I/II trial
IMGP-04. Targetable somatostatin receptor expression assessed by DOTATATE PET imaging in children and young adults with recurrent/progressive high-risk central nervous system (CNS) tumors: Initial screening results from the CONNECT2007 Lutathera Phase I/II trial Open
Somatostatin type-2A receptors (SST2A) regulate cell growth through downstream modulation of proliferation and apoptosis signaling, representing a potential therapeutic target. Membranous SST2A protein expression has been identified immuno…
View article: NR0B1 alters the 9-<i>cis</i>-retinoic acid response in Ewing Sarcoma cells
NR0B1 alters the 9-<i>cis</i>-retinoic acid response in Ewing Sarcoma cells Open
Pediatric cancers are often characterized by relatively low DNA mutation rates and are frequently driven instead by alterations in gene expression programs. In Ewing Sarcoma (EwS), these changes result from the activity of an oncogenic fus…
View article: PEDIA-BRAIN: A single nuclei multiomic encyclopedia of the human pons provides a resource for normal development and disease vulnerability
PEDIA-BRAIN: A single nuclei multiomic encyclopedia of the human pons provides a resource for normal development and disease vulnerability Open
The human pons relays sensory and motor information between the brain and the body. It is a key site for pathological processes, including diffuse midline gliomas (DMGs) and multiple sclerosis (MS) which predominantly arise in childhood an…
View article: MRD4U: A path to development for personalized liquid biopsy for children with central nervous system tumors
MRD4U: A path to development for personalized liquid biopsy for children with central nervous system tumors Open
These findings demonstrate applicability of our personalized MRD4U assay in early detection of disease recurrence. Unlike non-targeted or tumor-agnostic CSF liquid biopsy approaches, MRD4U leverages patient-specific genomic information to …
View article: Childhood cancer data initiative: expanded access to tumor molecular profiling for children, adolescents, and young adults
Childhood cancer data initiative: expanded access to tumor molecular profiling for children, adolescents, and young adults Open
The Molecular Characterization Initiative (MCI), a key effort of the National Cancer Institute’s Childhood Cancer Data Initiative (CCDI), was launched in 2022 in collaboration with the Children’s Oncology Group (COG) to bring comprehensive…
View article: Pediatric Cancer Genetics and Genomics
Pediatric Cancer Genetics and Genomics Open
Molecular profiling of DNA and RNA from pediatric cancers by next-generation sequencing has been demonstrated to improve diagnosis and prognosis and to identify somatic alterations indicating vulnerability to targeted therapies. Hence, muc…
View article: Variant calling from RNA-Seq data reveals allele-specific differential expression of pathogenic cancer variants
Variant calling from RNA-Seq data reveals allele-specific differential expression of pathogenic cancer variants Open
View article: Supplementary Figure S6 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Figure S6 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
Immunohistologic images
View article: Supplementary Table S4 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S4 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
Peptide sequences included in each subject's personalized NeoVax peptide vaccine
View article: Supplementary Figure S9 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Figure S9 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
Bar graph displaying number of validated variants for each subject
View article: Supplementary Table S7 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S7 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
RNA-sequencing pseudo counts generated via Salmon algorithm
View article: Supplementary Figure S8 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Figure S8 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
CDR3beta sequences ranked by ratio
View article: Supplementary Table S10 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S10 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
Differential expression analysis of nCounter CAR-T characterization panel gene expression analyzed via ROSALIND software
View article: Supplementary Figure S7 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Figure S7 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
CDR3beta sequences ranked by abundance
View article: Supplementary Table S5 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S5 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
immunoSEQ resolved TCR sequences for each subject PBMCs pre- and post-NeoVax
View article: Supplementary Table S8 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S8 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
CIBERSORTx relative percents of deconvoluted immunocytes
View article: Supplementary Table S9 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S9 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
Immunohistochemistry (IHC) quantification of CD3+ and CD8+ T cells from tumor blocks
View article: Supplementary Table S2 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S2 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
Mutect2 called and validated variants for each subject and each tumor region from whole exome sequencing data
View article: Supplementary Table S6 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S6 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
TCR clonal analysis via immunoSEQ ANALYZER software and The Immune Epitope Database (IEDB) TCRMatch results
View article: Supplementary Table S1 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S1 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
Representativeness of study participants
View article: Supplementary Table S3 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S3 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
pVAC-Seq predicted neoantigens for each subject and each tumor region from whole exome sequencing data
View article: Supplementary Table S8 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S8 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
CIBERSORTx relative percents of deconvoluted immunocytes
View article: Supplementary Table S2 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S2 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
Mutect2 called and validated variants for each subject and each tumor region from whole exome sequencing data
View article: Supplementary Table S6 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S6 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
TCR clonal analysis via immunoSEQ ANALYZER software and The Immune Epitope Database (IEDB) TCRMatch results
View article: Supplementary Table S4 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S4 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
Peptide sequences included in each subject's personalized NeoVax peptide vaccine
View article: Supplementary Table S3 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S3 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
pVAC-Seq predicted neoantigens for each subject and each tumor region from whole exome sequencing data
View article: Supplementary Table S1 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Supplementary Table S1 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma Open
Representativeness of study participants