The Cancer Genome Atlas

Tools & Applications

• Broad Institute FireCloud by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• ISB Cancer Genomics Cloud by Institute for Systems Biology
  
• TCGA Cancers Selected for Study by National Cancer Institute
  
• Using TCGA Data, Resources, and Materials by National Cancer Institute
  

Publications

• "Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons" by Galen F. Gao, Joel S. Parker, et al.
  
• A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples by Han Chen, Chunyan Li, et al.
  
• An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics by Jianfang Liu, Tara Lichtenberg, et al.
  
• Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer by Katherine A. Hoadley, Christina Yau, et al.
  
• Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas by Yang Liu, Nilay S. Sethi, et al.
  
• Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients by André Kahles, Kjong-Van Lehmann, et al.
  
• Comprehensive Characterization of Cancer Driver Genes and Mutations by Matthew H. Bailey, Collin Tokheim, et al.
  
• Genomic and Functional Approaches to Understanding Cancer Aneuploidy by Alison M. Taylor, Juliann Shih, et al.
  
• Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas by Theo A. Knijnenburg, Linghua Wang, et al.
  
• Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas by Joshua D. Campbell, Christina Yau, et al.
  
• Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types by Zhongqi Ge, Jake S. Leighton, et al.
  
• Machine Learning Detects Pan-Cancer Ras Pathway Activation in The Cancer Genome Atlas by Gregory P. Way, Francisco Sanchez-Vega, et al.
  
• Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation by Tathiane M. Malta, Artem Sokolov, et al.
  
• Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers by Xinxin Peng, Zhongyuan Chen, et al.
  
• Oncogenic Signaling Pathways in The Cancer Genome Atlas by Francisco Sanchez-Vega, Marco Mina, et al.
  
• Pan-Cancer Alterations of the MYC Oncogene and its Proximal Network Across The Cancer Genome Atlas by Franz X. Schaub, Varsha Dhankani, et al.
  
• Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context by Hua-Sheng Chiu, Sonal Somvanshi, et al.
  
• Pathogenic Germline Variants in 10,389 Adult Cancers by Kuan-lin Huang, R. Jay Mashl, et al.
  
• Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines by Kyle Ellrott, Matthew H. Bailey, et al.
  
• Spatial Organization And Molecular Correlation Of Tumor-Infiltrating Lymphocytes Using Deep Learning On Pathology Images by Joel Saltz, Rajarsi Gupta, et al.
  
• The chromatin accessibility landscape of primary human cancers by M. Ryan Corces, Jeffrey M. Granja, et al.
  
• The Immune Landscape of Cancer by Vésteinn Thorsson, David L. Gibbs, et al.
  

Therapeutically Applicable Research to Generate Effective Treatments (TARGET)

Tools & Applications

• Broad Institute FireCloud by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• ISB Cancer Genomics Cloud by Institute for Systems Biology
  
• TARGET data matrix by National Cancer Institute
  

Publications

• A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor by Gadd S, Huff V, Walz AL, et al.
  
• Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia by Yang JJ, Cheng C, Devidas M, et al.
  
• Biomarker significance of plasma and tumor miR-21, miR-221, and miR-106a in osteosarcoma by Nakka M, Allen-Rhoades W, Li Y, et al.
  
• CSF3R mutations have a high degree of overlap with CEBPA mutations in pediatric AM by Maxson JE, Ries RE, Wang YC, et al.
  
• Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism by Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD, Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, et al.
  
• Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways by Chun HJ, Lim EL, Heravi-Moussavi A, et al.
  
• Genomic classification and identification of the cell of origin of pediatric mixed phenotype acute leukemia by Thomas B. Alexander, Zhaohui Gu, Ilaria Iacobucci, et al.
  
• Genomics in childhood acute myeloid leukemia comes of age by Brunner AM, Graubert TA.
  
• Identification and analyses of extra-cranial and cranial rhabdoid tumor molecular subgroups reveal tumors with cytotoxic T cell infiltration by Hye-Jung E. Chun, Pascal D. Johann, Katy Milne et al.
  
• MicroRNA Expression-Based Model Indicates Event-Free Survival in Pediatric Acute Myeloid Leukemia by Lim EL, Trinh DL, Ries RE, et al.
  
• MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours by Perlman EJ, Gadd S, Arold ST, et al.
  
• Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors by Walz AL, Ooms A, Gadd S, et al.
  
• Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations by Eleveld TF, Oldridge DA, Bernard V, Koster J, et al.
  
• Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group by Ooms AH, Gadd S, Gerhard DS, et al.
  
• TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney by Gooskens SL, Gadd S, Guidry Auvil JM, et al.
  
• The genetic landscape of high-risk neuroblastoma by Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, et al.
  
• The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia by Yu Liu, John Easton, Ying Shao, et al.
  
• The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions by Bolouri H, Farrar JE, Triche T Jr, et al.
  

Gabriella Miller Kids First Pediatric Research Program (Kids First)

Tools & Applications

• CAVATICA by Seven Bridges Genomics
  
• Kids First DRC Portal by Kids First DRC
  
• Kids First DRC Source Code by Kids First DRC
  
• PedcBioPortal by cBioPortal
  

Publications

• Clinically Relevant and Minimally Invasive Tumor Surveillance of Pediatric Diffuse Midline Gliomas Using Patient-Derived Liquid Biopsy by Eshini Panditharatna, Lindsay B Kilburn, et al.
  
• Decreased ACKR3 (CXCR7) function causes oculomotor synkinesis in mice and humans. by Mary C Whitman, Noriko Miyake, et al.
  
• Deleterious de novo variants of X-linked ZC4H2 in females cause a variable phenotype with neurogenic arthrogryposis multiplex congenita. by Suzanna G M Frints, Friederike Hennig, et al.
  
• Development and Clinical Validation of a Large Fusion Gene Panel for Pediatric Cancers. by Fengqi Chang, Fumin Lin, et al.
  
• Elucidation of de novo small insertion/deletion biology with parent-of-origin phasing. by Allison H Seiden, Felix Richter, et al.
  
• Genome-Wide Association Study Identifies a Susceptibility Locus for Comitant Esotropia and Suggests a Parent-of-Origin Effect by Sherin Shaaban, Sarah MacKinnon et al.
  
• Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. by Madison R Bishop, Kimberly K Diaz Perez, et al.
  
• Genomic Analyses Implicate Noncoding De Novo Variants in Congenital Heart Disease. by Felix Richter, Sarah U Morton, et al.
  
• Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma. by Laura Egolf, Zalman Vaksman, et al.
  
• Germline microsatellite genotypes differentiate children with medulloblastoma. by Samuel Rivero-Hinojosa, Nicholas Kinney, et al.
  
• MACF1 Mutations Encoding Highly Conserved Zinc-Binding Residues of the GAR Domain Cause Defects in Neuronal Migration and Axon Guidance by William B Dobyns, Kimberly A Aldinger, et al.
  
• MAGEL2-Related Disorders: A study and case series. by Jameson Patak, James Gilfert, et al.
  
• Phenotype delineation of ZNF462 related syndrome. by Paul Kruszka, Tommy Hu, et al.
  
• The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. by Deanne M Taylor, Bruce J Aronow, et al.
  
• Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21. by Nandita Mukhopadhyay, Madison Bishop, et al.
  

Cell Painting Gallery

Tutorials

• Cell Painting wiki by Multiple Authors
  
• Center for Open Bioimage Analysis (COBA) YouTube Channel - video tutorials of CellProfiler and other softwares by Multiple Authors
  
• Image-based Profiling Handbook - for processing image-based profiling datasets using CellProfiler and pycytominer by Multiple Authors
  
• Image-based profiling introductory exercise - data and an exercise on exploring image-based profiles, including understanding the various data levels by Beth Cimini
  
• Scientific Community Image Forum - for software-oriented aspects of scientific imaging including analysis, processing, and acquisition by Multiple Authors
  

Tools & Applications

• Accelerating Drug Discovery with high-throughput Cell Painting on AWS by Chris Kaspar
  
• Deep Profiler - Morphological profiling using deep learning by Multiple Authors
  
• Distributed CellProfiler - Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure by Multiple Authors
  
• Image-based Profiling Recipe by Multiple Authors
  
• Pycytominer - Data processing functions for profiling perturbations by Multiple Authors
  

Publications

• A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay by Bray M-A, Gustafsdottir SM, Rohban MH, Singh S, Ljosa V, Sokolnicki KL, Bittker JA, Bodycombe NE, Dancik V, Hasaka TP, Hon CS, Kemp MM, Li K, Walpita D, Wawer MJ, Golub TR, Schreiber SL, Clemons PA, Shamji AF, & Carpenter AE
  
• Cell Painting predicts impact of lung cancer variants by Caicedo JC, Arevalo J, Piccioni F, Bray MA, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, & Singh S
  
• Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes by Bray M-A, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, & Carpenter AE
  
• Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects by Singh S, Wu X, Ljosa V, Bray M-A, Piccioni F, Root DE, Doench JG, Boehm JS, & Carpenter AE
  
• Multiplex Cytological Profiling Assay to Measure Diverse Cellular States by Gustafsdottir SM, Ljosa V, Sokolnicki KL, Wilson JA, Walpita D, Kemp MM, Seiler KP, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, and Shamji AF
  
• Systematic morphological profiling of human gene and allele function via Cell Painting by Rohban MH, Singh S, Wu X, Berthet JB, Bray M-A, Shrestha Y, Varelas X, Boehm JS, & Carpenter AE
  
• Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling by Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, BodycombeNE, Marton MA, Sokolnicki KL, Bray M-A, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CSK, Duvall JR, Wilson JA, Bittker JA, Dancik V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, & Clemons PA
  

Cancer Cell Line Encyclopedia (CCLE)

Tools & Applications

• Broad Institute Cancer Cell Line Encyclopedia by The Broad Institute of MIT & Harvard
  
• Cancer Genomics Cloud by Seven Bridges
  
• Genomic Data Commons by National Cancer Institute
  
• ISB CGC BigQuery tables by Institute for Systems Biology
  

Publications

• Next-generation characterization of the Cancer Cell Line Encyclopedia by Ghandi, M., Huang F. et al.
  
• Pharmacogenomic agreement between two cancer cell line data sets by The Cancer Cell Line Encyclopedia Consortium & The Genomics of Drug Sensitivity in Cancer Consortium
  
• The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity by Barretina Caponigro Stransky et al.
  
• The landscape of cancer cell line metabolism by Li, H. et al.
  

CIViC (Clinical Interpretation of Variants in Cancer)

Tutorials

• Introduction to Clinical Interpretation of Somatic Cancer Variants by The Griffith Lab
  

Tools & Applications

• CIViCpy - an analysis toolkit and SDK for extracting and analyzing knowledge from the CIViC knowledgebase by The CIViCpy Team
  

Publications

• A community approach to the cancer-variant-interpretation bottleneck by Kilannin Krysiak et al.
  
• CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer by Malachi Griffith et al.
  
• CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase by Kilannin Krysiak et al.
  
• CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase by Alex H Wagner et al.
  
• Standard operating procedure for curation and clinical interpretation of variants in cancer by Arpad M Danos et al.
  

Clinical Proteomic Tumor Analysis Consortium 2 (CPTAC-2)

Tools & Applications

• Cancer Genomics Cloud by Seven Bridges
  
• CPTAC Data Portal by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• Proteomic Data Commons by National Cancer Institute
  

Publications

• Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer by Hui Zhang, Tao Liu, Zhen Zhang, Samuel H. Payne, Bai Zhang, Jason E. McDermott, Jian-Ying Zhou, Vladislav A. Petyuk, Li Chen, Debjit Ray, Shisheng Sun, Feng Yang, Lijun Chen, Jing Wang, Punit Shah, Seong Won Cha, Paul Aiyetan, Sunghee Woo, Yuan Tian, Marina A. Gritsenko, Therese R. Clauss, Caitlin Choi, Matthew E. Monroe, Stefani Thomas, Song Nie, Chaochao Wu, Ronald J. Moore, Kun-Hsing Yu, David L. Tabb, David Fenyö, Vineet Bafna, Yue Wang, Henry Rodriguez, Emily S. Boja, Tara Hiltke, Robert C. Rivers, Lori Sokoll, Heng Zhu, Ie-Ming Shih, Leslie Cope, Akhilesh Pandey, Bing Zhang, Michael P. Snyder, Douglas A. Levine, Richard D. Smith, Daniel W. Chan, Karin D. Rodland, the CPTAC Investigators
  
• Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities by Suhas Vasaikar, Chen Huang, Xiaojing Wang. Vladislav A. Petyuk, Sara R. Savage, Bo Wen, Yongchao Dou, Yun Zhang, Zhiao Shi, Osama A. Arshad, Marina A. Gritsenko, Lisa J. Zimmerman, Jason E. McDermott, Therese R. Clauss, Ronald J. Moore, Rui Zhao, Matthew E. Monroe, Yi-Ting Wang, Matthew C. Chambers, Robbert J.C. Slebos, Ken S. Lau, Qianxing Mo, Li Ding, Matthew Ellis, Mathangi Thiagarajan, Christopher R. Kinsinger, Henry Rodriguez, Richard D. Smith, Karin D. Rodland, Daniel C. Liebler, Tao Liu, Bing Zhang, Clinical Proteomic Tumor Analysis Consortium
  
• Proteomic analysis of colon and rectal carcinoma using standard and customized databases by Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC
  

ICGC on AWS

Tutorials

• AWS Pancancer Workflow Launcher by Solomon Shorser
  

Publications

• Analyses of non-coding somatic drivers in 2,693 cancer whole genomes by Rheinbay et al (2020)
  
• Genomic basis of RNA alterations in cancer by PCAWG Transcriptome Core Group et al. (2020)
  
• Pan-cancer analysis of whole genomes by The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020)
  
• Patterns of somatic structural variation in human cancer genomes by Li et al. (2020)
  
• The evolutionary history of 2,658 cancers by Gerstung et al (2020)
  
• The repertoire of mutational signatures in human cancer by Alexandrov et al (2020)
  

Clinical Proteomic Tumor Analysis Consortium 3 (CPTAC-3)

Tools & Applications

• Cancer Genomics Cloud by Seven Bridges
  
• CPTAC Data Portal by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  
• Proteomic Data Commons by National Cancer Institute
  

Publications

• Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics by Clark DJ, Hu Y, Bocik W, Chen L, Schnaubelt M, Roberts R, Shah P, Whiteley G, Zhang H
  
• Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma by Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L1, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geizler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H; Clinical Proteomic Tumor Analysis Consortium
  

CAncer MEtastases in LYmph nOdes challeNge (CAMELYON) Dataset

Tools & Applications

• ASAP Viewer by Geert Litjens
  
• CAMELYON Challenge by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

Publications

• 1399 H&E-stained sentinel lymph node sections of breast cancer patients: the CAMELYON dataset by Geert Litjens, et al.
  
• Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer by Babak Ehteshami Bejnordi, et al.
  
• From Detection of Individual Metastases to Classification of Lymph Node Status at the Patient Level: The CAMELYON17 Challenge by Peter Bandi, et al.
  

CoMMpass from the Multiple Myeloma Research Foundation

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• "Identification of Initiating Trunk Mutations and Distinct Molecular Subtypes: An Interim Analysis of the Mmrf Commpass Study" by Jonathan J Keats, PhD, Gil Speyer, Legendre Christophe, Christofferson Austin, Kristi Stephenson, BS, Ahmet Kurdoglu, Megan Russell, Aldrich Jessica, Cuyugan Lori, Jonathan Adkins, Jackie McDonald, Adrienne Helland, Alex Blanski, Meghan Hodges, Dan Rohrer, Sundar Jagannath, MD, David Siegel, MD PhD, Ravi Vij, MD MBA, Gregory Orloff, MD, Todd Zimmerman, MD, Ruben Niesvizky, MD, Darla Liles, MD, Joseph W. Fay, Jeffrey L. Wolf, MD PhD, Robert M. Rifkin, Norma C Gutierrez, The MMRF CoMMpass Network, Jen Toups, Mary Derome, MS, Winnie Liang, PhD, Seunchan Kim, Daniel Auclair, PhD, Pamela G. Kidd, MD, Scott Jewell, PhD, John David Carpten, PhD, Sagar Lonial, MD
  
• "Interim Analysis Of The MMRF CoMMpass Trial: a Longitudinal Study In Multiple Myeloma Relating Clinical Outcomes To Genomic and Immunophenotypic Profiles" by Keats JJ, Craig DW, Liang W, Venkata Y, Kurdoglu A, Aldrich J, Auclair D, Allen K, Harrison B, Jewell S, Kidd PG, Correll M, Jagannath S, Siegel DS, Vij R, Orloff G, Zimmerman TM, MMRF CoMMpass Network, Capone W, Carpten J, Lonial S.
  
• "Interim Analysis of the Mmrf Commpass Trial: Identification of Novel Rearrangements Potentially Associated with Disease Initiation and Progression" by Sagar Lonial, MD, Venkata D Yellapantula, Winnie Liang, PhD, Ahmet Kurdoglu, BS, Jessica Aldrich, MSc, Christophe M. Legendre, MD, Kristi Stephenson, Jonathan Adkins, Jackie McDonald, Adrienne Helland, Megan Russell, Austin Christofferson, Lori Cuyugan, Dan Rohrer, Alex Blanski, Meghan Hodges, Mmrf CoMMpass Network, Mary Derome, Daniel Auclair, PhD, Pamela G. Kidd, MD, Scott Jewell, PhD, David Craig, PhD, John Carpten, PhD, Jonathan J. Keats, PhD
  
• "Molecular Predictors of Outcome and Drug Response in Multiple Myeloma: An Interim Analysis of the Mmrf CoMMpass Study" by Jonathan J Keats, PhD, Gil Speyer, Austin Christofferson, Christophe Legendre, PhD, Jessica Aldrich, Megan Russell, Lori Cuyugan, Jonathan Adkins, Alex Blanski, Meghan Hodges, Dan Rohrer, Sundar Jagannath, MD, Ravi Vij, MD, Gregory Orloff, MD, Todd Zimmerman, MD, Ruben Niesvizky, MD, Darla Liles, MD, Joseph W. Fay, Jeffrey L. Wolf, MD, Robert M Rifkin, Norma C Gutierrez, MD PhD, Mmrf CoMMpass Network, Jennifer Yesil, MS, Mary Derome, MS, Seungchan Kim, PhD, Winnie Liang, PhD, Pamela G. Kidd, MD, Scott Jewell, PhD, John David Carpten, PhD, Daniel Auclair, PhD, Sagar Lonial, MD FACP
  

MONKEY

Tools & Applications

• ASAP Viewer by Geert Litjens
  
• MONKEY Challenge by Computational Pathology Group Radboudumc, Nijmegen
  
• MONKEY challenge tutorials by Computational Pathology Group Radboudumc, Nijmegen
  
• Structured description of the MONKEY Challenge by Linda Studer, Dominique van Midden, Fazael Ayatollahi, Jeroen van der Laak
  
• Whole slide data - python package for working with wholeslide images and annotations files by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

Molecular Profiling to Predict Response to Treatment (phs001965)

Tools & Applications

• Childhood Cancer Data Initiative Data Catalog by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  

Publications

• Finding the way to Wilms tumor by comparing the primary and relapse tumor samples by Filippo Spreafico, Sara Ciceri, et al.
  
• Genetic changes associated with relapse in favorable histology Wilms tumor: A Children's Oncology Group AREN03B2 study by Samantha Gadd, Vicki Huff, et al.
  

Allen Ivy Glioblastoma Atlas

Tutorials

• Accessing Ivy Glioblastoma Atlas Project data by Allen Institute for Brain Science
  

Tools & Applications

• Ivy Glioblastoma Atlas Project by Allen Institute for Brain Science
  

Publications

• An anatomic transcriptional atlas of human glioblastoma by Ralph Puchalski, et al.
  

Beat Acute Myeloid Leukemia (AML) 1.0

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Clinical resistance to crenolanib in acute myeloid leukemia due to diverse molecular mechanisms by Zhang H, Savage S, Schultz AR, Bottomly D, White L, Segerdell E, et al.
  
• Functional Genomic Landscape of Acute Myeloid Leukemia by Jeffrey W. Tyner, Cristina E. Tognon, Dan Bottomly et al.
  

Broad Genome References

Tutorials

• Using Amazon FSx for Lustre for Genomics Workflows on AWS by W. Lee Pang
  AWS BatchAmazon FSx

Tools & Applications

• Genomics Workflows on AWS - Cromwell on AWS by W. Lee Pang
  

Publications

• Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA by Willey J. C., Morrison T. B., Austermiller B., Crawford E. E., et al (2021)
  

COBRA

Tools & Applications

• ASAP Viewer by Geert Litjens
  
• COBRA Tools & Labels by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  
• Whole slide data - python package for working with wholeslide images and annotations files by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

Clinical Trial Sequencing Project - Diffuse Large B-Cell Lymphoma

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• A multiprotein supercomplex controlling oncogenic signalling in lymphoma by Phelan JD, Young RM, Webster DE, Roulland S, Wright GW, Kasbekar M, Shaffer AL 3rd, Ceribelli M, Wang JQ, Schmitz R, Nakagawa M, Bachy E, Huang DW, Ji Y, Chen L, Yang Y, Zhao H, Yu X, Xu W, Palisoc MM, Valadez RR, Davies-Hill T, Wilson WH, Chan WC, Jaffe ES, Gascoyne RD, Campo E, Rosenwald A, Ott G, Delabie J, Rimsza LM, Rodriguez FJ, Estephan F, Holdhoff M, Kruhlak MJ, Hewitt SM, Thomas CJ, Pittaluga S, Oellerich T, Staudt LM
  
• Genetics and Pathogenesis of Diffuse Large B Cell Lymphoma by Roland Schmitz, Ph.D., George W. Wright, Ph.D., Da Wei Huang, M.D., Calvin A. Johnson, Ph.D., James D. Phelan, Ph.D., James Q. Wang, Ph.D., Sandrine Roulland, Ph.D., Monica Kasbekar, Ph.D., Ryan M. Young, Ph.D., Arthur L. Shaffer, Ph.D., Daniel J. Hodson, M.D., Ph.D., Wenming Xiao, Ph.D., et al.
  

Exceptional Responders Initiative

Tools & Applications

• GDC Legacy Archive by National Cancer Institute
  
• Genomic Data Commons by National Cancer Institute
  

Publications

• The Exceptional Responders Initiative: Feasibility of a National Cancer Institute Pilot Study by Barbara A. Conley, Lou Staudt, et al.
  

Foundation Medicine Adult Cancer Clinical Dataset (FM-AD)

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer Pathogenesis by Ryan J. Hartmaier, Lee A. Albacker, Juliann Chmielecki, Mark Bailey, Jie He, Michael E. Goldberg, Shakti Ramkissoon, James Suh, Julia A. Elvin, Samuel Chiacchia, Garrett M. Frampton, Jeffrey S. Ross, Vincent Miller, Philip J. Stephens and Doron Lipson
  
• Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity. by Beltran H, Yelensky R, Frampton GM, Park K, Downing SR, MacDonald TY, Jarosz M, Lipson D, Tagawa ST, Nanus DM, Stephens PJ, Mosquera JM, Cronin MT, Rubin MA
  

National Cancer Institute Imaging Data Commons (IDC) Collections

Tutorials

• IDC "Getting started" tutorial series by Imaging Data Commons team
  

Tools & Applications

• IDC Portal by Imaging Data Commons team
  

Publications

• NCI Imaging Data Commons by Fedorov A, Longabaugh W, Pot D, Clunie D, Pieper S, Aerts H, et al.
  

Cancer Genome Characterization Initiatives - Burkitt Lymphoma, HIV+ Cervical Cancer

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma by Grande B. M., Gerhard D. S., Jiang A., Griner N. B., Abramson J. S., Alexander T. B., et al.
  

EMory BrEast Imaging Dataset (EMBED)

Tutorials

• Sample Notebook by Emory-HITI
  

Publications

• The EMory BrEast imaging Dataset (EMBED): A Racially Diverse, Granular Dataset of 3.4M Screening and Diagnostic Mammograms by Jiwoong J. Jeong, Brianna L. Vey, Ananth Reddy, Thomas Kim, Thiago Santos, Ramon Correa, Raman Dutt, Marina Mosunjac, Gabriela Oprea-Ilies, Geoffrey Smith, Minjae Woo, Christopher R. McAdams, Mary S. Newell, Imon Banerjee, Judy Gichoya, Hari Trivedi
  

Genomic Characterization of Metastatic Castration Resistant Prostate Cancer

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genomic characterization of metastatic castration-resistant prostate cancer patients undergoing PSMA radioligand therapy: A single-center experience by Swayamjeet Satapathy, Chandan K Das, et al.
  

Integrative Analysis of Lung Adenocarcinoma in Environment and Genetics Lung cancer Etiology (Phase 2)

Tools & Applications

• EAGLE - Environment And Genetics in Lung cancer Etiology by National Cancer Institute Division of Cancer Epidemiology and Genetics
  
• Genomic Data Commons by National Cancer Institute
  

LEarning biOchemical Prostate cAncer Recurrence from histopathology sliDes challenge (LEOPARD) Dataset

Tools & Applications

• ASAP Viewer by Geert Litjens
  
• LEOPARD Challenge by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

National Cancer Institute Center for Cancer Research - Diffuse Large B Cell Lymphoma (DLBCL) Genomics and Expression

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genetics and Pathogenesis of Diffuse Large B Cell Lymphoma by Roland Schmitz, Ph.D., George W. Wright, Ph.D., Da Wei Huang, M.D., et al.
  

Oregon Health & Science University Chronic Neutrophilic Leukemia Dataset

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Genomic landscape of neutrophilic leukemias of ambiguous diagnosis by Zhang H, Wilmot B, Bottomly D et al.
  

Pancreatic Cancer Organoid Profiling

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

Publications

• Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer by Tiriac H, Belleau P, Engle DD, Plenker D, Deschênes A, Somerville TD, et al.
  

TIGER Training

Tools & Applications

• TIGER Challenge by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  
• Whole slide data - python package for working with wholeslide images and annotations files by Diagnostic Image Analysis Group, Radboudumc, Nijmegen
  

GATK Test Data

Tools & Applications

• Genomics Workflows on AWS - Cromwell on AWS by W. Lee Pang
  

Human Cancer Models Initiative (HCMI) Cancer Model Development Center

Tools & Applications

• Genomic Data Commons by National Cancer Institute
  

NYUMets Brain Dataset

Publications

• Longitudinal deep neural networks for assessing metastatic brain cancer on a massive open benchmark. by Link et al (2023)
  

recount3

Tutorials

• recount3 quick start guide by Leonardo Collado-Torres