A5061355669- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Sarcoma Diagnosis and Treatment
- Lung Cancer Research Studies
- Protein Degradation and Inhibitors
- Peptidase Inhibition and Analysis
- Genomics and Rare Diseases
- Advanced Breast Cancer Therapies
- Molecular Biology Techniques and Applications
- Neuroblastoma Research and Treatments
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- Gene expression and cancer classification
- Acute Myeloid Leukemia Research
- CAR-T cell therapy research
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Acute Lymphoblastic Leukemia research
- Cancer Research and Treatments
- DNA Repair Mechanisms
- RNA Interference and Gene Delivery
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Glioma Diagnosis and Treatment
- Hematopoietic Stem Cell Transplantation
City College of San Francisco
2018-2025
University of California, San Francisco
2018-2024
Memorial Sloan Kettering Cancer Center
2023
University of California System
2023
Boston Children's Hospital
2023
Harvard University
2023
Massachusetts Institute of Technology
2023
UCSF Benioff Children's Hospital
2020
UCSF Helen Diller Family Comprehensive Cancer Center
2020
Stanford Health Care
2017
Osteosarcoma is a highly aggressive cancer for which treatment has remained essentially unchanged more than 30 years. characterized by widespread and recurrent somatic copy-number alterations (SCNA) structural rearrangements. In contrast, few point mutations in protein-coding genes have been identified, suggesting that within SCNAs are key oncogenic drivers this disease. rearrangements heterogeneous across osteosarcoma cases, the need genome-informed approach to targeted therapy. To identify...
Abstract Summary: NGSUtils is a suite of software tools for manipulating data common to next-generation sequencing experiments, such as FASTQ, BED and BAM format files. These provide stable modular platform management analysis. Availability implementation: available under BSD license works on Mac OS X Linux systems. Python 2.6+ virtualenv are required. More information source code may be obtained from the website: http://ngsutils.org. Contact: yunliu@iupui.edu Supplemental information:...
Chromosomal translocation that results in fusion of the genes encoding RNA-binding protein EWS and transcription factor FLI1 (EWS-FLI1) is pathognomonic for Ewing sarcoma. EWS-FLI1 alters gene expression through mechanisms are not completely understood. We performed RNA sequencing (RNAseq) analysis on primary pediatric human mesenchymal progenitor cells (pMPCs) expressing order to identify targets this oncoprotein. determined long noncoding RNA-277 (Ewing sarcoma–associated transcript 1...
// Sekyung Oh 1, 2, * , Ryan A. Flynn 3, Stephen N. Floor 4 James Purzner 5, 6 Lance Martin Brian T. Do Simone Schubert 1 Dedeepya Vaka Sorana Morrissy 7, 8 Yisu Li 9 Marcel Kool 10 Volker Hovestadt 11 David T.W. Jones Paul Northcott Thomas Risch 12 Hans-Jörg Warnatz Marie-Laure Yaspo Christopher M. Adams 13 D. Leib Marcus Breese 14 Marco Marra Malkin 15 Peter Lichter Jennifer Doudna 4, 16, 17, 18 Stefan Pfister Michael Taylor 8, 9, 19 Howard Y. Chang 20, # Yoon-Jae Cho 21, 22,...
Pediatric hepatoblastoma is the most common primary liver cancer in infants and children. Studies of that focus exclusively on tumor cells demonstrate sparse somatic mutations a cell origin, hepatoblast, across patients. In contrast to homogeneity these studies would suggest, tumors have high degree heterogeneity can portend poor prognosis. this study, we use single-cell transcriptomic techniques analyze resected human pediatric specimens, identify five signatures may account for observed...
Abstract Most circulating tumor DNA (ctDNA) assays are designed to detect recurrent mutations. Pediatric sarcomas share few mutations but rather characterized by translocations and copy-number changes. We applied Cancer Personalized Profiling deep Sequencing (CAPP-Seq) for detection of found in the most common pediatric sarcomas. also ichorCNA combined off-target reads from our hybrid capture simultaneously alterations (CNA). analyzed 64 prospectively collected plasma samples 17 patients...
Models to study metastatic disease in rare cancers are needed advance preclinical therapeutics and gain insight into biology. Osteosarcoma is a cancer with complex genomic landscape which outcomes for patients poor. As osteosarcoma genomes highly heterogeneous, multiple models fully elucidate key aspects of biology recapitulate clinically relevant phenotypes.
Abstract The FET family of intrinsically disordered proteins (FUS, EWSR1, TAF15) are frequent 5’ oncogenic transcription factor (TF) fusion partners in a diversity sarcomas and leukemias. These TF oncoproteins often the sole driver alteration these cancers due to difficulty pharmacologic targeting TFs, precision medicine approaches have been lacking. Here we focus on pediatric bone tumor Ewing sarcoma (ES) as model for class rearranged cancers. ES patients with relapsed or metastatic disease...
Abstract Background Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative events from RNA-seq experiments is important for understanding the of transcripts and investigating regulation splicing. Results We developed Alt Event Finder, a tool identifying novel using transcript annotation derived genome-guided construction tools, such as Cufflinks Scripture. With proper combination alignment reconstruction...
Gliomatosis peritonei is a rare pathologic finding that associated with ovarian teratomas and malignant mixed germ cell tumors. The occurrence of gliomatosis as mature glial implant can impart an improved prognosis to patients immature teratoma, making prompt accurate diagnosis important. We describe case recurrent teratoma in 10-yr-old female patient, which comparative analysis the RNA sequencing gene expression data from patient's tumor was used effectively aid peritonei.
Overlapping myelodysplastic/myeloproliferative neoplasms (MDS/MPN) are clonal hematopoietic disorders with features of myelodysplasia and myeloproliferation. The only well-characterized MDS/MPN in children is juvenile myelomonocytic leukemia, an aggressive disorder infants toddlers. biochemical hallmark this disease hyperactivation the Ras/MAPK signaling pathway caused by mutations Ras genes more than 90% patients. Translocations involving receptor tyrosine kinases have been identified rare...
Abstract Models to study metastatic disease in rare cancers are needed advance preclinical therapeutics and gain insight into biology, especially for highly aggressive with a propensity spread. Osteosarcoma is cancer complex genomic landscape which outcomes patients poor. As osteosarcoma genomes heterogeneous, large panel of models fully elucidate key aspects biology recapitulate clinically-relevant phenotypes. We describe the development characterization patient-derived xenografts (PDXs)...
While oncogenes promote cancer cell growth, unrestrained proliferation represents a significant stressor to cellular homeostasis networks such as the DNA damage response (DDR). To enable oncogene tolerance, many cancers disable tumor suppressive DDR signaling through genetic loss of pathways and downstream effectors (e.g., ATM or p53 suppressor mutations). Whether how can help "self-tolerize" by creating analogous functional deficiencies in physiologic is not known. Here we focus on Ewing...
<p>Copy number and count data for tumor suppressor genes oncogenes in primary tumors, PDXs, PDX-derived cell lines</p>
<p>Supplementary figures and tables</p>
<div>AbstractPurpose:<p>Models to study metastatic disease in rare cancers are needed advance preclinical therapeutics and gain insight into biology. Osteosarcoma is a cancer with complex genomic landscape which outcomes for patients poor. As osteosarcoma genomes highly heterogeneous, multiple models fully elucidate key aspects of biology recapitulate clinically relevant phenotypes.</p>Experimental Design:<p>Matched patient samples, patient-derived xenografts (PDX),...
<div>AbstractPurpose:<p>Models to study metastatic disease in rare cancers are needed advance preclinical therapeutics and gain insight into biology. Osteosarcoma is a cancer with complex genomic landscape which outcomes for patients poor. As osteosarcoma genomes highly heterogeneous, multiple models fully elucidate key aspects of biology recapitulate clinically relevant phenotypes.</p>Experimental Design:<p>Matched patient samples, patient-derived xenografts (PDX),...
<p>Copy number and count data for tumor suppressor genes oncogenes in primary tumors, PDXs, PDX-derived cell lines</p>
<p>Supplementary figures and tables</p>
Abstract We have leveraged long-read and spatial sequencing modalities to identify cancer-specific oncogenic alterations for treatment of osteosarcomas. Osteosarcoma is archetypal cancers driven by aneuploidy structural rearrangement rather than point mutations. The functional consequences many SVs stem from their effect on multidimensional genome organization. can enable enhancer hijacking, alter boundaries topologically associated domains (TADs), move gene loci different regulatory...
Abstract Pediatric cancer patients are commonly profiled with gene-panel sequencing tests that yield few actionable results, in part due to the complex genomic alterations define these malignancies. We hypothesized integration of whole-genome (WGS) and RNA (RNAseq), would lead a more comprehensive understanding diseases. Our study is uniquely focused on metastatic relapsed disease, whereas previous studies primary cases. also prioritized longitudinal profiling, including deep sequencing,...
The biotechnology industry has long recognized the need for robust methods tracking samples and data; however, it is only with recent widespread adoption of genomic scale experiments that smaller academic facilities have also begun to appreciate value laboratory information management systems (LIMS) use in through many procedures involved, including automated data collection analysis. We designed an extensible LIMS database backend collectively called Labrat LIMS. extremely flexible...