A5049097819- Cancer Genomics and Diagnostics
- Cancer Treatment and Pharmacology
- Health Systems, Economic Evaluations, Quality of Life
- RNA modifications and cancer
- Economic and Financial Impacts of Cancer
- Cancer Immunotherapy and Biomarkers
- Cancer-related molecular mechanisms research
- Genetic factors in colorectal cancer
- Breast Cancer Treatment Studies
- Advanced Breast Cancer Therapies
- Myasthenia Gravis and Thymoma
- Biomedical Ethics and Regulation
- HER2/EGFR in Cancer Research
- Colorectal Cancer Treatments and Studies
- RNA Research and Splicing
- Microscopic Colitis
- PARP inhibition in cancer therapy
- BRCA gene mutations in cancer
- Hereditary Neurological Disorders
- Renal cell carcinoma treatment
- Cancer Cells and Metastasis
- Lung Cancer Treatments and Mutations
- Genomics and Rare Diseases
- Peripheral Neuropathies and Disorders
- Gene expression and cancer classification
Indiana University – Purdue University Indianapolis
2015-2025
Indiana University School of Medicine
2015-2025
Caris Life Sciences (United States)
2022-2025
Indiana University Health
2012-2023
Indiana University Melvin and Bren Simon Comprehensive Cancer Center
2017-2023
Indiana University
2009-2022
University School
2021-2022
University of Indianapolis
2010-2021
Indiana University Indianapolis
2017-2020
University of Michigan
2020
No biomarkers have been identified to predict outcome with the use of an antiangiogenesis agent for cancer. Vascular endothelial growth factor (VEGF) genetic variability has associated altered risk breast cancer and variable promoter activity. Therefore, we evaluated association VEGF genotype efficacy toxicity in E2100, a phase III study comparing paclitaxel versus plus bevacizumab as initial chemotherapy metastatic
Highlights•Multi-omics definition of four robust molecular TET subtypes associated with survival•Thymomas have the lowest mutational burden among adult cancers•Enrichment HRAS, NRAS, TP53, and recurrent GTF2I mutations are observed•Expression autoimmune targets aneuploidy links thymoma to myasthenia gravisSummaryThymic epithelial tumors (TETs) one rarest malignancies. Among TETs, is most predominant, characterized by a unique association diseases, followed thymic carcinoma, which less common...
A significant proportion of patients with early-stage triple-negative breast cancer (TNBC) are treated neoadjuvant chemotherapy. Sequencing circulating tumor DNA (ctDNA) after surgery, along enumeration cells (CTCs), may be used to detect minimal residual disease and assess which experience recurrence.To determine whether the presence ctDNA CTCs chemotherapy in TNBC is independently associated recurrence clinical outcomes.A preplanned secondary analysis was conducted from March 26, 2014,...
Colorectal cancer (CRC) consensus molecular subtypes (CMS) have different immunological, stromal cell, and clinicopathological characteristics. Single-cell characterization of CMS subtype tumor microenvironments is required to elucidate mechanisms stroma cell contributions pathogenesis which may advance subtype-specific therapeutic development. We interrogate racially diverse human CRC samples analyze multiple independent external cohorts for a total 487,829 single cells enabling...
Taxane-induced peripheral neuropathy (TIPN) is an important survivorship issue for many cancer patients. Currently, there are no clinically implemented biomarkers to predict which patients might be at increased risk TIPN. We present a comprehensive approach identification of genetic variants
Next-generation sequencing to detect circulating tumor DNA is a minimally invasive method for genotyping and monitoring therapeutic response. The majority of studies have focused on detecting from patients with metastatic disease. Herein, we tested whether could be used as biomarker predict relapse in triple-negative breast cancer residual disease after neoadjuvant chemotherapy. In this study, analyzed samples 38 early-stage matched tumor, blood, plasma. Extracted underwent library...
Patients with metastatic solid tumors who had progressed on at least one line of standard care therapy were referred to the Indiana University Health Precision Genomics Program. Tumor samples submitted for DNA & RNA next-generation sequencing, fluorescence in situ hybridization, and immunohistochemistry actionable targets. A multi-disciplinary tumor board reviewed all results. For each patient, ratio progression-free survival (PFS) genomically guided divided by PFS their prior was...
Abstract Purpose: Anthracycline-induced congestive heart failure (CHF) is a rare but serious toxicity associated with this commonly employed anticancer therapy. The ability to predict which patients might be at increased risk prior exposure would valuable optimally counsel risk-to-benefit ratio for each patient. Herein, we present genome-wide approach biomarker discovery two validation cohorts CHF from adult planning receive anthracycline. Experimental Design: We performed association study...
High-throughput sequencing provides the means to determine allelic decomposition for any gene of interest-the number copies and exact sequence content each copy a gene. Although many clinically functionally important genes are highly polymorphic have undergone structural alterations, no high-throughput data analysis tool has yet been designed effectively solve full problem. Here we introduce combinatorial optimization framework that successfully resolves this challenging problem, including...
Abstract Background Natural killer (NK) cells are non-antigen specific innate immune that can be redirected to targets of interest using multiple strategies, although none currently FDA-approved. We sought evaluate NK cell infiltration into tumors develop an improved understanding which histologies may most amenable cell-based therapies in the developmental pipeline. Methods DNA (targeted/whole-exome) and RNA (whole-transcriptome) sequencing was performed from 45 cancer types ( N = 90,916...
Abstract Immune checkpoint inhibitors (ICIs) have changed the treatment paradigm for many cancers but not shown benefit in prostate cancer (PCa). Chronic inflammation contributes to immunosuppressive tumor microenvironment (TME) and is associated with poor response ICIs. The primary source of inflammatory cytokine production inflammasome. Here, we identify PIM kinases as regulators inflammasome activation tumor-associated macrophages (TAMs). Analysis clinical data from a cohort naïve,...
The US Food and Drug Administration approves tissue-agnostic therapies to target tumor biomarkers regardless of type. In light the growing number such approvals in recent years, a better understanding their relative clinical benefit across cancer types is required. To address this need, we analyzed indications (TMB-High, MSI-High/MMRd, BRAFV600E mutations, NTRK RET fusions) database 295,316 molecularly-profiled samples with associated outcomes data. Here, show that 21.5% tumors harbored at...
Abstract Background Over 10,000 long intergenic non-coding RNAs (lincRNAs) have been identified in the human genome. Some well characterized and known to participate various stages of gene regulation. In post-transcriptional process, another class well-known small RNA, or microRNA (miRNA), is very active inhibiting mRNA. Though similar features between mRNA lincRNA revealed several recent studies, a few isolated miRNA-lincRNA relationships observed. Despite these advances, comprehensive...
Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer with lack of predictive biomarkers. We conducted study to assess DNA damage repair (DDR) gene mutations as biomarker in PDAC patients treated FOLFIRINOX.Indiana University Simon Cancer Center pancreatic database was used identify metastatic PDAC, FOLFIRINOX and had tissue available for sequencing. Baseline demographic, clinical, pathologic information gathered. isolation targeted sequencing performed using the Ion AmpliSeq protocol....
Acquired and intrinsic resistance to receptor tyrosine kinase inhibitors (RTKi) represents a major hurdle in improving the management of clear cell renal carcinoma (ccRCC). Recent reports suggest that drug is driven by tumor adaptation via epigenetic mechanisms activate alternative survival pathways. The histone methyl transferase EZH2 frequently altered many cancers, including ccRCC. To evaluate its role ccRCC RTKi, we established characterized spontaneously metastatic, patient-derived...
Abstract Chemotherapy with or without radiation is the standard therapy for anaplastic thyroid cancer (ATC), although response rate not high and durable. We describe a 62-year-old male who was diagnosed ATC initially treated thyroidectomy lymph node dissection, followed by chemotherapy. Next generation sequencing then performed to guide tumor found have BRAF programmed death-ligand 1 (PD-L1) positivity that subsequently vemurafenib nivolumab. This led substantial regression of nodules....
Background: Metaplastic breast cancer is one of the most therapeutically challenging forms because its highly heterogeneous and chemoresistant nature. We have previously demonstrated that ribosomal protein L39 (RPL39) gain-of-function mutation A14V oncogenic activity in triple-negative this may be mediated through inducible nitric oxide synthase (iNOS). The function RPL39 other subtypes currently unknown. objective study was to determine role mechanism action metaplastic cancer. Methods:...
The cancer-risk-associated rs6983267 single nucleotide polymorphism (SNP) and the accompanying long noncoding RNA CCAT2 in highly amplified 8q24.21 region have been implicated cancer predisposition, although causality has not established. Here, using allele-specific transgenic mice, we demonstrate that overexpression leads to spontaneous myeloid malignancies. We further identified is overexpressed bone marrow peripheral blood of myelodysplastic/myeloproliferative neoplasms (MDS/MPN)...