Joel S. Parker
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View article: Associations of the HER2DX Genomic Test with Biological and Pathological Features in HER2-positive Breast Cancer
Associations of the HER2DX Genomic Test with Biological and Pathological Features in HER2-positive Breast Cancer Open
Background: HER2DX is a validated genomic assay used to support treatment decisions in early-stage HER2-positive (HER2+) breast cancer. It provides three scores: relapse risk, likelihood of pathologic complete response (pCR), and ERBB2 mRN…
View article: Supplementary Table S2 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)
Supplementary Table S2 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727) Open
Supplementary table 2 - Model estimates for logistic regression models of objective response rate and linear regression models of restricted PFS by treatment group
View article: Figure 3 from Impact of Duration of Neoadjuvant Aromatase Inhibitors on Molecular Expression Profiles in Estrogen Receptor–positive Breast Cancers
Figure 3 from Impact of Duration of Neoadjuvant Aromatase Inhibitors on Molecular Expression Profiles in Estrogen Receptor–positive Breast Cancers Open
Differential single-gene expression changes between baseline and surgery of the 17 genes included in the FOS and JUN module scores in the POETIC cohort. Differential expression in the treated samples from POETIC subset (A) and in th…
View article: Supplementary Figure S2 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)
Supplementary Figure S2 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727) Open
Changes in A. CIN70, B. RPS and C. PARPi7 from treatment naïve primary tumours to post-treatment metastatic samples in an independent dataset. Multiple metastatic samples are included for some patients. 𝛃 coefficients and p-values presente…
View article: Figure 4 from Impact of Duration of Neoadjuvant Aromatase Inhibitors on Molecular Expression Profiles in Estrogen Receptor–positive Breast Cancers
Figure 4 from Impact of Duration of Neoadjuvant Aromatase Inhibitors on Molecular Expression Profiles in Estrogen Receptor–positive Breast Cancers Open
Single-gene expression changes of genes in common between baseline and surgery in the different cohorts. A, Scatterplot of differentially expressed genes between baseline and surgery measured by log2 FC among the entire s…
View article: Supplementary Figure S1 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)
Supplementary Figure S1 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727) Open
Additional associations between signatures. A. Distribution of CIN70 by HRD score and genomic scars (NtAI tertiles, AiCna tertiles and HLAMP). B Distribution of RPS by HRD score and genomic scars (NtAI tertiles, AiCna tertiles and HLAMP). …
View article: Supplementary Figure S5 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)
Supplementary Figure S5 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727) Open
Heatmap showing clustering of all module scores filtered for a significant interaction with treatment. Our original clusters are shown against the new clusters at the top of the heatmap.
View article: Figure 1 from Impact of Duration of Neoadjuvant Aromatase Inhibitors on Molecular Expression Profiles in Estrogen Receptor–positive Breast Cancers
Figure 1 from Impact of Duration of Neoadjuvant Aromatase Inhibitors on Molecular Expression Profiles in Estrogen Receptor–positive Breast Cancers Open
Differences in intrinsic subtype classification from baseline to surgery in the POETIC subset and the NeoAI study. Changes of intrinsic subtype classifications in all the POETIC-treated samples (A); in POETIC Luminal B–treated sampl…
View article: Supplementary Figure S4 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)
Supplementary Figure S4 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727) Open
This is an example of DDR-deficient case with high TILs and low gene-expression measurements. These cases were confirmed to have high TIL content (black delineation) and are characterized by both high tumour area- stromal area ratio as wel…
View article: Supplementary Table S4 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)
Supplementary Table S4 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727) Open
Supplementary Table 4 - Representativeness of Study Participants
View article: Figure 6 from Impact of Duration of Neoadjuvant Aromatase Inhibitors on Molecular Expression Profiles in Estrogen Receptor–positive Breast Cancers
Figure 6 from Impact of Duration of Neoadjuvant Aromatase Inhibitors on Molecular Expression Profiles in Estrogen Receptor–positive Breast Cancers Open
Boxplots showing changes in gene expression from baseline to surgery of the two immune-related signatures (“durvalumab” and “immune-tolerance”) among H-H and H-L Ki67 response categories in the POETIC-treated subset (A) and in the N…
View article: Supplementary Table S1 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)
Supplementary Table S1 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727) Open
Supplementary table 1 - Biomarkers of interest
View article: Supplementary Table S3 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)
Supplementary Table S3 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727) Open
Supplemetary table 3 - Change in signature scores from primary to recurrence
View article: Supplementary Figure S3 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727)
Supplementary Figure S3 from Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727) Open
Heatmap of signatures used for clustering by the resulting novel clusters.
View article: A Prognostic Model Based on PAM50 and Clinical Variables (PAM50MET) for Metastatic Hormone Receptor–positive HER2-negative Breast Cancer
A Prognostic Model Based on PAM50 and Clinical Variables (PAM50MET) for Metastatic Hormone Receptor–positive HER2-negative Breast Cancer Open
PURPOSE: Predicting prognosis in HR+/HER2- metastatic breast cancer (MBC) might be clinically useful; however, no validated prognostic biomarkers exist in this setting to date. PATIENTS AND METHODS: In phase III, EGF3…
View article: Genomic heterogeneity and copy number variant burden are associated with poor recurrence‐free survival and 11q loss in human papillomavirus‐positive squamous cell carcinoma of the oropharynx
Genomic heterogeneity and copy number variant burden are associated with poor recurrence‐free survival and 11q loss in human papillomavirus‐positive squamous cell carcinoma of the oropharynx Open
BACKGROUND: Human papillomavirus-positive (HPV+) squamous cell carcinoma of the oropharynx (OPSCC) is the most prevalent HPV-associated malignancy in the United States. Favorable treatment outcomes have led to increased interest in treatme…
View article: Genomic Analysis of Germline Variation Associated with Survival of Patients with Colorectal Cancer Treated with Chemotherapy Plus Biologics in CALGB/SWOG 80405 (Alliance)
Genomic Analysis of Germline Variation Associated with Survival of Patients with Colorectal Cancer Treated with Chemotherapy Plus Biologics in CALGB/SWOG 80405 (Alliance) Open
PURPOSE: Irinotecan/5-fluorouracil (5-FU; FOLFIRI) or oxaliplatin/5-FU (FOLFOX), combined with bevacizumab or cetuximab, are approved, first-line treatments for metastatic colorectal cancer (mCRC). We aimed at identifying germline variants…
View article: Targeting dopamine receptor D2 as a novel therapeutic strategy in endometrial cancer
Targeting dopamine receptor D2 as a novel therapeutic strategy in endometrial cancer Open
View article: Rad18 mediates specific mutational signatures and shapes the genomic landscape of carcinogen-induced tumors in vivo
Rad18 mediates specific mutational signatures and shapes the genomic landscape of carcinogen-induced tumors in vivo Open
The E3 ubiquitin ligase Rad18 promotes a damage-tolerant and error-prone mode of DNA replication termed trans-lesion synthesis that is pathologically activated in cancer. However, the impact of vertebrate Rad18 on cancer genomes i…
View article: Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors
Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors Open
Chromatin accessibility states that influence gene expression and other nuclear processes can be altered in disease. The constellation of transcription factors and chromatin regulatory complexes in cells results in characteristic patterns …
View article: Validation of reference genes for whole blood gene expression analysis in cord blood of preterm and full-term neonates and peripheral blood of healthy adults
Validation of reference genes for whole blood gene expression analysis in cord blood of preterm and full-term neonates and peripheral blood of healthy adults Open
View article: Improved T-cell Receptor Diversity Estimates Associate with Survival and Response to Anti–PD-1 Therapy
Improved T-cell Receptor Diversity Estimates Associate with Survival and Response to Anti–PD-1 Therapy Open
T-cell receptor (TCR) repertoire profiling has emerged as a powerful tool for biological discovery and biomarker development in cancer immunology and immunotherapy. A key statistic derived from repertoire profiling data is diversity
View article: Rapid idiosyncratic mechanisms of clinical resistance to KRAS G12C inhibition
Rapid idiosyncratic mechanisms of clinical resistance to KRAS G12C inhibition Open
BACKGROUND The KRAS proto-oncogene is among the most frequently mutated genes in cancer, yet for 40 years it remained an elusive therapeutic target. Recently, allosteric inhibitors that covalently bind to KRAS G12C mutations have been appr…
View article: Cistrome analysis of YY1 uncovers a regulatory axis of YY1:BRD2/4-PFKP during tumorigenesis of advanced prostate cancer
Cistrome analysis of YY1 uncovers a regulatory axis of YY1:BRD2/4-PFKP during tumorigenesis of advanced prostate cancer Open
Castration-resistant prostate cancer (CRPC) is a terminal disease and the molecular underpinnings of CRPC development need to be better understood in order to improve its treatment. Here, we report that a transcription factor Yin Yang 1 (Y…
View article: Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profiling
Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profiling Open
View article: Reversing the Genomic, Epigenetic, and Triple-Negative Breast Cancer-Enhancing Effects of Obesity.
Reversing the Genomic, Epigenetic, and Triple-Negative Breast Cancer-Enhancing Effects of Obesity. Open
The reversibility of the procancer effects of obesity was interrogated in formerly obese C57BL/6 mice that lost weight via a nonrestricted low-fat diet (LFD) or 3 distinct calorie-restricted (CR) regimens (low-fat CR, Mediterranean-style C…
View article: Sequencing of genes of drug response in tumor DNA and implications for precision medicine in cancer patients
Sequencing of genes of drug response in tumor DNA and implications for precision medicine in cancer patients Open
View article: Peripheral Blood IL5RA Gene Expression as a Diagnostic Biomarker for Eosinophilic Esophagitis
Peripheral Blood IL5RA Gene Expression as a Diagnostic Biomarker for Eosinophilic Esophagitis Open
View article: CRTC1/MAML2 directs a PGC-1α-IGF-1 circuit that confers vulnerability to PPARγ inhibition
CRTC1/MAML2 directs a PGC-1α-IGF-1 circuit that confers vulnerability to PPARγ inhibition Open
View article: Author Correction: Stretching muscle cells induces transcriptional and splicing transitions and changes in SR proteins
Author Correction: Stretching muscle cells induces transcriptional and splicing transitions and changes in SR proteins Open