Abstract

The goal of this proposal is: To provide the scientific community with an unprecedented amount of assembled high-quality genome sequence, sufficient in quantity and quality to solve some of the central intellectual questions in genomics. In particular, the genome sequence will allow comparative studies to identify the vast majority of functional elements encoded in the human genome. It will also allow extensive characterization of the biological diversity in the animal and fungal kingdoms. We propose to do this, over a three-year period, by producing: Shotgun sequence: approximately 331 million reads yielding, approximately 205 Gb of high-quality raw bases, and approximately 32 Gb of high-quality draft genome assembly; Polished sequence: approximately 10 Gb; and Finished sequence: approximately 1.5 Gb. We also plan to aggressively improve the efficiency of the genome sequencing process. The cost of high quality draft sequence of a typical mammalian genome (about 2.7 Gb) will be approximately $25M in Year 1 and decrease to about $16M by Year 3.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
3U54HG003067-03S1
Application #
7292838
Study Section
Special Emphasis Panel (ZHG1)
Program Officer
Felsenfeld, Adam
Project Start
2003-11-10
Project End
2006-11-30
Budget Start
2005-11-01
Budget End
2006-11-30
Support Year
3
Fiscal Year
2006
Total Cost
$4,005,044
Indirect Cost

  Institution

Name
Massachusetts Institute of Technology
Department
Type
Organized Research Units
DUNS #
001425594
City
Cambridge
State
MA
Country
United States
Zip Code
02139

  Publications

Radovich, Milan; Pickering, Curtis R; Felau, Ina et al. (2018) The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell 33:244-258.e10
Shen, Hui; Shih, Juliann; Hollern, Daniel P et al. (2018) Integrated Molecular Characterization of Testicular Germ Cell Tumors. Cell Rep 23:3392-3406
Berger, Ashton C; Korkut, Anil; Kanchi, Rupa S et al. (2018) A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell 33:690-705.e9
Palkopoulou, Eleftheria; Lipson, Mark; Mallick, Swapan et al. (2018) A comprehensive genomic history of extinct and living elephants. Proc Natl Acad Sci U S A 115:E2566-E2574
Hoadley, Katherine A; Yau, Christina; Hinoue, Toshinori et al. (2018) Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell 173:291-304.e6
Grasso, Catherine S; Giannakis, Marios; Wells, Daniel K et al. (2018) Genetic Mechanisms of Immune Evasion in Colorectal Cancer. Cancer Discov 8:730-749
Marin-Valencia, Isaac; Novarino, Gaia; Johansen, Anide et al. (2018) A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features. J Med Genet 55:48-54
Schaub, Franz X; Dhankani, Varsha; Berger, Ashton C et al. (2018) Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Syst 6:282-300.e2
Kolde, Raivo; Franzosa, Eric A; Rahnavard, Gholamali et al. (2018) Host genetic variation and its microbiome interactions within the Human Microbiome Project. Genome Med 10:6
Ghosh, Shereen G; Becker, Kerstin; Huang, He et al. (2018) Biallelic Mutations in ADPRHL2, Encoding ADP-Ribosylhydrolase 3, Lead to a Degenerative Pediatric Stress-Induced Epileptic Ataxia Syndrome. Am J Hum Genet 103:431-439

Showing the most recent 10 out of 349 publications