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155 results on '"Learned, Katrina"'

1. Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors

Author

Sanders, Lauren M, Chandra, Rahul, Zebarjadi, Navid, Beale, Holly C, Lyle, A Geoffrey, Rodriguez, Analiz, Kephart, Ellen Towle, Pfeil, Jacob, Cheney, Allison, Learned, Katrina, Currie, Rob, Gitlin, Leonid, Vengerov, David, Haussler, David, Salama, Sofie R, and Vaske, Olena M

Subjects
Cancer, Digestive Diseases, Rare Diseases, Biotechnology, Human Genome, Genetics, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Humans, Proteomics, Multiomics, Neoplasms, Machine Learning, Cell Line
Abstract

Cancer cell lines have been widely used for decades to study biological processes driving cancer development, and to identify biomarkers of response to therapeutic agents. Advances in genomic sequencing have made possible large-scale genomic characterizations of collections of cancer cell lines and primary tumors, such as the Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Atlas (TCGA). These studies allow for the first time a comprehensive evaluation of the comparability of cancer cell lines and primary tumors on the genomic and proteomic level. Here we employ bulk mRNA and micro-RNA sequencing data from thousands of samples in CCLE and TCGA, and proteomic data from partner studies in the MD Anderson Cell Line Project (MCLP) and The Cancer Proteome Atlas (TCPA), to characterize the extent to which cancer cell lines recapitulate tumors. We identify dysregulation of a long non-coding RNA and microRNA regulatory network in cancer cell lines, associated with differential expression between cell lines and primary tumors in four key cancer driver pathways: KRAS signaling, NFKB signaling, IL2/STAT5 signaling and TP53 signaling. Our results emphasize the necessity for careful interpretation of cancer cell line experiments, particularly with respect to therapeutic treatments targeting these important cancer pathways.

Published
2022

2. A Functional Precision Medicine Pipeline Combines Comparative Transcriptomics and Tumor Organoid Modeling to Identify Bespoke Treatment Strategies for Glioblastoma.

Author

Reed, Megan, Lyle, A, De Loose, Annick, Maddukuri, Leena, Learned, Katrina, Beale, Holly, Kephart, Ellen, Cheney, Allison, van den Bout, Anouk, Lee, Madison, Hundley, Kelsey, Smith, Ashley, DesRochers, Teresa, Vibat, Cecile, Gokden, Murat, Salama, Sofie, Wardell, Christopher, Eoff, Robert, Vaske, Olena, and Rodriguez, Analiz

Subjects
Li Fraumeni, glioblastoma, organoid, precision medicine, transcriptomics, Adolescent, Adult, Child, Female, Gene Expression Regulation, Neoplastic, Germ-Line Mutation, Glioblastoma, Humans, Janus Kinase 1, Janus Kinase 2, Li-Fraumeni Syndrome, Male, Nitriles, Organoids, Precision Medicine, Pyrazoles, Pyrimidines, RNA-Seq, STAT1 Transcription Factor, STAT2 Transcription Factor, Transcriptome, Young Adult
Abstract

Li Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome caused by germline mutations in TP53. TP53 is the most common mutated gene in human cancer, occurring in 30-50% of glioblastomas (GBM). Here, we highlight a precision medicine platform to identify potential targets for a GBM patient with LFS. We used a comparative transcriptomics approach to identify genes that are uniquely overexpressed in the LFS GBM patient relative to a cancer compendium of 12,747 tumor RNA sequencing data sets, including 200 GBMs. STAT1 and STAT2 were identified as being significantly overexpressed in the LFS patient, indicating ruxolitinib, a Janus kinase 1 and 2 inhibitors, as a potential therapy. The LFS patient had the highest level of STAT1 and STAT2 expression in an institutional high-grade glioma cohort of 45 patients, further supporting the cancer compendium results. To empirically validate the comparative transcriptomics pipeline, we used a combination of adherent and organoid cell culture techniques, including ex vivo patient-derived organoids (PDOs) from four patient-derived cell lines, including the LFS patient. STAT1 and STAT2 expression levels in the four patient-derived cells correlated with levels identified in the respective parent tumors. In both adherent and organoid cultures, cells from the LFS patient were among the most sensitive to ruxolitinib compared to patient-derived cells with lower STAT1 and STAT2 expression levels. A spheroid-based drug screening assay (3D-PREDICT) was performed and used to identify further therapeutic targets. Two targeted therapies were selected for the patient of interest and resulted in radiographic disease stability. This manuscript supports the use of comparative transcriptomics to identify personalized therapeutic targets in a functional precision medicine platform for malignant brain tumors.

Published
2021

3. The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets

Author

Beale, Holly C, Roger, Jacquelyn M, Cattle, Matthew A, McKay, Liam T, Thompson, Drew KA, Learned, Katrina, Lyle, A Geoffrey, Kephart, Ellen T, Currie, Rob, Lam, Du Linh, Sanders, Lauren, Pfeil, Jacob, Vivian, John, Bjork, Isabel, Salama, Sofie R, Haussler, David, and Vaske, Olena M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Rare Diseases, Biotechnology, Cancer Genomics, Human Genome, Cancer, Child, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, Humans, Neoplasms, RNA, Reproducibility of Results, Sequence Analysis, RNA, Exome Sequencing, RNA-Seq, sequencing, depth, duplicate, unmapped, exonic, quality
Abstract

BackgroundThe reproducibility of gene expression measured by RNA sequencing (RNA-Seq) is dependent on the sequencing depth. While unmapped or non-exonic reads do not contribute to gene expression quantification, duplicate reads contribute to the quantification but are not informative for reproducibility. We show that mapped, exonic, non-duplicate (MEND) reads are a useful measure of reproducibility of RNA-Seq datasets used for gene expression analysis.FindingsIn bulk RNA-Seq datasets from 2,179 tumors in 48 cohorts, the fraction of reads that contribute to the reproducibility of gene expression analysis varies greatly. Unmapped reads constitute 1-77% of all reads (median [IQR], 3% [3-6%]); duplicate reads constitute 3-100% of mapped reads (median [IQR], 27% [13-43%]); and non-exonic reads constitute 4-97% of mapped, non-duplicate reads (median [IQR], 25% [16-37%]). MEND reads constitute 0-79% of total reads (median [IQR], 50% [30-61%]).ConclusionsBecause not all reads in an RNA-Seq dataset are informative for reproducibility of gene expression measurements and the fraction of reads that are informative varies, we propose reporting a dataset's sequencing depth in MEND reads, which definitively inform the reproducibility of gene expression, rather than total, mapped, or exonic reads. We provide a Docker image containing (i) the existing required tools (RSeQC, sambamba, and samblaster) and (ii) a custom script to calculate MEND reads from RNA-Seq data files. We recommend that all RNA-Seq gene expression experiments, sensitivity studies, and depth recommendations use MEND units for sequencing depth.

Published
2021

4. Identification of a differentiation stall in epithelial mesenchymal transition in histone H3–mutant diffuse midline glioma

Author

Sanders, Lauren M, Cheney, Allison, Seninge, Lucas, van den Bout, Anouk, Chen, Marissa, Beale, Holly C, Kephart, Ellen Towle, Pfeil, Jacob, Learned, Katrina, Lyle, A Geoffrey, Bjork, Isabel, Haussler, David, Salama, Sofie R, and Vaske, Olena M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Human Genome, Rare Diseases, Neurosciences, Pediatric Cancer, Cancer, Brain Cancer, Pediatric, Cancer Genomics, Biotechnology, Brain Disorders, Generic health relevance, Cell Differentiation, Child, Child, Preschool, Epithelial-Mesenchymal Transition, Glioma, Histones, Humans, Mutation, glioma, H3K27M mutation, epithelial mesenchymal transition
Abstract

BackgroundDiffuse midline gliomas with histone H3 K27M (H3K27M) mutations occur in early childhood and are marked by an invasive phenotype and global decrease in H3K27me3, an epigenetic mark that regulates differentiation and development. H3K27M mutation timing and effect on early embryonic brain development are not fully characterized.ResultsWe analyzed multiple publicly available RNA sequencing datasets to identify differentially expressed genes between H3K27M and non-K27M pediatric gliomas. We found that genes involved in the epithelial-mesenchymal transition (EMT) were significantly overrepresented among differentially expressed genes. Overall, the expression of pre-EMT genes was increased in the H3K27M tumors as compared to non-K27M tumors, while the expression of post-EMT genes was decreased. We hypothesized that H3K27M may contribute to gliomagenesis by stalling an EMT required for early brain development, and evaluated this hypothesis by using another publicly available dataset of single-cell and bulk RNA sequencing data from developing cerebral organoids. This analysis revealed similarities between H3K27M tumors and pre-EMT normal brain cells. Finally, a previously published single-cell RNA sequencing dataset of H3K27M and non-K27M gliomas revealed subgroups of cells at different stages of EMT. In particular, H3.1K27M tumors resemble a later EMT stage compared to H3.3K27M tumors.ConclusionsOur data analyses indicate that this mutation may be associated with a differentiation stall evident from the failure to proceed through the EMT-like developmental processes, and that H3K27M cells preferentially exist in a pre-EMT cell phenotype. This study demonstrates how novel biological insights could be derived from combined analysis of several previously published datasets, highlighting the importance of making genomic data available to the community in a timely manner.

Published
2020

5. Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor.

Author

Sanders, Lauren M, Rangaswami, Arun, Bjork, Isabel, Lam, Du Linh, Beale, Holly C, Kephart, Ellen Towle, Durbin, Ann, Learned, Katrina, Currie, Rob, Lyle, A Geoffrey, Pfeil, Jacob, Shah, Avanthi Tayi, Lee, Alex G, Leung, Stanley G, Behroozfard, Inge H, Breese, Marcus R, Peralez, Jennifer, Hazard, Florette K, Lacayo, Norman, Spunt, Sheri L, Haussler, David, Salama, Sofie R, Sweet-Cordero, E Alejandro, and Vaske, Olena M

Subjects
Humans, Glioma, Teratoma, Peritoneal Neoplasms, Ovarian Neoplasms, Rare Diseases, Prognosis, Sequence Analysis, RNA, Base Sequence, Child, Female, Whole Exome Sequencing, RNA-Seq, neoplasm of the nervous system, Sequence Analysis, RNA
Abstract

Gliomatosis peritonei is a rare pathologic finding that is associated with ovarian teratomas and malignant mixed germ cell tumors. The occurrence of gliomatosis as a mature glial implant can impart an improved prognosis to patients with immature ovarian teratoma, making prompt and accurate diagnosis important. We describe a case of recurrent immature teratoma in a 10-yr-old female patient, in which comparative analysis of the RNA sequencing gene expression data from the patient's tumor was used effectively to aid in the diagnosis of gliomatosis peritonei.

Published
2019

6. Barriers to accessing public cancer genomic data.

Author

Durbin, Ann, Currie, Robert, Kephart, Ellen, Beale, Holly, Sanders, Lauren, Pfeil, Jacob, Goldstein, Theodore, Salama, Sofie, Haussler, David, Vaske, Olena, Bjork, Isabel, and Learned, Katrina

Subjects
Datasets as Topic, Genomics, Humans, Information Dissemination, Neoplasms
Abstract

Although increasingly recognized as critical to genomic research, genomic data sharing is hindered by an absence of standards regarding timing, patient privacy, use agreement standards, and data characterization and quality. Only after months of identifying, permissioning for use, committing to terms restricting use and sharing, downloading, and assessing quality, is it possible to know whether or not a dataset can be used. In this paper, we evaluate the barriers to data sharing based on the Treehouse experience and offer recommendations for use agreement standards, data characterization and metadata standardization to enhance data sharing and outcomes for all pediatric cancer patients.

Published
2019

7. Barriers to accessing public cancer genomic data.

Author

Learned, Katrina, Durbin, Ann, Currie, Robert, Kephart, Ellen Towle, Beale, Holly C, Sanders, Lauren M, Pfeil, Jacob, Goldstein, Theodore C, Salama, Sofie R, Haussler, David, Vaske, Olena Morozova, and Bjork, Isabel M

Subjects
Humans, Neoplasms, Information Dissemination, Genomics, Datasets as Topic
Published
2019

8. The UCSC Genome Browser database: 2016 update

Author

Speir, Matthew L, Zweig, Ann S, Rosenbloom, Kate R, Raney, Brian J, Paten, Benedict, Nejad, Parisa, Lee, Brian T, Learned, Katrina, Karolchik, Donna, Hinrichs, Angie S, Heitner, Steve, Harte, Rachel A, Haeussler, Maximilian, Guruvadoo, Luvina, Fujita, Pauline A, Eisenhart, Christopher, Diekhans, Mark, Clawson, Hiram, Casper, Jonathan, Barber, Galt P, Haussler, David, Kuhn, Robert M, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Animals, Databases, Genetic, Disease, Genes, Genome, Genomics, Humans, Mice, Molecular Sequence Annotation, Software, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently. Some release highlights of this year include new and updated genome browsers for various assemblies, including bonobo and zebrafish; new gene annotation sets; improvements to track and assembly hub support; and a new interactive tool, the "Data Integrator", for intersecting data from multiple tracks. We have greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include updated gene prediction sets from GENCODE, more phenotype- and disease-associated variants from ClinVar and ClinGen, more genomic regulatory data, and a new multiple genome alignment.

Published
2016

9. The UCSC Genome Browser database: 2015 update

Author

Rosenbloom, Kate R, Armstrong, Joel, Barber, Galt P, Casper, Jonathan, Clawson, Hiram, Diekhans, Mark, Dreszer, Timothy R, Fujita, Pauline A, Guruvadoo, Luvina, Haeussler, Maximilian, Harte, Rachel A, Heitner, Steve, Hickey, Glenn, Hinrichs, Angie S, Hubley, Robert, Karolchik, Donna, Learned, Katrina, Lee, Brian T, Li, Chin H, Miga, Karen H, Nguyen, Ngan, Paten, Benedict, Raney, Brian J, Smit, Arian FA, Speir, Matthew L, Zweig, Ann S, Haussler, David, Kuhn, Robert M, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Animals, Cricetinae, Databases, Nucleic Acid, Dogs, Ebolavirus, Gene Expression, Genome, Genomics, Internet, Mice, Molecular Sequence Annotation, Phenotype, Rats, Software, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.

Published
2015

10. The UCSC Genome Browser database: 2014 update

Author

Karolchik, Donna, Barber, Galt P, Casper, Jonathan, Clawson, Hiram, Cline, Melissa S, Diekhans, Mark, Dreszer, Timothy R, Fujita, Pauline A, Guruvadoo, Luvina, Haeussler, Maximilian, Harte, Rachel A, Heitner, Steve, Hinrichs, Angie S, Learned, Katrina, Lee, Brian T, Li, Chin H, Raney, Brian J, Rhead, Brooke, Rosenbloom, Kate R, Sloan, Cricket A, Speir, Matthew L, Zweig, Ann S, Haussler, David, Kuhn, Robert M, and Kent, W James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Alleles, Animals, Databases, Genetic, Genome, Genome, Human, Genomics, Humans, Internet, Mice, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Sequence Alignment, Software, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser's web-based tools provide an integrated environment for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation 'tracks' for ∼90 organisms. Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data. New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype alleles for protein-coding genes and an expansion of data hubs that includes the capability to display remotely hosted user-provided assembly sequence in addition to annotation data. To improve European access, we have added a Genome Browser mirror (http://genome-euro.ucsc.edu) hosted at Bielefeld University in Germany.

Published
2014

11. 20. Comparative analysis of RNA expression identifies druggable targets in difficult-to-treat pediatric solid tumors

Author

Vasquez, Yvonne, primary, Sanders, Lauren, additional, Beale, Holly, additional, Lyle, Geoffrey, additional, Kephart, Ellen, additional, Learned, Katrina, additional, Thomson, Drew, additional, Peralez, Jennifer, additional, Li, Amy, additional, Huang, Min, additional, Pyke-Grimm, Kimberly, additional, Salama, Sofie, additional, Haussler, David, additional, Bjork, Isabel, additional, Tan, Serena, additional, Spunt, Sheri, additional, and Vaske, Olena, additional

Published
2023
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14. EXTH-96. BIOPROCESSING OF SURGICAL PEDIATRIC BRAIN TUMOR SPECIMENS FOR GENOME-GUIDED PERSONALIZED DRUG TESTING

Author

Nasajpour, Emon, primary, Lyle, Geoff, additional, Lancero, Hope, additional, Garcia, Cesar, additional, Learned, Katrina, additional, Gibson, Eden, additional, Tran, Caitlynn, additional, Schouten, Troy, additional, Vogel, Hannes, additional, Mahaney, Kelly, additional, Prolo, Laura, additional, Vaske, Olena, additional, Grant, Gerald, additional, and Petritsch, Claudia, additional

Published
2022
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16. 323 Generation of a functional precision medicine pipeline which combines comparative transcriptomics and tumor organoid modeling to identify bespoke treatment strategies for glioblastoma

Author

Reed, Megan R., primary, Lyle, A. Geoffrey, additional, De Loose, Annick, additional, Learned, Katrina, additional, Vibat, Cecile Rose T., additional, Wardell, Christopher P., additional, Eoff, Robert L., additional, Vaske, Olena M., additional, and Rodriguez, Analiz, additional

Published
2022
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17. A comparative encyclopedia of DNA elements in the mouse genome

Author

Yue, Feng, Cheng, Yong, Breschi, Alessandra, Vierstra, Jeff, Wu, Weisheng, Ryba, Tyrone, Sandstrom, Richard, Ma, Zhihai, Davis, Carrie, Pope, Benjamin D., Shen, Yin, Pervouchine, Dmitri D., Djebali, Sarah, Thurman, Robert E., Kaul, Rajinder, Rynes, Eric, Kirilusha, Anthony, Marinov, Georgi K., Williams, Brian A., Trout, Diane, Amrhein, Henry, Fisher-Aylor, Katherine, Antoshechkin, Igor, DeSalvo, Gilberto, See, Lei-Hoon, Fastuca, Meagan, Drenkow, Jorg, Zaleski, Chris, Dobin, Alex, Prieto, Pablo, Lagarde, Julien, Bussotti, Giovanni, Tanzer, Andrea, Denas, Olgert, Li, Kanwei, Bender, M. A., Zhang, Miaohua, Byron, Rachel, Groudine, Mark T., McCleary, David, Pham, Long, Ye, Zhen, Kuan, Samantha, Edsall, Lee, Wu, Yi-Chieh, Rasmussen, Matthew D., Bansal, Mukul S., Kellis, Manolis, Keller, Cheryl A., Morrissey, Christapher S., Mishra, Tejaswini, Jain, Deepti, Dogan, Nergiz, Harris, Robert S., Cayting, Philip, Kawli, Trupti, Boyle, Alan P., Euskirchen, Ghia, Kundaje, Anshul, Lin, Shin, Lin, Yiing, Jansen, Camden, Malladi, Venkat S., Cline, Melissa S., Erickson, Drew T., Kirkup, Vanessa M., Learned, Katrina, Sloan, Cricket A., Rosenbloom, Kate R., Lacerda de Sousa, Beatriz, Beal, Kathryn, Pignatelli, Miguel, Flicek, Paul, Lian, Jin, Kahveci, Tamer, Lee, Dongwon, James Kent, W., Ramalho Santos, Miguel, Herrero, Javier, Notredame, Cedric, Johnson, Audra, Vong, Shinny, Lee, Kristen, Bates, Daniel, Neri, Fidencio, Diegel, Morgan, Canfield, Theresa, Sabo, Peter J., Wilken, Matthew S., Reh, Thomas A., Giste, Erika, Shafer, Anthony, Kutyavin, Tanya, Haugen, Eric, Dunn, Douglas, Reynolds, Alex P., Neph, Shane, Humbert, Richard, Scott Hansen, R., De Bruijn, Marella, Selleri, Licia, Rudensky, Alexander, Josefowicz, Steven, Samstein, Robert, Eichler, Evan E., Orkin, Stuart H., Levasseur, Dana, Papayannopoulou, Thalia, Chang, Kai-Hsin, Skoultchi, Arthur, Gosh, Srikanta, Disteche, Christine, Treuting, Piper, Wang, Yanli, Weiss, Mitchell J., Blobel, Gerd A., Cao, Xiaoyi, Zhong, Sheng, Wang, Ting, Good, Peter J., Lowdon, Rebecca F., Adams, Leslie B., Zhou, Xiao-Qiao, Pazin, Michael J., Feingold, Elise A., Wold, Barbara, Taylor, James, Mortazavi, Ali, Weissman, Sherman M., Stamatoyannopoulos, John A., Snyder, Michael P., Guigo, Roderic, Gingeras, Thomas R., Gilbert, David M., Hardison, Ross C., Beer, Michael A., and Ren, Bing

Subjects
Man -- Genetic aspects, Genetic research, Human beings -- Genetic aspects, Genomes -- Comparative analysis, Mice -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases., Author(s): Feng Yue [1, 2]; Yong Cheng [3]; Alessandra Breschi [4]; Jeff Vierstra [5]; Weisheng Wu [6]; Tyrone Ryba [7]; Richard Sandstrom [5]; Zhihai Ma [3]; Carrie Davis [8]; Benjamin [...]

Published
2014
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18. Metastatic pediatric sclerosing epithelioid fibrosarcoma

Author

Woods, Andrew D., primary, Purohit, Reshma, additional, Mitchell, Laura Crocker, additional, Collier, John R., additional, Collier, Katherine A., additional, Lathara, Melvin, additional, Learned, Katrina, additional, Vaske, Olena, additional, Geiger, Heather, additional, Wrzeszczynski, Kazimierz O., additional, Jobanputra, Vaidehi, additional, Srinivasa, Ganapati, additional, Rudzinski, Erin R., additional, Whelan, Kimberly, additional, Beierle, Elizabeth, additional, Spunt, Sheri L., additional, Keller, Charles, additional, and Wadhwa, Aman, additional

Published
2021
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20. Abstract 3035: Identifying potential druggable targets for synovial sarcoma using comparative RNA-seq analysis

Author

Vasquez, Yvonne A., primary, Pfeil, Jacob, additional, Mueller, Letitia, additional, Beale, Holly, additional, Lyle, Alfred G., additional, Sanders, Lauren, additional, Learned, Katrina, additional, Kephart, Ellen, additional, van den Bout, Anouk, additional, Cheney, Allison, additional, Hosseinzadeh, Sahar, additional, Bjork, Isabel, additional, Salama, Sofie R., additional, and Vaske, Olena, additional

Published
2021
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21. Abstract 261: Long-read sequencing characterization of a patient with bilateral Wilms tumor of unknown etiology

Author

Cheney, Allison R., primary, Monlong, Jean, additional, Beale, Holly C., additional, Olsen, Hugh, additional, Kephart, Ellen Towle, additional, Learned, Katrina, additional, White, Shanna, additional, Martinez-Agosto, Julian A., additional, Federman, Noah, additional, Akeson, Mark, additional, Jain, Miten, additional, Chang, Vivian Y., additional, and Vaske, Olena M., additional

Published
2021
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22. An integrated encyclopedia of DNA elements in the human genome

Author

Dunham, Ian, Kundaje, Anshul, Aldred, Shelley F., Collins, Patrick J., Davis, Carrie A., Doyle, Francis, Epstein, Charles B., Frietze, Seth, Harrow, Jennifer, Kaul, Rajinder, Khatun, Jainab, Lajoie, Bryan R., Landt, Stephen G., Lee, Bum-Kyu, Pauli, Florencia, Rosenbloom, Kate R., Sabo, Peter, Safi, Alexias, Sanyal, Amartya, Shoresh, Noam, Simon, Jeremy M., Song, Lingyun, Trinklein, Nathan D., Altshuler, Robert C., Birney, Ewan, Brown, James B., Cheng, Chao, Djebali, Sarah, Dong, Xianjun, Ernst, Jason, Furey, Terrence S., Gerstein, Mark, Giardine, Belinda, Greven, Melissa, Hardison, Ross C., Harris, Robert S., Herrero, Javier, Hoffman, Michael M., Iyer, Sowmya, Kellis, Manolis, Kheradpour, Pouya, Lassmann, Timo, Li, Qunhua, Lin, Xinying, Marinov, Georgi K., Merkel, Angelika, Mortazavi, Ali, Parker, Stephen C. J., Reddy, Timothy E., Rozowsky, Joel, Schlesinger, Felix, Thurman, Robert E., Wang, Jie, Ward, Lucas D., Whitfield, Troy W., Wilder, Steven P., Wu, Weisheng, Xi, Hualin S., Yip, Kevin Y., Zhuang, Jiali, Bernstein, Bradley E., Green, Eric D., Gunter, Chris, Snyder, Michael, Pazin, Michael J., Lowdon, Rebecca F., Dillon, Laura A. L., Adams, Leslie B., Kelly, Caroline J., Zhang, Julia, Wexler, Judith R., Good, Peter J., Feingold, Elise A., Crawford, Gregory E., Dekker, Job, Elnitski, Laura, Farnham, Peggy J., Giddings, Morgan C., Gingeras, Thomas R., Guigo, Roderic, Hubbard, Timothy J., Kent, W. James, Lieb, Jason D., Margulies, Elliott H., Myers, Richard M., Stamatoyannopoulos, John A., Tenenbaum, Scott A., Weng, Zhiping, White, Kevin P., Wold, Barbara, Yu, Yanbao, Wrobel, John, Risk, Brian A., Gunawardena, Harsha P., Kuiper, Heather C., Maier, Christopher W., Xie, Ling, Chen, Xian, Mikkelsen, Tarjei S., Gillespie, Shawn, Goren, Alon, Ram, Oren, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Eaton, Matthew L., Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Xue, Chenghai, Williams, Brian A., Zaleski, Chris, Roder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Batut, Philippe, Bell, Ian, Bell, Kimberly, Chakrabortty, Sudipto, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jackie, Duttagupta, Radha, Fastuca, Megan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Li, Guoliang, Luo, Oscar J., Park, Eddie, Preall, Jonathan B., Presaud, Kimberly, Ribeca, Paolo, Robyr, Daniel, Ruan, Xiaoan, Sammeth, Michael, Sandhu, Kuljeet Singh, Schaeffer, Lorain, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Hayashizaki, Yoshihide, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory J., Ruan, Yijun, Carninci, Piero, Sloan, Cricket A., Learned, Katrina, Malladi, Venkat S., Wong, Matthew C., Barber, Galt P., Cline, Melissa S., Dreszer, Timothy R., Heitner, Steven G., Karolchik, Donna, Kirkup, Vanessa M., Meyer, Laurence R., Long, Jeffrey C., Maddren, Morgan, Raney, Brian J., Grasfeder, Linda L., Giresi, Paul G., Battenhouse, Anna, Sheffield, Nathan C., Showers, Kimberly A., London, Darin, Bhinge, Akshay A., Shestak, Christopher, Schaner, Matthew R., Ki Kim, Seul, Zhang, Zhuzhu Z., Mieczkowski, Piotr A., Mieczkowska, Joanna O., Liu, Zheng, McDaniell, Ryan M., Ni, Yunyun, Rashid, Naim U., Kim, Min Jae, Adar, Sheera, Zhang, Zhancheng, Wang, Tianyuan, Winter, Deborah, Keefe, Damian, Iyer, Vishwanath R., Zheng, Meizhen, Wang, Ping, Gertz, Jason, Vielmetter, Jost, Partridge, E., Varley, Katherine E., Gasper, Clarke, Bansal, Anita, Pepke, Shirley, Jain, Preti, Amrhein, Henry, Bowling, Kevin M., Anaya, Michael, Cross, Marie K., Muratet, Michael A., Newberry, Kimberly M., McCue, Kenneth, Nesmith, Amy S., Fisher-Aylor, Katherine I., Pusey, Barbara, DeSalvo, Gilberto, Parker, Stephanie L., Balasubramanian, Sreeram, Davis, Nicholas S., Meadows, Sarah K., Eggleston, Tracy, Newberry, J. Scott, Levy, Shawn E., Absher, Devin M., Wong, Wing H., Blow, Matthew J., Visel, Axel, Pennachio, Len A., Petrykowska, Hanna M., Abyzov, Alexej, Aken, Bronwen, Barrell, Daniel, Barson, Gemma, Berry, Andrew, Bignell, Alexandra, Boychenko, Veronika, Bussotti, Giovanni, Davidson, Claire, Despacio-Reyes, Gloria, Diekhans, Mark, Ezkurdia, Iakes, Frankish, Adam, Gilbert, James, Gonzalez, Jose Manuel, Griffiths, Ed, Harte, Rachel, Hendrix, David A., Hunt, Toby, Jungreis, Irwin, Kay, Mike, Khurana, Ekta, Leng, Jing, Lin, Michael F., Loveland, Jane, Lu, Zhi, Manthravadi, Deepa, Mariotti, Marco, Mudge, Jonathan, Mukherjee, Gaurab, Notredame, Cedric, Pei, Baikang, Rodriguez, Jose Manuel, Saunders, Gary, Sboner, Andrea, Searle, Stephen, Sisu, Cristina, Snow, Catherine, Steward, Charlie, Tapanari, Electra, Tress, Michael L., van Baren, Marijke J., Washietl, Stefan, Wilming, Laurens, Zadissa, Amonida, Zhang, Zhengdong, Brent, Michael, Haussler, David, Valencia, Alfonso, Addleman, Nick, Alexander, Roger P., Auerbach, Raymond K., Balasubramanian, Suganthi, Bettinger, Keith, Bhardwaj, Nitin, Boyle, Alan P., Cao, Alina R., Cayting, Philip, Charos, Alexandra, Cheng, Yong, Eastman, Catharine, Euskirchen, Ghia, Fleming, Joseph D., Grubert, Fabian, Habegger, Lukas, Hariharan, Manoj, Harmanci, Arif, Iyengar, Sushma, Jin, Victor X., Karczewski, Konrad J., Kasowski, Maya, Lacroute, Phil, Lam, Hugo, Lamarre-Vincent, Nathan, Lian, Jin, Lindahl-Allen, Marianne, Min, Renqiang, Miotto, Benoit, Monahan, Hannah, Moqtaderi, Zarmik, Mu, Xinmeng J., Ouyang, Zhengqing, Patacsil, Dorrelyn, Raha, Debasish, Ramirez, Lucia, Reed, Brian, Shi, Minyi, Slifer, Teri, Witt, Heather, Wu, Linfeng, Xu, Xiaoqin, Yan, Koon-Kiu, Yang, Xinqiong, Struhl, Kevin, Weissman, Sherman M., Penalva, Luiz O., Karmakar, Subhradip, Bhanvadia, Raj R., Choudhury, Alina, Domanus, Marc, Ma, Lijia, Moran, Jennifer, Victorsen, Alec, Auer, Thomas, Centanin, Lazaro, Eichenlaub, Michael, Gruhl, Franziska, Heermann, Stephan, Hoeckendorf, Burkhard, Inoue, Daigo, Kellner, Tanja, Kirchmaier, Stephan, Mueller, Claudia, Reinhardt, Robert, Schertel, Lea, Schneider, Stephanie, Sinn, Rebecca, Wittbrodt, Beate, Wittbrodt, Jochen, Partridge, E. Christopher, Jain, Gaurav, Balasundaram, Gayathri, Bates, Daniel L., Byron, Rachel, Canfield, Theresa K., Diegel, Morgan J., Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Garg, Kavita, Gist, Erica, Hansen, R. Scott, Boatman, Lisa, Haugen, Eric, Humbert, Richard, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tattyana V., Lee, Kristen, Lotakis, Dimitra, Maurano, Matthew T., Neph, Shane J., Neri, Fiedencio V., Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Rynes, Eric, Sanchez, Minerva E., Sandstrom, Richard S., Shafer, Anthony O., Stergachis, Andrew B., Thomas, Sean, Vernot, Benjamin, Vierstra, Jeff, Vong, Shinny, Weaver, Molly A., Yan, Yongqi, Zhang, Miaohua, Akey, Joshua M., Bender, Michael, Dorschner, Michael O., Groudine, Mark, MacCoss, Michael J., Navas, Patrick, Stamatoyannopoulos, George, Beal, Kathryn, Brazma, Alvis, Flicek, Paul, Johnson, Nathan, Lukk, Margus, Luscombe, Nicholas M., Sobral, Daniel, Vaquerizas, Juan M., Batzoglou, Serafim, Sidow, Arend, Hussami, Nadine, Kyriazopoulou-Panagiotopoulou, Sofia, Libbrecht, Max W., Schaub, Marc A., Miller, Webb, Bickel, Peter J., Banfai, Balazs, Boley, Nathan P., Huang, Haiyan, Li, Jingyi Jessica, Noble, William Stafford, Bilmes, Jeffrey A., Buske, Orion J., Sahu, Avinash D., Kharchenko, Peter V., Park, Peter J., Baker, Dannon, Taylor, James, and Lochovsky, Lucas

Subjects
Genetic research, Human genome -- Research, Genetic transcription -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research., Author(s): The ENCODE Project Consortium; Overall coordination (data analysis coordination); Ian Dunham [2]; Anshul Kundaje [3, 82]; Data production leads (data production); Shelley F. Aldred [4]; Patrick J. Collins [4]; [...]

Published
2012
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23. The UCSC Genome Browser database: extensions and updates 2013

Author

Meyer, Laurence R., Zweig, Ann S., Hinrichs, Angie S., Karolchik, Donna, Kuhn, Robert M., Wong, Matthew, Sloan, Cricket A., Rosenbloom, Kate R., Roe, Greg, Rhead, Brooke, Raney, Brian J., Pohl, Andy, Malladi, Venkat S., Li, Chin H., Lee, Brian T., Learned, Katrina, Kirkup, Vanessa, Hsu, Fan, Heitner, Steve, Harte, Rachel A., Haeussler, Maximilian, Guruvadoo, Luvina, Goldman, Mary, Giardine, Belinda M., Fujita, Pauline A., Dreszer, Timothy R., Diekhans, Mark, Cline, Melissa S., Clawson, Hiram, Barber, Galt P., Haussler, David, and Kent, James W.

Published
2013
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24. ENCODE Data in the UCSC Genome Browser: year 5 update

Author

Rosenbloom, Kate R., Sloan, Cricket A., Malladi, Venkat S., Dreszer, Timothy R., Learned, Katrina, Kirkup, Vanessa M., Wong, Matthew C., Maddren, Morgan, Fang, Ruihua, Heitner, Steven G., Lee, Brian T., Barber, Galt P., Harte, Rachel A., Diekhans, Mark, Long, Jeffrey C., Wilder, Steven P., Zweig, Ann S., Karolchik, Donna, Kuhn, Robert M., Haussler, David, and Kent, James W.

Published
2013
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25. The UCSC Genome Browser database: extensions and updates 2011

Author

Dreszer, Timothy R., Karolchik, Donna, Zweig, Ann S., Hinrichs, Angie S., Raney, Brian J., Kuhn, Robert M., Meyer, Laurence R., Wong, Mathew, Sloan, Cricket A., Rosenbloom, Kate R., Roe, Greg, Rhead, Brooke, Pohl, Andy, Malladi, Venkat S., Li, Chin H., Learned, Katrina, Kirkup, Vanessa, Hsu, Fan, Harte, Rachel A., Guruvadoo, Luvina, Goldman, Mary, Giardine, Belinda M., Fujita, Pauline A., Diekhans, Mark, Cline, Melissa S., Clawson, Hiram, Barber, Galt P., Haussler, David, and James Kent, W.

Published
2012
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26. ENCODE whole-genome data in the UCSC Genome Browser: update 2012

Author

Rosenbloom, Kate R., Dreszer, Timothy R., Long, Jeffrey C., Malladi, Venkat S., Sloan, Cricket A., Raney, Brian J., Cline, Melissa S., Karolchik, Donna, Barber, Galt P., Clawson, Hiram, Diekhans, Mark, Fujita, Pauline A., Goldman, Mary, Gravell, Robert C., Harte, Rachel A., Hinrichs, Angie S., Kirkup, Vanessa M., Kuhn, Robert M., Learned, Katrina, Maddren, Morgan, Meyer, Laurence R., Pohl, Andy, Rhead, Brooke, Wong, Matthew C., Zweig, Ann S., Haussler, David, and Kent, W. James

Published
2012
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27. The UCSC Genome Browser database: update 2011

Author

Fujita, Pauline A., Rhead, Brooke, Zweig, Ann S., Hinrichs, Angie S., Karolchik, Donna, Cline, Melissa S., Goldman, Mary, Barber, Galt P., Clawson, Hiram, Coelho, Antonio, Diekhans, Mark, Dreszer, Timothy R., Giardine, Belinda M., Harte, Rachel A., Hillman-Jackson, Jennifer, Hsu, Fan, Kirkup, Vanessa, Kuhn, Robert M., Learned, Katrina, Li, Chin H., Meyer, Laurence R., Pohl, Andy, Raney, Brian J., Rosenbloom, Kate R., Smith, Kayla E., Haussler, David, and Kent, W. James

Published
2011
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28. ENCODE whole-genome data in the UCSC genome browser (2011 update)

Author

Raney, Brian J., Cline, Melissa S., Rosenbloom, Kate R., Dreszer, Timothy R., Learned, Katrina, Barber, Galt P., Meyer, Laurence R., Sloan, Cricket A., Malladi, Venkat S., Roskin, Krishna M., Suh, Bernard B., Hinrichs, Angie S., Clawson, Hiram, Zweig, Ann S., Kirkup, Vanessa, Fujita, Pauline A., Rhead, Brooke, Smith, Kayla E., Pohl, Andy, Kuhn, Robert M., Karolchik, Donna, Haussler, David, and Kent, W. James

Published
2011
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31. Abstract 5464: Determining accuracy of RNA sequencing data for gene expression profiling of single samples

Author

Beale, Holly C., primary, Roger, Jacquelyn M., additional, Cattle, Matthew A., additional, McKay, Liam T., additional, Learned, Katrina, additional, Lyle, Geoff, additional, Kephart, Ellen T., additional, Currie, Rob, additional, Lam, Du Linh, additional, Sanders, Lauren, additional, Pfeil, Jacob, additional, Vivian, John, additional, Bjork, Isabel, additional, Salama, Sofie R., additional, Haussler, David, additional, and Vaske, Olena M., additional

Published
2020
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32. Abstract 6154: H3K27M gliomas are characterized by a stall in the epithelial-mesenchymal transition

Author

CHENEY, ALLISON R., primary, Sanders, Lauren M., additional, Seninge, Lucas, additional, Beale, Holly C., additional, Kephart, Ellen Towle, additional, Pfeil, Jacob, additional, Learned, Katrina, additional, Lyle, A. Geoffrey, additional, Bjork, Isabel, additional, Haussler, David, additional, Salama, Sofie R., additional, and Vaske, Olena M., additional

Published
2020
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33. Abstract A44: Comparative gene expression analysis for identification and prioritization of therapeutic targets in a cohort of childhood cancers

Author

Sanders, Lauren M., primary, Lyle, A. Geoffrey, additional, Beale, Holly C., additional, Kephart, Ellen Towle, additional, Learned, Katrina, additional, Peralez, Jennifer, additional, Lacayo, Norman, additional, Rangaswami, Arun, additional, Spunt, Sheri L., additional, Bjork, Isabel, additional, Haussler, David, additional, Salama, Sofie R., additional, and Vaske, Olena M., additional

Published
2020
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34. Abstract B06: Candidate differentiation stall in epithelial mesenchymal transition in H3K27M diffuse midline glioma

Author

Cheney, Allison R., primary, Sanders, Lauren M., additional, Seninge, Lucas, additional, Beale, Holly C., additional, Kephart, Ellen Towle, additional, Pfeil, Jacob, additional, Learned, Katrina, additional, Lyle, A. Geoffrey, additional, Bjork, Isabel, additional, Haussler, David, additional, Salama, Sofie R., additional, and Vaske, Olena M., additional

Published
2020
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35. ENCODE whole-genome data in the UCSC Genome Browser

Author

Rosenbloom, Kate R., Dreszer, Timothy R., Pheasant, Michael, Barber, Galt P., Meyer, Laurence R., Pohl, Andy, Raney, Brian J., Wang, Ting, Hinrichs, Angie S., Zweig, Ann S., Fujita, Pauline A., Learned, Katrina, Rhead, Brooke, Smith, Kayla E., Kuhn, Robert M., Karolchik, Donna, Haussler, David, and Kent, W. James

Published
2010
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36. The UCSC Genome Browser database: update 2010

Author

Rhead, Brooke, Karolchik, Donna, Kuhn, Robert M., Hinrichs, Angie S., Zweig, Ann S., Fujita, Pauline A., Diekhans, Mark, Smith, Kayla E., Rosenbloom, Kate R., Raney, Brian J., Pohl, Andy, Pheasant, Michael, Meyer, Laurence R., Learned, Katrina, Hsu, Fan, Hillman-Jackson, Jennifer, Harte, Rachel A., Giardine, Belinda, Dreszer, Timothy R., Clawson, Hiram, Barber, Galt P., Haussler, David, and Kent, W. James

Published
2010
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37. Framework for determining accuracy of RNA sequencing data for gene expression profiling of single samples

Author

Beale, Holly C., Roger, Jacquelyn M., Cattle, Matthew A., McKay, Liam T., Learned, Katrina, Lyle, A. Geoffrey, Kephart, Ellen T., Currie, Rob, Lam, Du Linh, Sanders, Lauren, Pfeil, Jacob, Vivian, John, Bjork, Isabel, Salama, Sofie R., Haussler, David, and Vaske, Olena M.

Abstract

Background The clinical value of identifying aberrant gene expression in tumors is becoming increasingly evident. In order for multi-gene expression analysis to achieve wider adoption and eventually be developed as a Clinical Laboratory Improvement Amendments (CLIA)-approved test, the input sample requirements, sensitivity, specificity and reference ranges must be quantified. Methods We analyzed paired-end Illumina RNA sequencing (RNA-Seq) data from 1088 tumor samples from 29 projects. We categorized reads based on where and how well they map to the genome, as well as their PCR duplicate status. We subsampled 5 deeply sequenced samples, identified exceptionally highly expressed genes and samples with similar gene expression profiles. Results We addressed variability in RNA-Seq dataset composition by defining reference ranges for four types of reads found in sequencing data: unmapped (0-13%); mapped duplicate (2-66%); mapped non exonic (0-26%) and mapped, exonic, non-duplicate (MEND, 27-76%). With 20 million MEND reads, we detected over-expressed genes (“up-outlier” genes) with a median sensitivity of 96.1% and specificity of 99.8%; sample similarity had 96.6% sensitivity and 100.0% specificity. Conclusions This strategy for measuring RNA-Seq data content and identifying thresholds could be applied to a clinical test of a single sample, specifying minimum inputs and defining the sensitivity and specificity. We estimate that a sample sequenced to the depth of 70 million total reads will typically have sufficient data for accurate gene expression analysis.

Published
2019
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38. Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor.

Author

Sanders, Lauren, Sanders, Lauren, Rangaswami, Arun, Bjork, Isabel, Lam, Du, Beale, Holly, Kephart, Ellen, Durbin, Ann, Learned, Katrina, Currie, Rob, Lyle, A, Pfeil, Jacob, Shah, Avanthi, Lee, Alex, Leung, Stanley, Behroozfard, Inge, Breese, Marcus, Peralez, Jennifer, Hazard, Florette, Lacayo, Norman, Spunt, Sheri, Salama, Sofie, Sweet-Cordero, E, Vaske, Olena, Haussler, David, Sanders, Lauren, Sanders, Lauren, Rangaswami, Arun, Bjork, Isabel, Lam, Du, Beale, Holly, Kephart, Ellen, Durbin, Ann, Learned, Katrina, Currie, Rob, Lyle, A, Pfeil, Jacob, Shah, Avanthi, Lee, Alex, Leung, Stanley, Behroozfard, Inge, Breese, Marcus, Peralez, Jennifer, Hazard, Florette, Lacayo, Norman, Spunt, Sheri, Salama, Sofie, Sweet-Cordero, E, Vaske, Olena, and Haussler, David

Abstract

Gliomatosis peritonei is a rare pathologic finding that is associated with ovarian teratomas and malignant mixed germ cell tumors. The occurrence of gliomatosis as a mature glial implant can impart an improved prognosis to patients with immature ovarian teratoma, making prompt and accurate diagnosis important. We describe a case of recurrent immature teratoma in a 10-yr-old female patient, in which comparative analysis of the RNA sequencing gene expression data from the patients tumor was used effectively to aid in the diagnosis of gliomatosis peritonei.

Published
2019

39. An encyclopedia of mouse DNA elements (Mouse ENCODE)

Author

Stamatoyannopoulos, John A, Snyder, Michael, Hardison, Ross, Ren, Bing, Gingeras, Thomas, Gilbert, David M, Groudine, Mark, Bender, Michael, Kaul, Rajinder, Canfield, Theresa, Giste, Erica, Johnson, Audra, Zhang, Mia, Balasundaram, Gayathri, Byron, Rachel, Roach, Vaughan, Sabo, Peter J, Sandstrom, Richard, Stehling, A Sandra, Thurman, Robert E, Weissman, Sherman M, Cayting, Philip, Hariharan, Manoj, Lian, Jin, Cheng, Yong, Landt, Stephen G, Ma, Zhihai, Wold, Barbara J, Dekker, Job, Crawford, Gregory E, Keller, Cheryl A, Wu, Weisheng, Morrissey, Christopher, Kumar, Swathi A, Mishra, Tejaswini, Jain, Deepti, Byrska-Bishop, Marta, Blankenberg, Daniel, Lajoie, Bryan R, Jain, Gaurav, Sanyal, Amartya, Chen, Kaun-Bei, Denas, Olgert, Taylor, James, Blobel, Gerd A, Weiss, Mitchell J, Pimkin, Max, Deng, Wulan, Marinov, Georgi K, Williams, Brian A, Fisher-Aylor, Katherine I, Desalvo, Gilberto, Kiralusha, Anthony, Trout, Diane, Amrhein, Henry, Mortazavi, Ali, Edsall, Lee, McCleary, David, Kuan, Samantha, Shen, Yin, Yue, Feng, Ye, Zhen, Davis, Carrie A, Zaleski, Chris, Jha, Sonali, Xue, Chenghai, Dobin, Alex, Lin, Wei, Fastuca, Meagan, Wang, Huaien, Guigo, Roderic, Djebali, Sarah, Lagarde, Julien, Ryba, Tyrone, Sasaki, Takayo, Malladi, Venkat S, Cline, Melissa S, Kirkup, Vanessa M, Learned, Katrina, Rosenbloom, Kate R, Kent, W James, Feingold, Elise A, Good, Peter J, Pazin, Michael, Lowdon, Rebecca F, and Adams, Leslie B

Published
2012
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40. Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer

Author

Vaske, Olena M., primary, Bjork, Isabel, additional, Salama, Sofie R., additional, Beale, Holly, additional, Tayi Shah, Avanthi, additional, Sanders, Lauren, additional, Pfeil, Jacob, additional, Lam, Du L., additional, Learned, Katrina, additional, Durbin, Ann, additional, Kephart, Ellen T., additional, Currie, Rob, additional, Newton, Yulia, additional, Swatloski, Teresa, additional, McColl, Duncan, additional, Vivian, John, additional, Zhu, Jingchun, additional, Lee, Alex G., additional, Leung, Stanley G., additional, Spillinger, Aviv, additional, Liu, Heng-Yi, additional, Liang, Winnie S., additional, Byron, Sara A., additional, Berens, Michael E., additional, Resnick, Adam C., additional, Lacayo, Norman, additional, Spunt, Sheri L., additional, Rangaswami, Arun, additional, Huynh, Van, additional, Torno, Lilibeth, additional, Plant, Ashley, additional, Kirov, Ivan, additional, Zabokrtsky, Keri B., additional, Rassekh, S. Rod, additional, Deyell, Rebecca J., additional, Laskin, Janessa, additional, Marra, Marco A., additional, Sender, Leonard S., additional, Mueller, Sabine, additional, Sweet-Cordero, E. Alejandro, additional, Goldstein, Theodore C., additional, and Haussler, David, additional

Published
2019
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41. Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor

Author

Sanders, Lauren M., primary, Rangaswami, Arun, additional, Bjork, Isabel, additional, Lam, Du Linh, additional, Beale, Holly C., additional, Kephart, Ellen Towle, additional, Durbin, Ann, additional, Learned, Katrina, additional, Currie, Rob, additional, Lyle, A. Geoffrey, additional, Pfeil, Jacob, additional, Shah, Avanthi Tayi, additional, Lee, Alex G., additional, Leung, Stanley G., additional, Behroozfard, Inge H., additional, Breese, Marcus R., additional, Peralez, Jennifer, additional, Hazard, Florette K., additional, Lacayo, Norman, additional, Spunt, Sheri L., additional, Haussler, David, additional, Salama, Sofie R., additional, Sweet-Cordero, E. Alejandro, additional, and Vaske, Olena M., additional

Published
2019
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42. The case for using Mapped Exonic Non-Duplicate (MEND) read counts in RNA-Seq experiments: examples from pediatric cancer datasets

Author

Beale, Holly C., primary, Roger, Jacquelyn M., additional, Cattle, Matthew A., additional, McKay, Liam T., additional, Thomson, Drew K. A., additional, Learned, Katrina, additional, Lyle, A. Geoffrey, additional, Kephart, Ellen T., additional, Currie, Rob, additional, Lam, Du Linh, additional, Sanders, Lauren, additional, Pfeil, Jacob, additional, Vivian, John, additional, Bjork, Isabel, additional, Salama, Sofie R., additional, Haussler, David, additional, and Vaske, Olena M., additional

Published
2019
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43. GENE-11. SHARED LONG NON-CODING RNA DYSREGULATION IN HISTONE H3 K27M GLIOMAS AND PF-A EPENDYMOMAS

Author

Sanders, Lauren, primary, Cheney, Allison, additional, Field, Andrew, additional, Beale, Holly, additional, Kephart, Ellen, additional, Learned, Katrina, additional, Bjork, Isabel, additional, Durbin, Ann, additional, Lyle, Geoff, additional, Pfeil, Jacob, additional, Salama, Sofie, additional, Haussler, David, additional, and Vaske, Olena, additional

Published
2019
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44. DIPG-07. GENOMIC ANALYSIS METHODS FOR IDENTIFICATION OF CANCER DRIVER PATHWAYS IN CHILDHOOD BRAIN TUMORS

Author

Sanders, Lauren, primary, Rose-Dey, Brittany, additional, Beale, Holly, additional, Pfeil, Jacob, additional, Kephart, Ellen, additional, Learned, Katrina, additional, Durbin, Ann, additional, Bjork, Isabel, additional, Currie, Rob, additional, Morozova, Olena, additional, Agnihotri, Sameer, additional, Salama, Sofie, additional, and Haussler, David, additional

Published
2018
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45. Abstract LB-338: A critical evaluation of genomic data sharing: Barriers to accessing pediatric cancer genomic datasets: a Treehouse Childhood Cancer Initiative experience

Author

Learned, Katrina, primary, Durbin, Ann, additional, Currie, Robert, additional, Beale, Holly, additional, Lam, Du Linh, additional, Goldstein, Theodore, additional, Salama, Sofie R., additional, Haussler, David, additional, Morozova, Olena, additional, and Bjork, Isabel, additional

Published
2017
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46. The UCSC Genome Browser database: 2016 update.

Author

Speir, Matthew, Speir, Matthew, Zweig, Ann, Rosenbloom, Kate, Raney, Brian, Paten, Benedict, Nejad, Parisa, Lee, Brian, Learned, Katrina, Karolchik, Donna, Hinrichs, Angie, Heitner, Steve, Harte, Rachel, Guruvadoo, Luvina, Fujita, Pauline, Eisenhart, Christopher, Diekhans, Mark, Clawson, Hiram, Casper, Jonathan, Barber, Galt, Kuhn, Robert, Kent, W, Haussler, David, Haeussler, Maximilian, Speir, Matthew, Speir, Matthew, Zweig, Ann, Rosenbloom, Kate, Raney, Brian, Paten, Benedict, Nejad, Parisa, Lee, Brian, Learned, Katrina, Karolchik, Donna, Hinrichs, Angie, Heitner, Steve, Harte, Rachel, Guruvadoo, Luvina, Fujita, Pauline, Eisenhart, Christopher, Diekhans, Mark, Clawson, Hiram, Casper, Jonathan, Barber, Galt, Kuhn, Robert, Kent, W, Haussler, David, and Haeussler, Maximilian

Abstract

For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently. Some release highlights of this year include new and updated genome browsers for various assemblies, including bonobo and zebrafish; new gene annotation sets; improvements to track and assembly hub support; and a new interactive tool, the Data Integrator, for intersecting data from multiple tracks. We have greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include updated gene prediction sets from GENCODE, more phenotype- and disease-associated variants from ClinVar and ClinGen, more genomic regulatory data, and a new multiple genome alignment.

Published
2016

47. The UCSC Genome Browser database: 2016 update

Author

Speir, Matthew L., primary, Zweig, Ann S., additional, Rosenbloom, Kate R., additional, Raney, Brian J., additional, Paten, Benedict, additional, Nejad, Parisa, additional, Lee, Brian T., additional, Learned, Katrina, additional, Karolchik, Donna, additional, Hinrichs, Angie S., additional, Heitner, Steve, additional, Harte, Rachel A., additional, Haeussler, Maximilian, additional, Guruvadoo, Luvina, additional, Fujita, Pauline A., additional, Eisenhart, Christopher, additional, Diekhans, Mark, additional, Clawson, Hiram, additional, Casper, Jonathan, additional, Barber, Galt P., additional, Haussler, David, additional, Kuhn, Robert M., additional, and Kent, W. James, additional

Published
2015
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50. The UCSC Genome Browser database: 2015 update

Author

Rosenbloom, Kate R., primary, Armstrong, Joel, additional, Barber, Galt P., additional, Casper, Jonathan, additional, Clawson, Hiram, additional, Diekhans, Mark, additional, Dreszer, Timothy R., additional, Fujita, Pauline A., additional, Guruvadoo, Luvina, additional, Haeussler, Maximilian, additional, Harte, Rachel A., additional, Heitner, Steve, additional, Hickey, Glenn, additional, Hinrichs, Angie S., additional, Hubley, Robert, additional, Karolchik, Donna, additional, Learned, Katrina, additional, Lee, Brian T., additional, Li, Chin H., additional, Miga, Karen H., additional, Nguyen, Ngan, additional, Paten, Benedict, additional, Raney, Brian J., additional, Smit, Arian F. A., additional, Speir, Matthew L., additional, Zweig, Ann S., additional, Haussler, David, additional, Kuhn, Robert M., additional, and Kent, W. James, additional

Published
2014
Full Text
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