The People & Partnerships of the Tisch
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Q&A: Mount Sinai's Andrew Kasarskis on Teaching Students How To
REPRINTED FROM October 25, 2012 Q&A: Mount Sinai’s Andrew Kasarskis on Teaching Students how to Analyze their Own Genomes Name: Andrew Kasarskis The elective course, called “Practical Analysis of Your Per- Age: 39 sonal Genome,” is offered through the Genetics and Genomic Position: Vice chair and associate Sciences training area within Mount Sinai’s Graduate School professor, Department of Genetics of Biological Sciences, and 20 students, including MD and and Genomic Sciences; co-director, PhD students, medical residents, genetic counseling students, Institute for Genomics and Multi- and junior faculty members, were selected to participate. scale Biology, Mount Sinai School of Last week, Clinical Sequencing News met with Andrew Medicine, since 2011 Kasarskis, vice chair of the Department of Genetics and Experience and Education: Genomic Sciences, to talk about the design of the course and Senior director, multiscale biology, what he and his colleagues hope students will take away from Pacific Biosciences, 2010-2011; Head of strategic initiatives, it. Below is an edited version of the conversation. Sage Bionetworks, and affiliate investigator, Fred Hutchinson Cancer Research Center, 2009-2010; Scientific director of How did you select students for this course? genetics and other positions, Rosetta Inpharmatics (owned We had a lot more interest than we had slots — at least a by Merck), 2002-2009; Senior scientist and other positions, factor of five, if you include all the faculty interest — so we DoubleTwist, 2000-2002; Scientific curator, department of had to select. We put in place a few prerequisites, and we had genetics, Stanford University School of Medicine, 1998-2000; PhD a lot of instructor input as to who we were going to select. -
2018 Annual Meeting Trevi Fountain (Fontana Di Trevi), Rome November 14 - 17, 2018 Rome Cavalieri Hotel • Rome, Italy
Connective Tissue Oncology Society 2018 Annual Meeting Trevi Fountain (Fontana di Trevi), Rome November 14 - 17, 2018 Rome Cavalieri Hotel • Rome, Italy Wednesday, 14 November, 2018 12:00 pm - 6:00 pm Registration Salon de Cavalieri 1 & Gallery 6:00 pm - 8:00 pm Welcome Reception San Pietro Gallery Thursday, 15 November, 2018 6:00 am - 7:00 am Registration Salon de Cavalieri 1 & Gallery 7:00 am - 8:00 am Coffee and Posters Salon de Cavalieri 1 & Gallery 8:00 am - 5:30 pm 4th International Sarcoma Nurse and Allied Caravaggio Room Professionals Meeting (iSNAP) - "Collaboration in Sarcoma Care - Realizing Better Outcomes" 9:00 am - 11:00 am – SARC PROGRAM – Salon del Cavalieri 2,3,4 Chawla/Rosenfeld Developmental Therapeutics Symposium Emerging and Novel Biologically Targeted Approaches for Sarcoma Patients Introduction Elizabeth Lawlor, MD, PhD Robert Maki, MD, PhD Enhancing Activity of B7-H3 CAR T Cells for Pediatric Sarcomas Robbie Majzner, MD Discussion / Q & A Translating PARP Inhibition as a TherapeuticSARC Target @ into CTOS Benefit for Patients with Sarcoma November 15, 2018 Sandra Strauss, MD, PhD 9:00 AM - 11:00 AM Rome Cavalieri Hotel Discussion / Q & A Rome, Italy Epigenetic Changes following the Loss of PRC2 in MPNST: Emerging Therapeutic Opportunities Keila Torres, MD, PhD Chawla/Rosenfeld Developmental Therapeutics Symposium Discussion / Q & A 2019 Career DevelopmentEmerging and Update novel biologically targeted approaches for sarcoma patients Elizabeth Lawlor, MD, PhD 9:00 AM Elizabeth Lawlor, MD, PhD Introduction Robert -
We Will Find a Cure Together 2016 Annual Report Table of Contents
WE WILL FIND A CURE TOGETHER 2016 ANNUAL REPORT TABLE OF CONTENTS LETTER FROM THE CO-FOUNDERS 3 WHAT WE DO AND WHY IT MATTERS 5 DTRF-FUNDED RESEARCH 6 FINANCIALS 7 THIRD INTERNATIONAL DTRF DESMOID TUMOR RESEARCH WORKSHOP 9 OUR COMMUNITY 10 ANNUAL SIGNATURE DTRF EVENTS 11 DTRF ANNUAL PATIENT MEETING 12 OUR TEAM 13 A LETTER FROM THE CO-FOUNDERS Dear Friends, Thank you for your interest in our Annual Report as we press forward to find new treatments for desmoid tumors! 2016 has been a year of exciting developments: PRO Tool. We continue our work in developing the first validated Patient Reported Outcome (PRO) tool in desmoid tumors with Dr. Mrinal Gounder of Memorial Sloan Kettering Cancer Center and Quintiles. We have had great success in recruiting patients to aid in this process. This tool, which will provide the framework for collecting data on the patient’s experience with a particular treatment, is intended to facilitate a new regulatory endpoint that can be used in all future clinical trials. It will be a great advancement in the field for researchers worldwide and is intended to facilitate future FDA approval of treatments for desmoid tumors. We anticipate that the PRO will be trial-ready in early 2017. DTRF Desmoid Tumor Patient Registry. We’re also nearing the Jeanne Whiting, President/Co-founder and Marlene finish line of accomplishing our goal of establishing a desmoid Portnoy, Executive Director/Co-founder tumor patient registry. DTRF was fortunate to be one of twenty rare disease organizations selected for a natural history study project initiated by the National Organization of Rare Disorders (NORD), in partnership with the FDA. -
Patientderived Xenografts for Individualized Care in Advanced Sarcoma
Original Article Patient-Derived Xenografts for Individualized Care in Advanced Sarcoma Justin Stebbing, MA, FRCP, FRCPath, PhD1; Keren Paz, PhD2; Gary K. Schwartz, MD3; Leonard H. Wexler, MD3; Robert Maki, MD, PhD4; Raphael E. Pollock, MD, PhD5; Ronnie Morris, MD2; Richard Cohen, MD6; Arjun Shankar, MD6; Glen Blackman, MBBS7; Victoria Harding, MD1; David Vasquez, MD2; Jonathan Krell, MD, PhD1; Daniel Ciznadija, PhD2; Amanda Katz, MD2; and David Sidransky, MD8 BACKGROUND: Patients with advanced, metastatic sarcoma have a poor prognosis, and the overall benefit from the few standard-of- care therapeutics available is small. The rarity of this tumor, combined with the wide range of subtypes, leads to difficulties in con- ducting clinical trials. The authors previously reported the outcome of patients with a variety of common solid tumors who received treatment with drug regimens that were first tested in patient-derived xenografts using a proprietary method (“TumorGrafts”). METHODS: Tumors resected from 29 patients with sarcoma were implanted into immunodeficient mice to identify drug targets and drugs for clinical use. The results of drug sensitivity testing in the TumorGrafts were used to personalize cancer treatment. RESULTS: Of 29 implanted tumors, 22 (76%) successfully engrafted, permitting the identification of treatment regimens for these patients. Although 6 patients died before the completion of TumorGraft testing, a correlation between TumorGraft results and clinical outcome was observed in 13 of 16 (81%) of the remaining individuals. No patients progressed during the TumorGraft-predicted therapy. CONCLUSIONS: The current data support the use of the personalized TumorGraft model as an investigational platform for therapeu- tic decision-making that can guide treatment for rare tumors such as sarcomas. -
Abstract Book
PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017 ABSTRACT BOOK Poster Presenters: Poster space is assigned by abstract page number. Please find the page that your abstract is on and put your poster on the poster board with the corresponding number (e.g., if your abstract is on page 50, put your poster on board #50). Proceedings papers with oral presentations #2-39 are not assigned poster space. Papers are organized first by session, then the last name of the first author. Presenting authors’ names are underlined. TABLE OF CONTENTS PROCEEDINGS PAPERS WITH ORAL PRESENTATION COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION 1 IDENTIFICATION AND ANALYSIS OF BACTERIAL GENOMIC METABOLIC SIGNATURES ... 2 Nathan Bowerman, Nathan Tintle, Matthew DeJongh, Aaron A. Best WHEN SHOULD WE NOT TRANSFER FUNCTIONAL ANNOTATION BETWEEN SEQUENCE PARALOGS? ............................................................................................................................................................. 3 Mengfei Cao, Lenore J. Cowen PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION ................................................................................................................................... 4 Sheng Wang, Meng Qu, Jian Peng ON THE POWER AND LIMITS OF SEQUENCE SIMILARITY BASED CLUSTERING OF PROTEINS INTO FAMILIES ............................................................................................................................... 5 Christian Wiwie, Richard Röttger IMAGING -
Sarcoma Journal an Exciting Initiative in Peer-Reviewed Professional Education and Advocacy PAGE 4
VOL 1 | NO 1 | FALL 2017 WWW.SARCOMAJOURNAL.COM theSARCOMA Official Journal of The Sarcoma Foundation JOURNAL of America™ FEATURE ARTICLE Sof t Tissue Sarcoma: Diagnosis and treatment PAGE 7 EDITORIAL Introducing The Sarcoma Journal An exciting initiative in peer-reviewed professional education and advocacy PAGE 4 CASE REPORT Bilateral chylothorax in an AIDS patient with newly diagnosed Kaposi sarcoma PAGE 20 CASE REPORT Pulmonary sarcomatoid carcinoma presenting Premier Issue as a necrotizing cavitary lung lesion Diagnostic dilemma PAGE 22 › EDITORIAL‹ VIEWS AND NEWS BY WILLIAM D. TAP, MD | Editor-In-Chief Introducing The Sarcoma Journal—The Official Journal of the Sarcoma Foundation of America™: An Exciting Initiative in Peer-Reviewed Professional Education and Patient Advocacy › I WELCOME YOUR he Sarcoma Journal — Official ing affiliations with the Sarcoma Foun- PARTICIPATION IN Journal of the Sarcoma Founda- dation of America and its comprehensive THE SUCCESS OF THE tion of America™ represents a program of sarcoma research, patient sup- SARCOMA JOURNAL Tnew and exciting initiative in pro- port and education and advocacy. As you fessional education. We invite you to share explore the first issue of the journal, you BY SUBMITTING in the excitement surrounding the launch will discover how our editorial content is MANUSCRIPTS, of a medical journal designed to be your an extension of this three-tiered approach. INTERESTING CASE most authoritative and comprehensive The SFA program is characterized by a STUDIES, ORIGINAL source of scientific information on the di- multi-dimensional and uniquely coordi- RESEARCH, AND TOPIC agnosis and treatment of sarcomas and sar- nated outreach program of videos and we- PERSPECTIVES—AS coma sub-types. -
Sarcoma European & Latin American Network (Selnet
Sarcomas SARCOMA EUROPEAN & LATIN AMERICAN NETWORK (SELNET) RECOMMENDATIONS ON PRIORITIZATION IN SARCOMA CARE DURING COVID-19 PANDEMIC a,b a,b c d JAVIER MARTIN-BROTO,MDPHD , NADIA HINDI, MD, SAMUEL AGUIAR JR MD, RONALD BADILLA-GONZÁLEZ, MD, e f g h,i,j VICTOR CASTRO-OLIDEN, MD, MATIAS CHACÓN, MD, RAQUEL CORREA-GENEROSO, MD, ENRIQUE DE ALAVA,MDPHD, k l m n DAVIDE MARÍA DONATI, MD, MIKAEL ERIKSSON, MD, MARTIN FALLA-JIMENEZ, MD, GISELA GERMAN, MD, o p q e MARIA LETICIA GOBO SILVA, MD, FRANCOIS GOUIN, MD, ALESSANDRO GRONCHI, MD, JUAN CARLOS HARO-VARAS, MD, r s t u NATALIA JIMÉNEZ-BRENES, MD, BERND KASPER, MD, CELSO ABDON LOPES DE MELLO, MD, ROBERT MAKI,MDPHD, a v w x PAULA MARTÍNEZ-DELGADO,PHD, HECTOR MARTÍNEZ-SAID, MD, JORGE LUIS MARTINEZ-TLAHUEL, MD, JOSE MANUEL MORALES-PÉREZ, MD, y z aa FRANCISCO CRISTOBAL MUÑOZ-CASARES, MD, SUELY A. NAKAGAWA, MD, EDUARDO JOSE ORTIZ-CRUZ,MDPHD, bb cc a dd EMANUELA PALMERINI,MDPHD, SHREYASKUMAR PATEL, MD, DAVID S. MOURA,PHD, SILVIA STACCHIOTTI, MD, ee ff f gg MARIE PIERRE SUNYACH, MD, CLAUDIA M. VALVERDE, MD, FEDERICO WAISBERG, MD, JEAN-YVES BLAY,MDPHD aGroup of Advanced Therapies and Biomarkers in Sarcoma, Institute of Biomedicine of Seville (IBIS, HUVR, CSIC, Universidad de Sevilla), Sevilla, Spain; bDepartment of medical oncology, University Hospital Virgen del Rocio, Seville, Spain; cDepartment of Pelvic Surgery, A.C. Camargo Cancer Center, S~ao Paulo, Brazil; dDepartment of medical oncology, Rafael Angel Calderón Guardia Hospital, San José, Costa Rica; eDepartment of medical oncology, Instituto Nacional -
Second International DTRF Desmoid Tumor Research Workshop October 18, 2015 Participant Profiles
Second International DTRF Desmoid Tumor Research Workshop October 18, 2015 Participant Profiles updated on 10.27.15 Mushriq Al-Jazrawe, University of Toronto, Laboratory Medicine & Pathobiology Mushriq received his bachelor of science at the University of Toronto in Genes, Genetics, and Biotechnology. He is currently a PhD candidate in the Department of Laboratory Medicine & Pathobiology, University of Toronto in Dr. Benjamin Alman lab, studying the role of platelet- derived growth factor signaling and microRNAs in desmoid tumors. Benjamin Alman, MD, Department Chair, Orthopedic Surgery, Duke University Dr. Alman is an orthopaedic clinician-scientist, whose research focuses on understanding role of developmentally important processes in pathologic and reparative process involving the musculoskeletal system. The long-term goal of his work is to use this knowledge to identify improved therapeutic approaches to orthopaedic disorders. He makes extensive use of genetically modified mice to model human disease, and has used this approach to identify new drug therapies for musculoskeletal tumors and to improve the repair process in cartilage, skin, and bone. He also works on cellular heterogeneity in sarcomas, and has identified a subpopulation of tumor initiating cells in musculoskeletal tumors. In this work, he also has identified specific cell populations that are responsible for joint and bone development. He has was recently recruited from the University of Toronto to Duke University to chair the department of orthopaedics, which was established in 2010, and includes a large musculoskeletal research component. He has half his time protected for his research work. Dr. Alman is the Principal Investigator in the DTRF-funded collaborative project, "Collaboration for a Cure: Identifying new therapeutic targets for desmoid tumors." Profile here. -
Clinical Recommendations Margins)
Annals of Oncology 20 (Supplement 4): iv132–iv136, 2009 clinical recommendations doi:10.1093/annonc/mdp153 Soft tissue sarcomas: ESMO Clinical Recommendations for diagnosis, treatment and follow-up P. G. Casali1, L. Jost2, S. Sleijfer3, J. Verweij3 & J.-Y. Blay4 On behalf of the ESMO Guidelines Working Group* 1Department of Cancer Medicine, Istituto Nazionale dei Tumori, Milan, Italy; 2Department of Oncology, Kantonsspital, Bruderholz, Switzerland; 3Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands; 4INSERM U590, Claude Bernard University and Department of Oncology, Edouard Herriot Hospital, Lyon, France The following recommendations apply to adult-type soft tissue performed by a trained surgeon, or discussed between the sarcomas arising from limbs and superficial trunk. surgeon and the radiologist. It should be planned in such a way Recommendations on retroperitoneal sarcomas, desmoid-type that the biopsy pathway and the scar can be safely removed on fibromatosis and uterine sarcomas are provided separately at definitive surgery, and should be preceded by imaging the end of the chapter with regard to those main aspects by [contrast-enhanced magnetic resonance imaging (MRI) is the which they differ from more frequent soft tissue sarcomas. In preferred method for limb and superficial trunk lesions]. general, the main principles of diagnosis and treatment may Histological diagnosis should be made according to the well apply to all soft tissue sarcomas, including the rarest World Health Organization (WHO) classification. The presentations [e.g. visceral sarcomas other than gastrointestinal malignancy grade should be provided in all cases in which this stromal tumors (GIST), head and neck sarcomas], which is feasible based on available systems. -
Speaker Bios
Second International Chordoma Research Workshop April 3–5, 2008 Speaker Biographies Christopher Austin, M.D. Dr. Christopher Austin is Director of the NIH Chemical Genomics Center (NCGC) and Senior Advisor to the Director for Translational Research at the National Human Genome Research Institute (NHGRI). NCGC, part of the NIH Roadmap Molecular Libraries initiative, develops small‐molecule probes for biological functions and new paradigms for high‐throughput screening, chemistry, and cheminformatics. In his role as Senior Advisor for Translational Research, he initiated the Knockout Mouse Project, which is producing knockout mice for all mouse genes, and an in‐depth transcriptome map of the mouse. Dr. Austin came to NIH from Merck and Co., where he directed research programs in genomics‐based target discovery, pharmacogenomics, and DNA microarray technologies, with a focus on neuropsychiatric diseases. Dr. Austin received his A.B. from Princeton University and M.D. from Harvard University. He did clinical training in neurology at Massachusetts General Hospital, followed by a fellowship in genetics at Harvard. Laurence Baker, D.O. Dr. Laurence Baker is Professor of Internal Medicine and Pharmacology in the Departments of Internal Medicine and Pharmacology, Division of Hematology/Oncology, University of Michigan Medical School. He received his medical degree from the University of Osteopathic Medicine and Surgery in Des Moines, Iowa, in 1966. He did a medical residency at Detroit Osteopathic Hospital, which was followed by an oncology fellowship at Wayne State University. He joined the faculty of the Department of Oncology at Wayne State upon completion of his fellowship in 1972. In 1987, Dr. Baker became the Director of the Meyer L. -
SPRING 2011 Accelerating Science, Advancing Medicine
Dean’s Quarterly SPRING 2011 ACCELERATING SCIENCE, ADVANCING MEDICINE Becoming an Engine of Discovery I am pleased to outline the strategic plan for the Center for Discovery and Innovation (CDI) at The Mount Sinai Medical Center. This entity, designed to capitalize on the unprecedented opportunities of 21st century biomedicine, will bring together some 30 renowned translational scientists, many of whom are successful drug developers and patent-holders already, with the charge of translating discovery into therapeutics and generating new intellectual property. Under the direction of a senior leader with Experimental Therapeutics Institute in five key international stature in translational medicine areas: small-molecule drug discovery, monoclonal and the successful development of therapeutic antibodies and purified proteins, high-content interventions, the CDI discovery group will screening/RNAi, induced pluripotent stem cells, identify the most promising research within all of and systems pharmacology and network analysis Mount Sinai’s disease-focused institutes with the facilities. goal of illuminating new disease targets and the The success of the CDI enterprise and the Dennis S. Charney, MD, is the Anne and Joel Ehrenkranz molecules that treat those targets. scientists it recruits and supports will ultimately Dean of Mount Sinai School of Medicine and the Executive Vice President for Academic Affairs of The Mount Sinai This new era of growth will span years and will be measured by the discoveries made, and the Medical Center. require great institutional commitment and applications developed, to predict, prevent, investment, and the results will be breathtaking. and treat disease. I look forward to sharing with The CDI is structured to focus on five areas that you the progress and results of CDI throughout To learn more, visit www.mountsinai.org/Charney represent the most pressing global disease burden: the coming years. -
Genomechronicler: the Personal Genome Project UK Genomic Report Generator Pipeline
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.06.873026; this version posted September 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline José Afonso Guerra-Assunção1,2*, Lucia Conde2, Ismail Moghul3, Amy P. Webster3, Simone Ecker3, Olga Chervova3, Christina Chatzipantsiou4, Pablo P. Prieto4, Stephan Beck3, Javier Herrero2 1Infection and Immunity, University College London, London, United Kingdom 2Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, United Kingdom 3Medical Genomics, UCL Cancer Institute, University College London, London, United Kingdom 4Lifebit, 9 Appold St, EC2A 2AP London, United Kingdom * Correspondence: Corresponding Author [email protected] Keywords: Personal Genomics, PGP-UK, Genomic Report, Open Consent, Participant Engagement, Open Source, Cloud Computing. Abstract In recent years, there has been a significant increase in whole genome sequencing data of individual genomes produced by research projects as well as direct to consumer service providers. While many of these sources provide their users with an interpretation of the data, there is a lack of free, open tools for generating reports exploring the data in an easy to understand manner. GenomeChronicler was developed as part of the Personal Genome Project UK (PGP-UK) to address this need. PGP-UK provides genomic, transcriptomic, epigenomic and self-reported phenotypic data under an open-access model with full ethical approval.