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Title: An Integrated Program in Microbial Genome Sequencing and Analysis

Abstract

Under this award, numerous genome sequences were generated, analyzed, published and made publicly available.

Authors:
; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
The Institute for Genomic Research
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
860806
Report Number(s):
DOEER619611
TRN: US200710%%42
DOE Contract Number:
FC02-95ER61962
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; MICROORGANISMS; DNA SEQUENCING; GENETICS; DATA ANALYSIS; RESEARCH PROGRAMS; genomics; microbial genomics; functional genomics; sequencing

Citation Formats

Claire M. Fraser, Ph.D., J.E. Eisen, Ph.D., W. Nierman, Ph.D., K. Nelson, Ph.D., H. Tettelin, Ph.D., J. Heidelberg, Ph.D., O. White, Ph.D., B. Methe, Ph.D., N. El-Sayed, Ph.D., S. Gill, Ph.D., S. Peterson, Ph.D., J. Quackenbush, Ph.D., and T. Read, Ph.D. An Integrated Program in Microbial Genome Sequencing and Analysis. United States: N. p., 2005. Web. doi:10.2172/860806.
Claire M. Fraser, Ph.D., J.E. Eisen, Ph.D., W. Nierman, Ph.D., K. Nelson, Ph.D., H. Tettelin, Ph.D., J. Heidelberg, Ph.D., O. White, Ph.D., B. Methe, Ph.D., N. El-Sayed, Ph.D., S. Gill, Ph.D., S. Peterson, Ph.D., J. Quackenbush, Ph.D., & T. Read, Ph.D. An Integrated Program in Microbial Genome Sequencing and Analysis. United States. doi:10.2172/860806.
Claire M. Fraser, Ph.D., J.E. Eisen, Ph.D., W. Nierman, Ph.D., K. Nelson, Ph.D., H. Tettelin, Ph.D., J. Heidelberg, Ph.D., O. White, Ph.D., B. Methe, Ph.D., N. El-Sayed, Ph.D., S. Gill, Ph.D., S. Peterson, Ph.D., J. Quackenbush, Ph.D., and T. Read, Ph.D. Wed . "An Integrated Program in Microbial Genome Sequencing and Analysis". United States. doi:10.2172/860806. https://www.osti.gov/servlets/purl/860806.
@article{osti_860806,
title = {An Integrated Program in Microbial Genome Sequencing and Analysis},
author = {Claire M. Fraser, Ph.D. and J.E. Eisen, Ph.D. and W. Nierman, Ph.D. and K. Nelson, Ph.D. and H. Tettelin, Ph.D. and J. Heidelberg, Ph.D. and O. White, Ph.D. and B. Methe, Ph.D. and N. El-Sayed, Ph.D. and S. Gill, Ph.D. and S. Peterson, Ph.D. and J. Quackenbush, Ph.D. and T. Read, Ph.D.},
abstractNote = {Under this award, numerous genome sequences were generated, analyzed, published and made publicly available.},
doi = {10.2172/860806},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Nov 30 00:00:00 EST 2005},
month = {Wed Nov 30 00:00:00 EST 2005}
}

Technical Report:

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  • The goal of human genome project is to characterize and sequence entire genomes of human and several model organisms, thus providing complete sets of information on the entire structure of transcribed, regulatory and other functional regions for these organisms. In the past years, a number of useful genetic and physical markers on human and mouse genomes have been made available along with the advent of BAC library resources for these organisms. The advances in technology and resource development made it feasible to efficiently construct genome-wide physical BAC contigs for human and other genomes. Currently, over 30,000 mapped STSs and 27,000more » mapped Unigenes are available for human genome mapping. ESTs and cDNAs are excellent resources for building contig maps for two reasons. Firstly, they exist in two alternative forms--as both sequence information for PCR primer pairs, and cDoreen genomic libraries efficiently for large number of DNA probes by combining over 100 cDNA probes in each hybridization. Second, the linkage and order of genes are rather conserved among human, mouse and other model organisms. Therefore, gene markers have advantages over random anonymous STSs in building maps for comparative genomic studies.« less
  • We developed a great deal of expertise in building large BAC libraries from a variety of DNA sources including humans, mice, corn, microorganisms, worms, and Arabidopsis. We greatly improved the technology for screening these libraries rapidly and for selecting appropriate BACs and mapping BACs to develop large overlapping contigs. We became involved in supplying BACs and BAC contigs to a variety of sequencing and mapping projects and we began to collaborate with Drs. Adams and Venter at TIGR and with Dr. Leroy Hood and his group at University of Washington to provide BACs for end sequencing and for mapping andmore » sequencing of large fragments of chromosome 16. Together with Dr. Ian Dunham and his co-workers at the Sanger Center we completed the mapping and they completed the sequencing of the first human chromosome, chromosome 22. This was published in Nature in 1999 and our BAC contigs made a major contribution to this sequencing effort. Drs. Shizuya and Ding invented an automated highly accurate BAC mapping technique. We also developed long-term collaborations with Dr. Uli Weier at UCSF in the design of BAC probes for characterization of human tumors and specific chromosome deletions and breakpoints. Finally the contribution of our work to the human genome project has been recognized in the publication both by the international consortium and the NIH of a draft sequence of the human genome in Nature last year. Dr. Shizuya was acknowledged in the authorship of that landmark paper. Dr. Simon was also an author on the Venter/Adams Celera project sequencing the human genome that was published in Science last year.« less
  • The 14 plenary session presentations focused on nematode; yeast; fruit fly; plants; mycobacteria; and man. In addition there were presentations on a variety of technical innovations including database developments and refinements, bioelectronic genesensors, computer-assisted multiplex techniques, and hybridization analysis with DNA chip technology. This document includes a list of exhibitors and abstracts of sessions.
  • The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. As the result of a different DHS project, we have selected for and isolated a large number of ciprofloxacin resistant B. anthracis Sterne isolates. These isolates vary in the concentrations of ciprofloxacin that they can tolerate, suggesting multiple mutations in the samples. In collaboration with University of Houston, Eureka Genomics and Oak Ridge National Laboratory, we analyzedmore » the ciprofloxacin resistant B. anthracis Sterne isolates by microarray hybridization, Illumina and Roche 454 sequencing to understand the error rates and sensitivity of the different methods. The report provides an assessment of the results and a complete set of all protocols used and all data generated along with information to interpret the protocols and data sets.« less