(Dbgap) Data Submission, Access, and Management (NOT-OD-17-044) February 21, 2017 – April 7, 2017
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Whole-Genome Shotgun Assembly and Analysis of the Genome
R ESEARCH A RTICLE of the human genome, it contains a comparable complement of protein-coding genes, as in- Whole-Genome Shotgun ferred from random genomic sampling (3). Subsequently, more-targeted analyses (5–9) Assembly and Analysis of the showed that the Fugu genome has remarkable homologies to the human sequence. The intron- Genome of Fugu rubripes exon structure of most genes is preserved be- tween Fugu and human, in some cases with Samuel Aparicio,2,1* Jarrod Chapman,3 Elia Stupka,1* conserved alternative splicing (10). The relative Nik Putnam,3 Jer-ming Chia,1 Paramvir Dehal,3 compactness of the Fugu genome is accounted Alan Christoffels,1 Sam Rash,3 Shawn Hoon,1 Arian Smit,4 for by the proportional reduction in the size of introns and intergenic regions, in part owing to Maarten D. Sollewijn Gelpke,3 Jared Roach,4 Tania Oh,1 3 1 3 1 the relative scarcity of repeated sequences like Isaac Y. Ho, Marie Wong, Chris Detter, Frans Verhoef, those that litter the human genome. Conserva- 3 1 3 3 Paul Predki, Alice Tay, Susan Lucas, Paul Richardson, tion of synteny was discovered between hu- Sarah F. Smith,5 Melody S. Clark,5 Yvonne J. K. Edwards,5 mans and Fugu (5, 6), suggesting the possibil- Norman Doggett,6 Andrey Zharkikh,7 Sean V. Tavtigian,7 ity of identifying chromosomal elements from Dmitry Pruss,7 Mary Barnstead,8 Cheryl Evans,8 Holly Baden,8 the common ancestor. Noncoding sequence Justin Powell,9 Gustavo Glusman,4 Lee Rowen,4 Leroy Hood,4 comparisons detected core conserved regulato- ry elements in mice (11). -
The Path to New Therapies for Schizophrenia and Bipolar Illness
THE JOURNAL • PERSPECTIVE • www.fasebj.org The Path to New Therapies for Schizophrenia and Bipolar Illness Edward M. Scolnick1 Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA ABSTRACT: Schizophrenia and bipolar illness are two of the most serious forms of mental illness. Until relatively recently, almost nothing was known about the molecular pathogenesis of either illness. The single largest risk factor that predisposes people to schizophrenia or bipolar illness is genetic risk. Heritability is high, and the incidence is significantly higher in identical twins than in nonidentical twins. Despite decades of work aimed at identifying the genes involved in these two illnesses, virtually no progress had been made until the past decade. With the knowledge and technologies that have been gained from the Human Genome Project, it has been possible to begin to understand the underlying genetics and to use the new information to begin the effort to discover new and better medicines to treat these illnesses. This article will describe the past decade of work toward this goal and articulate both the promise that now exists and what is still needed to bring dramatic and tangible change to patients.—Scolnick, E. M. The path to new therapies for schizophrenia and bipolar illness. FASEB J. 31, 1254–1259 (2017). www.fasebj.org KEY WORDS: genetics • pharmacology • progress In the fall of 2004, I became an associate member of the bipolar illness for many years. Virtually no reproducible Broad Institute, founded on the principle of collaboration results had been achieved. The Broad Institute had a su- among scientists at the Massachusetts Institute of Tech- perb group of scientific experts in human genetics, a field nology, Harvard, and Harvard-affiliated hospitals. -
28Th Course in Medical Genetics
European School of Genetic Medicine th 28 Course in Medical Genetics Bertinoro University Residential Centre Via Frangipane, 6 – Bertinoro Course Directors: H. Brunner (Nijmegen, The Netherlands), G.Romeo (Bologna, Italy), B.Wirth (Cologne, Germany) 1 28th Course in Medical Genetics CONTENTS PROGRAMME 3 ABSTRACTS OF LECTURES 7 ABSTRACTS OF STUDENTS POSTERS 37 STUDENTS WHO IS WHO 40 FACULTY WHO IS WHO 51 2 Arrival: Saturday May 16 Sunday, May 17 Morning Session: Introduction to Human Genome Analysis 8.30 – 9.00 Registration to the course 9.00 – 9.30 Introduction to the course G. Romeo 9.30 – 10.15 Medical Genetics Today D. Donnai 10.15 – 11.00 Genotypes & phenotypes H. Brunner 11.00 – 11.30 Coffee Break 11.30 – 12.15 Introduction in Next Generation Sequencing technologies and applications J. Veltman 12.15 – 13.00 How to deal with next generation sequencing output. C. Gilissen 13.10 – 14.00 Lunch Break Afternoon Session: 14.30 – 16.00 Concurrent Workshops 16.00-16.30 Coffee Break 16.30 – 18.00 Concurrent Workshops 3 Monday, May 18 Morning Session: Approaches to Clinical and Molecular Genetics 9.00 – 9.50 Linkage and association (in a conceptual and historic perspective) A. Read 9.50- 10.40 Arrays and CNVs E. Klopocki 10.40 – 11.10 Coffee Break 11.10 – 12.00 Molecular syndromology in the NGS-era: which phenotype, which family, which strategy? Applications to aging research B. Wollnik 12.00 – 12.50 Bottlenecks in understanding mitochondrial diseases P. Chinnery 13.10 – 14.00 Lunch Break Afternoon Session: 14.30 – 16.00 Concurrent Workshops – including Ethics by Andrew Read 16.00-16.30 Coffee Break 16.30 – 18.00 Concurrent Workshops 18.30 – 19.30 Poster Viewing Session 4 Tuesday, May 19 Morning Session: Gene regulation and complex genetic disorders 9.00 - 9.50 Preventing and treating mitochondrial diseases Patrick Chinnery 9.50 – 10.40 Epigenetics and disease K. -
A Rare Variant in D-Amino Acid Oxidase Implicates NMDA Receptor Signaling and Cerebellar Gene Networks in Risk for Bipolar Disorder
medRxiv preprint doi: https://doi.org/10.1101/2021.06.02.21258261; this version posted June 5, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Submitted Manuscript: Confidential Template updated: February 2021 Title: A rare variant in D-amino acid oxidase implicates NMDA receptor signaling and cerebellar gene networks in risk for bipolar disorder Authors: Naushaba Hasin (1), Lace M. Riggs (2,3), Tatyana Shekhtman (4), Justin Ashworth (5), Robert Lease (1,6), Rediet T. Oshone (1), Elizabeth M. Humphries (1,7), Judith A. Badner (8), Pippa A. Thompson (9), David C. Glahn (10), David W. Craig (11), Howard J. Edenberg (12), Elliot S. Gershon (13), Francis J. McMahon (14), John I. Nurnberger (15), Peter P. Zandi (16), John R. Kelsoe (4), Jared C. Roach (5), Todd D. Gould (3,17,18), and Seth A. Ament* (1,3) Affiliations: 1. Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA 2. Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA 3. Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA 4. Department of Psychiatry, University of California San Diego, La Jolla, CA, USA 5. Institute for Systems Biology, Seattle, WA, USA 6. Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA 7. Program in Molecular Epidemiology, University of Maryland School of Medicine, Baltimore, MD, USA 8. -
GWG Dec 2012 Nominee Bios2
Agenda Item #12 ICOC Meeting December 12, 2012 CIRM Scientific and Medical Research Funding Working Group Biographical information of candidates nominated to serve as Scientific Members of the Working Group Stephen Friend, MD, PhD Dr. Friend is the President of Sage Bionetworks. He received his BA in philosophy, his PhD in biochemistry, and his MD from Indiana University. He is an authority in the field of cancer biology and a leader in efforts to make large scale, data-intensive biology broadly accessible to the entire research community. Dr. Friend has been a senior advisor to the National Cancer Institute (NCI), several biotech companies, a Trustee of the American Association for Cancer Research (AACR), and is an American Association for the Advancement of Science (AAAS) and Ashoka Fellow as well as an editorial board member of Open Network Biology. Dr. Friend was previously Senior Vice President and Franchise Head for Oncology Research at Merck & Co., Inc. where he led Merck’s Basic Cancer Research efforts. Prior to joining Merck, Dr. Friend was recruited by Dr. Leland Hartwell to join the Fred Hutchinson Cancer Research Center’s Seattle Project, an advanced institute for drug discovery. While there Drs. Friend and Hartwell developed a method for examining large patterns of genes that led them to co-found Rosetta Inpharmatics in 2001. Dr. Friend has also held faculty positions at Harvard Medical School from 1987 to 1995 and at Massachusetts General Hospital from 1990 to 1995. Christie Gunter, PhD Dr. Gunter is the HudsonAlpha director of research affairs. She earned her BS degree in both genetics and biochemistry from the University of Georgia in 1992, and a PhD in genetics from Emory University in 1998. -
Final Program
© Istock FINAL PROGRAM SUMMARY Organizing & Scientifc Committees 3 Final program 4 Life Achievement Award 4 Program at a glance 5 Wednesday, December 4 6 Thursday, December 5 8 Friday, December 6 12 Saturday, December 7 16 Posters presentation 19 Theme 1: Clinical trials: Methodology 20 Theme 2: Clinical trials: Results 23 Theme 3: Clinical trials: Imaging 24 Theme 4: Clinical trials: Biomarkers including plasma 26 Theme 5: Clinical trials: Cognitive and functional endpoints 29 Theme 6: Cognitive assessment and clinical trials 31 Theme 7: Behavioral disorders and clinical trials 33 Theme 8: Health economics and clinical trials 33 Theme 9: Epidemiology and clinical trials 33 Theme 10: Clinical Trials: Animals Models 34 Theme 11: New therapies and clinical trials 34 Privileged partners 37 CTAD 2019 General information 38 San Diego ©Terry Healy - Graphic designer: Kom Graphik ©Terry CTAD Organizing Committee Jacques Touchon MD, PhD University Hospital of Montpellier CTAD Scientific Committee France Susan ABUSHAKRA (San Francisco); Paul AISEN (San Diego); Kaj BLENNOW (Molndal); Merce BOADA Paul Aisen MD (Barcelona); Maria CARRILLO (Chicago); Mony John DE Alzheimer’s LEON (New York); Steven DEKOSKY (Gainesville); Rachelle Therapeutic Research Institute (ATRI) DOODY (Basel); Bruno DUBOIS (Paris); Howard FELDMAN University of Southern California (USC), (San Diego); Nick FOX (London); Giovanni B. FRISONI San Diego, USA (Brescia, Geneva); Lutz FROELICH (Mannheim); Serge GAUTHIER (Montreal); Ezio GIACOBINI (Geneva); Michael GRUNDMANN (San Diego); Harald HAMPEL (Woodcliff Bruno Vellas MD, PhD Lake); Takeshi IWATSUBO (Tokyo); Ara KHACHATURIAN University (Washington DC); Zaven KHACHATURIAN (Washington Hospital of Toulouse DC); Virginia LEE (Philadelphia); Constantine G. France LYKETSOS (Baltimore); José Luis MOLINUEVO (Barcelona); Jean-Marc ORGOGOZO (Bordeaux); Ronald PETERSEN Mike Weiner MD (Rochester); Craig W. -
Aarhus University Honorary Doctorate Seminar Friday 13 September 2019 at 10.00 – 11.15
Department of Biomedicine Center for Genomics Personalized Medicine and Personalized Medicine Aarhus University Honorary Doctorate Seminar Friday 13 September 2019 at 10.00 – 11.15 Professor Mark Daly, Institute for Molecular Medicine Finland. Analytic and Translational Genetics Unit, USA. Broad Institute of Harvard and MIT, USA. Talk: Global partnerships: From Psychiatric Genetics to FinnGen and opportunities in discovery, prevention and personalized medicine. Venue: Eduard Biermann Auditory, The Lakeside Theatres, Aarhus University, Bartholins Allé 3, 8000 Aarhus C. Programme 10.00 – 10.05 Welcome by Anders Børglum 10.05 – 10.50 AU Honorary Doctorate lecture by Mark Daly 10.50 – 11.15 Open discussion Biosketch: Mark Daly, PhD, was appointed Director of the Institute for Molecular Medicine Finland (FIMM) in February 2018. He retains also his affiliations in Boston at the Harvard Medical School, Massachusetts General Hospital and as an institute member of the Broad Institute and co-director of the Program in Medical and Population Genetics. Daly received his B.S. in physics from the Massachusetts Institute of Technology and his Ph.D. in human genetics from Leiden University, Netherlands. He received the Curt Stern Award from the American Society of Human Genetics in 2014 and is a member of the National Academy of Medicine. Department of Biomedicine Center for Genomics Personalized Medicine and Personalized Medicine His research primarily focuses on the development and application of statistical methods for the discovery and interpretation of genetic variation responsible for complex human disease. In addition to foundational work in human genetics methodology, his lab has made major contributions to gene discovery in inflammatory bowel disease, autism and schizophrenia - primarily through catalyzing global collaborative research efforts which he continues to help lead. -
Implementing Physician Education Programs
Informatic Imperatives for Sequencing in Large-Scale Studies Daniel MacArthur Analytic and Translational Genetics Unit, Massachusetts General Hospital Broad Institute of Harvard and MIT Harvard Medical School 1000 Genomes Project Consortium Acknowledgments • Shane McCarthy (Sanger) • Mark DePristo, Ryan Poplin and Khalid Shakir (Broad) • Mark Daly and David Altshuler (MGH/Broad) • 1000 Genomes Analysis Group A plausible near-future scenario • we have exome sequence and complex phenotype data available for 100,000 individuals from multiple sources • one petabyte of raw data • goals: – create accurate, consistent variant calls across all samples – harmonized, cleaned phenotype data – data are not just accessible but usable by researchers from the wider community Key challenges • Logistics: moving, storing and crunching large data-sets • Harmonization: integrating and cleaning data from multiple sources • Analysis: extracting useful information from massive, structured data-sets • Access: making data available and usable for many different audiences Logistics: data management • 100,000 exomes 1 petabyte raw data – with 10 Gbit connection, 1-6 months – may be faster to use truck full of hard drives • data storage is not free: – expect ~$1M/year for 100K exomes • ~10x greater for WGS; less with compression • but community now has extensive experience in handling large sequence data: logistical problems are soluble Logistics: QC and meta-data • sample-tracking: – genetic data: easy ID of duplicates, sample swaps, pedigree and population errors -
Whole-Genome Shotgun Assembly and Analysis of the Genome Of
R ESEARCH A RTICLE of the human genome, it contains a comparable complement of protein-coding genes, as in- Whole-Genome Shotgun ferred from random genomic sampling (3). Subsequently, more-targeted analyses (5–9) Assembly and Analysis of the showed that the Fugu genome has remarkable homologies to the human sequence. The intron- Genome of Fugu rubripes exon structure of most genes is preserved be- tween Fugu and human, in some cases with Samuel Aparicio,2,1* Jarrod Chapman,3 Elia Stupka,1* conserved alternative splicing (10). The relative Nik Putnam,3 Jer-ming Chia,1 Paramvir Dehal,3 compactness of the Fugu genome is accounted Alan Christoffels,1 Sam Rash,3 Shawn Hoon,1 Arian Smit,4 for by the proportional reduction in the size of introns and intergenic regions, in part owing to Maarten D. Sollewijn Gelpke,3 Jared Roach,4 Tania Oh,1 3 1 3 1 the relative scarcity of repeated sequences like Isaac Y. Ho, Marie Wong, Chris Detter, Frans Verhoef, those that litter the human genome. Conserva- 3 1 3 3 Paul Predki, Alice Tay, Susan Lucas, Paul Richardson, tion of synteny was discovered between hu- Sarah F. Smith,5 Melody S. Clark,5 Yvonne J. K. Edwards,5 mans and Fugu (5, 6), suggesting the possibil- Norman Doggett,6 Andrey Zharkikh,7 Sean V. Tavtigian,7 ity of identifying chromosomal elements from Dmitry Pruss,7 Mary Barnstead,8 Cheryl Evans,8 Holly Baden,8 the common ancestor. Noncoding sequence 9 4 4 4 comparisons detected core conserved regulato- Justin Powell, Gustavo Glusman, Lee Rowen, Leroy Hood, Downloaded from ry elements in mice (11). -
Ryan L. Collins
RYAN LEWIS COLLINS Ph.D. Candidate, Bioinformatics and Integrative Genomics Ph.D. Program, Harvard Medical School 185 Cambridge St., Floor 5 Boston, MA, 02114 NSF Graduate Research Fellow, Talkowski Laboratory, Massachusetts General Hospital (603) 290-2200 Team Leader, Population Genetics & Genome Biology, Broad-SV Group, Broad Institute of MIT and Harvard www.RyanLCollins.com [email protected] § Professional status: third-year Ph.D. § Career objective: to advance knowledge § Scientific interests: structural variation, candidate at Harvard Medical School of the structure-function dynamics in the chromatin, genome topology, sequencing studying human genome structure & human genome, and their implications for technologies, interpretation of genetic function in the lab of Dr. Michael development, disease, population genetics, variation, gene regulation & regulatory Talkowski at Massachusetts General and precision medicine, ideally by leading elements, statistics, predictive modeling, Hospital and The Broad Institute. an independent research group. bioinformatics, and clinical genetics. EDUCATION DEGREES Ph.D. Harvard Medical School, Boston, MA, USA 2016-Present Division of Medical Sciences: Bioinformatics and Integrative Genomics Thesis Title The properties of natural selection on structural variation in the human genome Advisor Michael E. Talkowski, Ph.D. Dissertation Committee Shamil Sunyaev, Ph.D.; Mark Daly, Ph.D.; James Gusella, Ph.D.; Marcin Imielinski, M.D., Ph.D. A.B. Dartmouth College, Hanover, NH, USA 2009-2013 Department -
A Personal View of Molecular Technology and How It Has Changed Biology Leroy Hood President and Director, Institute for Systems Biology, Seattle, Washington 98103
A Personal View of Molecular Technology and How It Has Changed Biology Leroy Hood President and Director, Institute for Systems Biology, Seattle, Washington 98103 Received June 27, 2002 I have had the pleasure of practicing biology and technology development for the past 35 yearssfirst at the National Institutes of Health (NIH) for 3 years, then at the California Institute of Technology (Caltech) for 22 years, subsequently at the University of Washington (UW) for 8 years, and finally at the Institute for Systems Biology (ISB) for the past 2 years. In each case, my geographical transitions were prompted by exciting new opportunities and evolving visions of how biology should be practiced. The technology developments I have been associated with over this period helped to catalyze two emerg- Figure 1. Quotes from Freeman J. Dyson, Imagined Worlds ing paradigm changes in biology: systems biology and predic- (Harvard University Press: Cambridge, MA, 1998). tive/preventive medicine. Table 1. Colleagues for Instrument and Strategy Development My career has been driven by two imperatives from my Ph.D. advisor, Bill Dreyer (Caltech). First, ªAlways practice biology Ruedi Aebersold protein blotting, protein microsequencing at the leading edge.º For much of my career, this leading edge Bruce Birren pulse-field gel electrophoresis Alan Blanchard ink-jet DNA synthesizer was molecular immunology.1-14 Second, ªWith new technolo- Ian Clark-Lewis long peptides gies, biologists have the chance to open up new horizons for Cecilie Boysen BAC shotgun sequencing exploration in biology.º Indeed, Freeman Dyson made this Pat Griffin mass spectrometry and proteins point eloquently (Figure 1). -
The Genome Analysis Toolkit: a Mapreduce Framework for Analyzing Next-Generation DNA Sequencing Data
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation McKenna, A., M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, et al. “The Genome Analysis Toolkit: A MapReduce Framework for Analyzing Next-Generation DNA Sequencing Data.” Genome Research 20, no. 9 (September 1, 2010): 1297–1303. As Published http://dx.doi.org/10.1101/gr.107524.110 Publisher Cold Spring Harbor Laboratory Press Version Final published version Citable link http://hdl.handle.net/1721.1/88421 Terms of Use Creative Commons Attribution-Noncommerical Detailed Terms http://creativecommons.org/licenses/by-nc/3.0/ Downloaded from genome.cshlp.org on June 16, 2014 - Published by Cold Spring Harbor Laboratory Press The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data Aaron McKenna, Matthew Hanna, Eric Banks, et al. Genome Res. 2010 20: 1297-1303 originally published online July 19, 2010 Access the most recent version at doi:10.1101/gr.107524.110 Supplemental http://genome.cshlp.org/content/suppl/2010/07/14/gr.107524.110.DC1.html Material References This article cites 26 articles, 13 of which can be accessed free at: http://genome.cshlp.org/content/20/9/1297.full.html#ref-list-1 Creative This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the Commons first six months after the full-issue publication date (see License http://genome.cshlp.org/site/misc/terms.xhtml).