Nikhil Wagle
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View article: Detection of heterogeneous resistance mechanisms to tyrosine kinase inhibitors from cell-free DNA
Detection of heterogeneous resistance mechanisms to tyrosine kinase inhibitors from cell-free DNA Open
Though there has been substantial progress in the development of anti-human epidermal growth factor receptor 2 (HER2) therapies to treat HER2-positive metastatic breast cancer (MBC) within the past two decades, most patients still experien…
SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data Open
Solid tumors are spatially heterogeneous in their genetic, molecular, and cellular composition, but recent spatial profiling studies have mostly charted genetic and RNA variation in tumors separately. To leverage the potential of RNA to id…
View article: Real-time genomic characterization of advanced pancreatic cancer to enable precision medicine
Real-time genomic characterization of advanced pancreatic cancer to enable precision medicine Open
Clinically relevant subtypes exist for pancreatic ductal adenocarcinoma (PDAC), but molecular characterization is not yet standard in clinical care. We implemented a biopsy protocol to perform time-sensitive whole-exome sequencing and RNA …
View article: Genomic mechanisms of resistance to tyrosine kinase inhibitors in HER2 amplified breast cancer
Genomic mechanisms of resistance to tyrosine kinase inhibitors in HER2 amplified breast cancer Open
Though there has been substantial progress in the development of anti-HER2 therapies to treat HER2-positive metastatic breast cancer (MBC) within the past two decades, most patients still experience disease progression and cancer-related d…
High FOXA1 levels induce ER transcriptional reprogramming, a pro-metastatic secretome, and metastasis in endocrine-resistant breast cancer Open
Aberrant activation of the forkhead protein FOXA1 is observed in advanced hormone-related cancers. However, the key mediators of high FOXA1 signaling remain elusive. We demonstrate that ectopic high FOXA1 (H-FOXA1) expression promotes estr…
View article: The Metastatic Breast Cancer Project: leveraging patient-partnered research to expand the clinical and genomic landscape of metastatic breast cancer and accelerate discoveries
The Metastatic Breast Cancer Project: leveraging patient-partnered research to expand the clinical and genomic landscape of metastatic breast cancer and accelerate discoveries Open
Capturing the full complexity of the clinical experiences of metastatic breast cancer (MBC) patients treated in a variety of settings is needed to better understand this disease and develop new treatment modalities. Yet, challenges exist t…
View article: A genomic score to predict local control among patients with brain metastases managed with radiation
A genomic score to predict local control among patients with brain metastases managed with radiation Open
Background Clinical predictors of local recurrence following radiation among patients with brain metastases (BrM) provide limited explanatory power. We developed a DNA-based signature of radiotherapeutic efficacy among patients with BrM to…
View article: A Gene Panel Associated With Abemaciclib Utility in <i>ESR1</i>-Mutated Breast Cancer After Prior Cyclin-Dependent Kinase 4/6-Inhibitor Progression
A Gene Panel Associated With Abemaciclib Utility in <i>ESR1</i>-Mutated Breast Cancer After Prior Cyclin-Dependent Kinase 4/6-Inhibitor Progression Open
PURPOSE For patients with hormone receptor–positive (HR+), human epidermal growth factor receptor 2–negative (HER2–) metastatic breast cancer (MBC), first-line treatment is endocrine therapy (ET) plus cyclin-dependent kinase 4/6 inhibition…
View article: Supplementary Figure 1 from Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib
Supplementary Figure 1 from Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib Open
PDF file 249K, Effect of pazopanib on S6K1 phosphorylation in cells expressing activating MTOR mutations
View article: Supplemental Figure 8 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Supplemental Figure 8 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer Open
Figure S8
View article: Supplemental Figure 7 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Supplemental Figure 7 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer Open
Figure S7
View article: Data from MAP Kinase Pathway Alterations in <i>BRAF</i>-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition
Data from MAP Kinase Pathway Alterations in <i>BRAF</i>-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition Open
Treatment of BRAF-mutant melanoma with combined dabrafenib and trametinib, which target RAF and the downstream MAP–ERK kinase (MEK)1 and MEK2 kinases, respectively, improves progression-free survival and response rates compared with dabraf…
View article: Supplementary Table S1 from Clinical Acquired Resistance to RAF Inhibitor Combinations in <i>BRAF</i>-Mutant Colorectal Cancer through MAPK Pathway Alterations
Supplementary Table S1 from Clinical Acquired Resistance to RAF Inhibitor Combinations in <i>BRAF</i>-Mutant Colorectal Cancer through MAPK Pathway Alterations Open
Supplementary Table S1. Patient characteristics and MAPK pathway reactivating resistance mechanisms of BRAF-mutant CRC patients with clinical acquired resistance to RAF/EGFR or RAF/MEK inhibitor combinations.
View article: Supplemental Table 2 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Supplemental Table 2 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer Open
Supplemental Table 2
View article: Supplementary Figure 1 from Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib
Supplementary Figure 1 from Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib Open
PDF file 249K, Effect of pazopanib on S6K1 phosphorylation in cells expressing activating MTOR mutations
View article: Supplemental Figure 3 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Supplemental Figure 3 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer Open
Figure S3
View article: Data from Real-time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine
Data from Real-time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine Open
Clinically relevant subtypes exist for pancreatic ductal adenocarcinoma (PDAC), but molecular characterization is not yet standard in clinical care. We implemented a biopsy protocol to perform time-sensitive whole-exome sequencing and RNA …
View article: Supplementary Table Legends from The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma
Supplementary Table Legends from The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma Open
PDF file 73K, This file contains legends for the five supplementary tables
View article: Supplementary Figure 3 from A Genome-Scale RNA Interference Screen Implicates NF1 Loss in Resistance to RAF Inhibition
Supplementary Figure 3 from A Genome-Scale RNA Interference Screen Implicates NF1 Loss in Resistance to RAF Inhibition Open
Supplementary Figure 3 PDF file - 474K, A375 cells lacking NF1 display resistance to selective RAF and MEK inhibitors in a colony formation assay but pan-RAF inhibition and ERK inhibition is more effective at suppression. (A) A375 cells in…
View article: Supplementary Table 5 from Somatic <i>ERCC2</i> Mutations Correlate with Cisplatin Sensitivity in Muscle-Invasive Urothelial Carcinoma
Supplementary Table 5 from Somatic <i>ERCC2</i> Mutations Correlate with Cisplatin Sensitivity in Muscle-Invasive Urothelial Carcinoma Open
Damaging scores for alterations. This table shows the damaging scores (Methods) for nonsynonymous alterations (missense, nonsense, splice site, frame shift) studied in this cohort. The damaging score was derived as follows: missense mutati…
View article: Supplemental Figure 10 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Supplemental Figure 10 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer Open
Figure S10
View article: Supplementary Figures 1-3 from High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing
Supplementary Figures 1-3 from High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing Open
PDF file - 325K
View article: Supplemental Figure 2 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Supplemental Figure 2 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer Open
Figure S2
Supplementary Table 1 from Somatic <i>ERCC2</i> Mutations Correlate with Cisplatin Sensitivity in Muscle-Invasive Urothelial Carcinoma Open
Treatment information and sequencing metrics for all patients The treatment information and raw sequencing metrics, including mean target coverage, for each case is listed here. In addition, the mutation rate data referred to in the Result…