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 Platypus genome explains animal's peculiar features; holds clues to evolution of mammals |
| May 7 2008 |
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The duck-billed platypus: part bird, part reptile, part mammal --- and the genome to prove it. An international consortium of scientists, led by the School of Medicine, has decoded the genome of the platypus, showing that the animal's peculiar mix of features is reflected in its DNA. An analysis of the genome, published in the journal Nature, can help scientists piece together a more complete picture of the evolution of all mammals, including humans. Also see the Science Daily, NPR, The New York Times, Nature coverage and Nature paper abstract. (more)
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| Mapping and sequencing of structural variation from eight human genomes |
| May 5 2008 |
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Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale—particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. (more)
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| University celebrates National DNA Day |
| April 25 2008 |
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National DNA Day is April 25. The day celebrates a most remarkable molecule, one that holds the instructions for life: DNA. DNA Day was created in 2003 to commemorate the completion of the Human Genome Project and the 50th anniversary of James Watson's and Francis Crick's discovery of DNA's double helical structure. (more)
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| Young scientists learn about DNA |
| April 25 2008 |
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ST. LOUIS (2008-04-25) National DNA Day was established to commemorate the discovery of the structure of DNA in 1953. Here in St. Louis, scientists from Washington University are leading experiments in area schools. (more)
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| Wilson leads quest to reveal the genome's secrets |
| April 17 2008 |
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In his youth, Richard K. Wilson, Ph.D., had two heroes: He lived with one, and the other had a Nobel Prize. Wilson's father was a high-school biology teacher who inspired in his son a passion for science. And James Watson, Ph.D., co-discoverer of the double-helical structure of DNA, inspired in Wilson a decades-long fascination with the genetic code that would shape his career. Today, as director of the Genome Sequencing Center (GSC), Wilson stands at the forefront of the genetics revolution --- one that promises to transform the way medicine is practiced and patients are treated. (more)
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| Brace yourselves: The 1,000 genomes project is underway |
| March 19 2008 |
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Washington University's David Dooling blogs that the school's genome center kicks off its work for the 1,000 Genomes Project this week. "This project, which aims to create a much deeper understanding of normal human variation, will begin by sequencing DNA from the well-characterized samples of the HapMap Project," he writes. Dooling also describes the three pilot projects planned for the effort, "each of which will generate an unprecedented amount of genomic information," he says. (more)
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| Washington University unveils draft sequence of corn genome |
| February 25 2008 |
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A team of scientists led by Washington University in St. Louis has begun to unlock the genetic secrets of corn, a crop vital to U.S. agriculture. The researchers have completed a working draft of the corn genome, an accomplishment that should accelerate efforts to develop better crop varieties to meet society's growing demands for food, livestock feed and fuel. (more)
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| Corn genome mapped |
| February 25 2008 |
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Scientists at the Genome Sequencing Center at Washington University have sequenced the corn genome. They say the sequencing will help researchers develop better crop varieties and help companies like Monsanto look for genes that make corn more nutritious or more efficient for ethanol production. (more)
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| Researchers map corn plant's genome |
| February 25 2008 |
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Scientists at universities and corporations are about to get a major leg up in their tireless --- and profitable --- effort to reinvent the corn plant. A group of researchers led by Washington University in St. Louis have mapped out the corn plant's massive genome, and is posting the research on the Internet. (more)
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| The impact of next-generation sequencing technology on genetics |
| February 20 2008 |
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If one accepts that the fundamental pursuit of genetics is to determine the genotypes that explain phenotypes, the meteoric increase of DNA sequence information applied toward that pursuit has nowhere to go but up. The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics, providing the ability to answer questions with heretofore unimaginable speed. These technologies will provide an inexpensive, genome-wide sequence readout as an endpoint to applications ranging from chromatin immunoprecipitation, mutation mapping and polymorphism discovery to noncoding RNA discovery. (more)
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| 1,000 human genomes to be sequenced |
| February 11 2008 |
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The School of Medicine will play a leading role in an international collaboration to sequence the genomes of 1,000 individuals by participating in the ambitious 1,000 Genomes Project, designed to create the most detailed picture to date of human genetic variation and assist in the identification of many genetic factors underlying common diseases. (more)
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| Pictures of data center construction |
| January 22 2008 |
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We have posted some pictures of the construction progress on our new data center. We will continue to post more pictures as more progress is made. (more)
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| International Consortium Announces the 1000 Genomes Project |
| January 22 2008 |
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An international research consortium announced the 1000 Genomes Project, an ambitious effort that will involve sequencing the genomes of at least a thousand people from around the world to create the most detailed and medically useful picture to date of human genetic variation. The project will receive major support from the Wellcome Trust Sanger Institute in Hinxton, England, the Beijing Genomics Institute, Shenzhen (BGI Shenzhen) in China and the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH). (more)
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| Lab Cultures --- To get more minorities in scientific research, first get them in the laboratory |
| November 16 2007 |
Fewer than 3 percent of PhDs awarded in science, mathematics and engineering go to African-Americans. For Latinos, the numbers are only slightly better. Nationwide, research institutions struggle to entice minorities to obtain advanced science degrees. "The problem is pervasive," says Richard K. Wilson, PhD, director of the School of Medicine's Genome Sequencing Center (GSC). But now a program can at least lure them into the lab.
With funding from the National Human Genome Research Institute, the GSC brought eight promising college students --- all minorities majoring in the sciences --- to Washington University this summer, where they received their first independent laboratory experience and close mentoring as part of the new Opportunities in Genomics Research program. (more)
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| Lung cancer's genetic alterations uncovered by genome researchers |
| November 15 2007 |
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School of Medicine scientists, working as part of an international research team, have completed a massive effort to map the genetic changes underlying the most commonly diagnosed form of lung cancer. The research provides an unprecedented view of the abnormal genetic landscape in lung cancer cells from patients with adenocarcinoma, the most common type of lung cancer in the United States accounting for about 30 percent of cases. (more)
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| Washington University researchers help finish genetic map of common lung cancer |
| November 5 2007 |
Researchers have completed a map of the genetic changes underlying a common form of lung cancer called adenocarcinoma.
Scientists at Washington University's Genome Sequencing Center participated in international research that uncovered 57 genomic changes that occur frequently in lung cancer patients. Only 15 changes were previously known. (more)
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| Data center construction will support advances in genome sequencing |
| October 30 2007 |
An important component of BioMed 21, the Genome Sequencing Center at Washington University in St. Louis is a gene-sequencing powerhouse and one of the four such centers in the world. It specializes in large-scale, high-throughput genome sequencing, supplying data that helps researchers at the School of Medicine identify the genetic factors that contribute to disease.
To meet the massive computing needs of the Genome Sequencing Center (GSC), a 16,000 square-foot data center is being constructed on Newstead Avenue across the street from the center's current facility on the medical campus. The data center will support 120 racks of highly dense data storage and computing solutions required by next-generation DNA sequencing technology.
Also see the coverage in the St. Louis Post-Dispatch. (more)
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| Uncovering clues as to what happens when we get cancer |
| October 25 2007 |
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The Genome Sequencing Center at Washington University is one of three in the country participating in the Cancer Genome Atlas Project. The three-year pilot study seeks to go deep into the blueprint of the human genome to find clues as to what happens when we get cancer. (more)
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| Secrets of Plant Genomes Revealed |
| September 28 2007 |
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Plant genome research is already revolutionizing the field of biology. Currently, scientists are unlocking the secrets of some of the most important plants in our lives, including corn, cotton and potatoes. Secrets of Plant Genomes: Revealed! takes viewers on a lively, upbeat journey that explores how these plants got to be the way they are and investigates how we can make better use of them in the future. (more)
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| SEQUENCING GENOMES - Almost as a Matter of Course |
| August 17 2007 |
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The Internet might provide a usefully, albeit simplistic, analogy for the amazing technical advances happening at Washington University's Genome Sequencing Center. Dial-up was amazing as you were introduced to the ever growing net. DSL was boggling as more and more information arrived even faster. And higher speed service? Your net-cup ran over as your computer filled with all the cyber goodies you hadn't anticipated receiving back in the recent past of dial-up days presenting you a sudden need for increased memory for the increasing items to be saved with the promise of even greater advances in the indeterminate future. (more)
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| SNPing Away at Genome-Wide Disease Association Studies |
| August 8 2007 |
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This year has seen a torrent of reports in scientific journals and mainstream media announcing the results of studies linking a gene variant to an increased risk for common diseases --- diabetes, Alzheimer's disease, and heart disease, for example. As the New York Times stated recently, "The sudden spate of new genes marks an acceleration, and perhaps a turning point, in the ability to find disease genes." (more)
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| Initial Orangutan and Marmoset Assemblies Completed |
| April 11 2007 |
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Washington University scientists recently completed initial assemblies of the orangutan and marmoset genomes. Analysis of these genomes and a comparison with human and the other primates will be carried out over the next several months. The National Human Genome Research Institute, one of the National Institutes of Health, funded the sequencing and assembly efforts. (more)
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| Rhesus Monkey Genome Reveals DNA Similarities with Chimps and Humans |
| April 11 2007 |
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Scientists have decoded the genome of the rhesus macaque monkey and compared it with the genomes of humans and their closest living relatives - the chimps - revealing that the three primate species share about 93 percent of the same DNA. The sequencing was completed by an international consortium of researchers, including scientists at the Genome Sequencing Center at Washington University School of Medicine in St. Louis, and is published in a special section of the April 13 issue of the journal Science. The research was funded by the National Human Genome Research Institute, one of the National Institutes of Health. (more)
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| PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data |
| April 6 2007 |
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Some 3 billion bits of genetic code make up the human genome, including numerous small insertions and deletions that are thought to be linked to diseases such as cystic fibrosis, hemophilia, muscular dystrophy and cancer, among others. So far, scientists attempting to identify these variations have had to manually sift through the genome - a tedious and time-consuming process. Now, researchers from Washington University School of Medicine have developed a computer software program, PolyScan, to automatically detect the insertions and deletions, as well as single nucleotide polymorphisms or SNPs, in DNA sequencing data. In a recent published study describing their development and evaluation of PolyScan, the scientists found that it could accurately identify 90 percent of the insertions and deletions and determine the number of bases involved, when examining a test gene set. Their results suggest that PolyScan will be very useful in identifying genetic variations in high-throughput re-sequencing data. (more)
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| Fat Bacteria in Human Guts Tied to Obesity |
| December 20 2006 |
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Many people worry about putting on a few pounds during the holiday season. But when you reach for a Christmas cookie, keep in mind that you're not the only one who's going to enjoy that tasty treat: It will also get eaten by the bacteria living in your gut. (more)
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| NHGRI Funds Large-Scale Sequencing Centers |
| November 20 2006 |
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The National Human Genome Research Institute (NHGRI) announced the results of the recent competition for support of its three large-scale sequencing centers, strengthening efforts to use the power of DNA sequencing to unlock the genomic secrets of human diseases. Also today, NHGRI and the National Cancer Institute (NCI), both part of the National Institutes of Health (NIH), announced that all three sequencing centers will devote a significant part of their efforts to The Cancer Genome Atlas (TCGA) Pilot Project, which is testing the feasibility of a large-scale, systematic approach to identify important genomic changes involved in cancer. (more)
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| GSC receives $156 million |
| November 20 2006 |
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The Genome Sequencing Center at Washington University School of Medicine in St. Louis has been awarded a $156 million, four-year grant to use the powerful tools of DNA sequencing to unlock the secrets of cancer and other human diseases. (more)
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| Anticipating the $1,000 genome |
| July 27 2006 |
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A new generation of DNA-sequencing platforms will become commercially available over the next few years. These instruments will enable re-sequencing of human genomes at a previously unimagined throughput and low cost. Here, I examine why the $1,000 human genome is an important goal for research and clinical diagnostics, and what will be required to achieve it. (more)
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| GSC receives funding for C. elegans microarrays |
| July 5 2006 |
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The Genome Sequencing Center at Washington University has received funding from NHGRI and HHMI to produce and distribute microarrays for use by C. elegans investigators. We feel that providing a common resource will enable comparability of microarray data sets between C. elegans laboratories. (more)
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| Gut microbes' partnership helps body extract energy from food, store it as fat |
| June 12 2006 |
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Researchers studying mutually beneficial interactions between members of our vast community of friendly gut microorganisms have shown that two common organisms collude and collaborate to increase the amount of calories harvested from a class of carbohydrates found in food sweeteners. (more)
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| Scientists solve 30-year-old mystery of mutant mouse's kidney woes |
| May 1 2006 |
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Researchers seeking insights into kidney failure in human infants have located the source of a 30-year-old mystery mutation that causes similar problems in a mouse line. (more)
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| Washington University's Sarah Elgin is re-funded by Howard Hughes Medical Institute |
| April 24 2006 |
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Sarah C. R. Elgin, Ph.D., professor of biology at Washington University in St. Louis, named a 'Howard Hughes Medical Institute (HHMI) Professor' in 2002, is one of eight scientists to have her original grant funding renewed in 2006. In 2002, Elgin was one of 20 'million dollar professors' to get funding when HHMI announced the program. Recently, HHMI announced the awarding of 20 new such professorships in 2006, in addition to renewal funding to help eight of the 2002 group find ways to sustain the parts of their programs that worked best and to disseminate them to the broader community of science educators. (more)
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| Solutions sought for carbon sequestration, hydrogen production |
| April 21 2006 |
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In just six months of collaboration, a Department of Energy "grand challenge project" led by the University has resulted in the sequencing and annotation of a cyanobacterium gene that could yield clues to how environmental conditions influence key carbon fixation processes at the gene-mRNA-protein levels in an organism. (more)
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| GSC Launches PrimerDB |
| April 5 2006 |
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The Genome Sequencing Center at Washington University School of Medicine announces the release of over 400,000 primer sequences to facilitate the amplification and re-sequencing of human genes. Paired primers spanning the exonic regions of more than fourteen-thousand human genes are currently available. (more)
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| Scientists probe the secrets of maize genome |
| March 17 2006 |
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The Genome Sequencing Center at Washington University is in full swing, sequencing the entire maize genome. (more)
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| New Chimp assembly available |
| March 15 2006 |
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The Genome Sequencing Center (GSC) at Washington University School of Medicine announces the availability of a new 6X draft sequence of the chimpanzee genome. As with the previous 4X draft sequence, the new assembly is derived from a captive born, male western chimpanzee named "Clint" (from the Yerkes Primate Research Center; Atlanta, USA). In addition to the 6x coverage whole genome shotgun derived assembly from "Clint", the assembly benefits from finished regions of chimpanzee chromosome 21 (1). The assembly also benefits from contributed Y chromosome sequence (2). Last, a finished 5 Mb region from chromosome 7 has been integrated into the assembly. This new assembly is now available on all of the major genome browsers and on our FTP server. Previously, the GSC, in conjunction with the Broad Institute (Cambridge, MA) published an analysis of the 4X draft chimpanzee genome sequence analysis in the September 1, 2005 issue of the journal Nature. The 4X draft established a reference for studies highlighting the differences and similarities with our closest living evolutionary relative. From our initial glimpse of the 4X chimpanzee genome, we recognized the need to continue efforts to address regions of discontinuity due to coverage limitations. As part of the recent 6X draft sequence assembly analysis, we employed a comprehensive chimpanzee physical map and other human genome sequence references to assess the continuity, accuracy and coverage of the current 6X draft chimpanzee sequence assembly. Some highlights of this analysis are (1) 38% of the previously identified genes increased in coverage, (2) overall high quality base pair coverage was increased to 97% from an existing 94%, (3) fewer sequence assembly order and orientation errors and (4) additional genes corresponding to human mRNAs were discovered that were not detected using the same criteria in the previous 4X assembly. We expect this new version of the assembly to allow us to more effectively catalog complete chimpanzee genes as well as important conserved regulatory elements of the chimpanzee genome. This work was funded by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH). 1. Courtesy of Todd Taylor and the Riken Genome Sciences Center; Watanabe et al., DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature. 2004 May 27;429(6990):382-8. 2. In collaboration with David Page's group at the Whitehead Institute; The DNA sequence of chimpanzee chromosome Y, unpublished; Hughes et al., Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee (Nature, 2005 437:100-3). The Genome Sequencing Center (GSC) at Washington University School of Medicine announces the availability of a new 6X draft sequence of the chimpanzee genome. As with the previous 4X draft sequence, the new assembly is derived from a captive born, male western chimpanzee named "Clint" (from the Yerkes Primate Research Center; Atlanta, USA). (more)
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| Partnering with community groups improves K-12 science education |
| February 17 2006 |
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The recent revolution in the life sciences- the sequencing of the human genome, and development of "high throughput" technologies- has created new opportunities for investigation, and created new challenges for educators. Sarah C.R. Elgin, Ph.D., professor of biology; biochemistry and molecular biophysics; and education in Arts & Sciences at Washington University in St. Louis, has been a proponent and creator of partnerships locally and nationwide to improve the life science education both in K-12 schools and at the undergraduate level. (more)
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| Researchers Assemble Second Non-Human Primate Genome |
| February 9 2006 |
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A multi-center team has deposited the draft genome sequence of the rhesus macaque monkey into free public databases for use by the worldwide research community, the National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH). (more)
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| New Genome and Epigenome Projects |
| December 15 2005 |
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Richard Wilson, Director of the Genome Sequencing Center, was interviewed by National Public Radio. He discussed the Cancer Genome Project at Washington University and the importance of epigenetic factors. (more)
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| 454 Life Sciences and the Genome Sequencing Center at Washington University School of Medicine in St. Louis Announce Collaborative Research Plan |
| December 7 2005 |
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454 Life Sciences Corporation, a majority-owned subsidiary of CuraGen Corporation (Nasdaq: CRGN), and the Genome Sequencing Center (GSC) at Washington University School of Medicine in St. Louis today announced a collaborative research plan to sequence disease-causing pathogens and to sequence RNA to analyze gene activity in tissue samples. Research will be performed on the 454 Life Sciences' Genome Sequencer 20 Systems at the GSC. (more)
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| Sequencing Maize |
| November 15 2005 |
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Washington University has received $29.5 million to sequence the corn genome. The Genome Sequencing Center has been chosen as the lead institution for a project, jointly sponsored by the National Science Foundation, the U. S. Department of Energy, and the U. S. Department of Agriculture, to sequence the maize genome. Other institutions that will participate are Arizona Genomics Institute (AGI) Tucson, AZ, Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, NY, and Iowa State University, Ames Iowa. (more)
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| Washington University receives $29.5 million to sequence corn genome |
| November 15 2005 |
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Researchers at the Genome Sequencing Center (GSC) at Washington University School of Medicine in St. Louis will lead the sequencing of the genome of maize, more popularly known to consumers as corn. (more)
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| New Genome Comparison Finds Chimps, Humans Very Similar at the DNA Level |
| August 31 2005 |
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The first comprehensive comparison of the genetic blueprints of humans and chimpanzees shows our closest livingrelatives share perfect identity with 96 percent of our DNA sequence, an international research consortium reported. (more)
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| Gene Sequence Study Takes a Stab at Personalized Medicine |
| May 20 2005 |
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Since its beginning 15 years ago, the Human Genome Project was sold to the public and to Congress as a biomedical effort that would ultimately bring a person's unique DNA sequence data to bear on preventing and treating disease. Now the National Human Genome Research Institute (NHGRI), which led the U.S. public sequencing effort, is about to take a controversial step toward that goal. (more)
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| Leading Genome Sequencing Center Turns to BlueArc Titan for DNA Analysis and Storage |
| May 17 2005 |
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BlueArc; Corporation, provider of the world's highest performance, most scalable network storage systems, today announced that the Genome Sequencing Center at Washington University in St. Louis has purchased a multi-tiered Titan system with more than 60 terabytes of capacity, to store and retain genetic research data. (more)
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| Scientists Analyze Chromosomes 2 and 4 |
| April 6 2005 |
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Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions. (more)
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| Researchers Compare Chicken, Human Genomes (see Nature) |
| December 8 2004 |
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An international research consortium has found that chickens and humans share more than half of their genes, but that their DNA sequences diverge in ways that may explain some of the important differences between birds and mammals. The consortium's analysis is published in the Dec. 9 issue of the journal Nature. (more)
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| A transcriptomic analysis of the phylum Nematoda |
| November 14 2004 |
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The phylum Nematoda occupies a huge range of ecological niches, from free-living microbivores to human parasites. We analyzed the genomic biology of the phylum using 265,494 expressed-sequence tag sequences, corresponding to 93,645 putative genes, from 30 species, including 28 parasites. From 35% to 70% of each species' genes had significant similarity to proteins from the model nematode Caenorhabditis elegans. More than half of the putative genes were unique to the phylum, and 23% were unique to the species from which they were derived. We have not yet come close to exhausting the genomic diversity of the phylum. We identified more than 2,600 different known protein domains, some of which had differential abundances between major taxonomic groups of nematodes. We also defined 4,228 nematode-specific protein families from nematode-restricted genes: this class of genes probably underpins species- and higher-level taxonomic disparity. Nematode-specific families are particularly interesting as drug and vaccine targets. (more)
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| Finishing the euchromatic sequence of the human genome |
| October 21 2004 |
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The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers 99% of the euchromatic genome and is accurate to an error rate of 1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead. (more)
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| WUSTL to play key role in sequencing moss genome |
| September 3 2004 |
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The University will be directly involved in sequencing the entire genome of the moss Physcomitrella patens at the Joint Genome Institute (JGI) in Walnut Creek, Calif. (more)
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| Geneticists Receive $2 Million Grant to Study Parasites That Infect 2 Billion |
| May 25 2004 |
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Scientists at the Genome Sequencing Center (GSC) at Washington University School of Medicine in St. Louis have received a four-year, $2 million National Institutes of Health (NIH) grant to study the genetics of two groups of parasitic roundworms, ascaris and hookworm. (more)
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| Chicken Genome Assembled |
| March 1 2004 |
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The National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), today announced that the first draft of the chicken genome sequence has been deposited into free public databases for use by biomedical and agricultural researchers around the globe. (more)
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| Parasitic and Free-Living Nematodes Comparative Gene Expression |
| February 11 2004 |
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Although developmental timing of gene expression is used to infer potential gene function, studies have yet to correlate this information between species. We analyzed 10,921 ESTs in 3311 clusters from first- and infective third-stage larva (L1, L3i) of the parasitic nematode Strongyloides stercoralis and compared the results to Caenorhabditis elegans, a species that has an L3i-like dauer stage. In the comparison of S. stercoralis clusters with stage-specific expression to C. elegans homologs expressed in either dauer or nondauer stages, matches between S. stercoralis L1 and C. elegans nondauer-expressed genes dominated, suggesting conservation in the repertoire of genes expressed during growth in nutrient-rich conditions. For example, S. stercoralis collagen transcripts were abundant in L1 but not L3i, a pattern consistent with C. elegans collagens. Although a greater proportion of S. stercoralis L3i than L1 genes have homologs among the C. elegans dauer-specific transcripts, we did not uncover evidence of a robust conserved L3i/dauer `expression signature.' Strikingly, in comparisons of S. stercoralis clusters to C. elegans homologs with RNAi knockouts, those with significant L1-specific expression were more than twice as likely as L3i-specific clusters to match genes with phenotypes. We also provide functional classifications of S. stercoralis clusters. (more)
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| Chimp Genome Assembled by Sequencing Centers |
| December 12 2003 |
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The National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), today announced the first draft version of the genome sequence of the chimpanzee and its alignment with the human genome. All of the data have been deposited into free public databases and are now available for use by scientists around the world. (more)
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| The Genome Sequence of C. briggsae: A Platform for Comparative Genomics |
| November 17 2003 |
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The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes. (more)
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| Washington University Launches BioMed 21 |
| November 18 2003 |
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Washington University Launches BioMed 21 --- a $300 Million Biomedical Science Initiative to Transform Genome Research into New Medical Treatments. (more)
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| NHGRI Funds Next Generation Of Large-Scale Sequencing Centers |
| November 7 2003 |
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The National Human Genome Research Institute (NHGRI) announced the selection of five centers to carry out a new generation of large-scale sequencing projects designed to maximize the promise of the Human Genome Project and dramatically expand our understanding of human health and disease. (more)
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| Y chromosome sequencing sheds light on infertility, mysteries of maleness |
| July 11 2003 |
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Two studies of the Y chromosome -- the chromosome for maleness -- provide new insights into the mysteries of maleness and the causes and diagnosis of male infertility. (more)
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| The DNA Sequence of Human Chromosome 7 (news) |
| July 9 2003 |
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Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame. (more)
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| Researchers Discover Use of Novel Mechanism Preserves Y Chromosome Genes |
| June 20 2003 |
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A detailed analysis of the just-completed sequence of the human Y chromosome - the chromosome that distinguishes males from females - has uncovered a novel mechanism by which it maintains its genetic integrity. The study is published in the current issue of Nature. (more)
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| Yeast Genomes Reveal New Sites of Gene Control |
| May 30 2003 |
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Researchers at Washington University School of Medicine in St. Louis have begun unraveling the network of genes and proteins that regulate the lives of cells. The investigators compared the genome of the yeast Saccharomyces cerevisiae (S. cerevisiae) to those of five other yeast species to identify all the locations at which molecules known as regulatory proteins attach to DNA to turn genes on and off. The study is published in the May 30 issue of the journal Science. (more)
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| SARS genome sequenced by researcher |
| May 2 2003 |
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While most of the world works to contain the spread of the virus that causes severe acute respiratory syndrome (SARS), the Genome Sequencing Center (GSC) in the School of Medicine has become part of the international effort to understand the microbe. (more)
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| Human Genome Project completed |
| April 18 2003 |
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University researchers and other members of the International Human Genome Consortium announced the successful completion of the Human Genome Project more than two years ahead of schedule at an April 14 news conference in Washington, D.C. (more)
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| Genome Sequencing Center Director Wilson says 'best is yet to come' |
| January 17 2003 |
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With the mapping of the human genome nearly complete, some scientists say that medicine has entered the post-genomics age. But Richard K. Wilson, Ph.D., professor of genetics and of molecular microbiology, disagrees. (more)
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| Mouse genome blueprint published |
| December 13 2002 |
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University researchers, working with a large team of international investigators, have published a draft sequence of the mouse genome -- the genetic blueprint of a mouse -- and an analysis comparing the mouse and human genomes. (more)
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| Initial Sequencing and Analysis of the Mouse Genome |
| December 5 2002 |
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The international Mouse Genome Sequencing Consortium announced the publication of a high-quality draft sequence of the mouse genome - the genetic blueprint of a mouse - together with a comparative analysis of the mouse and human genomes describing insights gleaned from the two sequences. The paper appears in the Dec. 5 issue of the journal Nature. (more)
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| Johnston, Wilson receive genetics appointments |
| August 23 2002 |
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H. Mark Johnston, Ph.D., professor of genetics, has been named interim head of the Department of Genetics in the School of Medicine, and Richard K. Wilson, Ph.D., associate professor of genetics and of molecular microbiology, has been named director of the Genome Sequencing Center. (more)
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| New C.briggsae WGS assembly BLAST database available |
| July 12 2002 |
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The GSC provides blast databases of the current C. briggsae whole genome shotgun assembly (default) and the finished data (13 Mb). The whole genome assembly is experimental and subject to change. Almost all the genome should be present, but we know there is some redundancy so you may get duplicate matches, and there will also be sequence errors and missassemblies. Please treat the results of searches as preliminary unpublished data. In particular, we reserve the right to publish the results of any large scale analyses, and if you wish to use the results of specific searches in a publication you should (a) acknowledge the sequencing centers (the Sanger Institute and the Genome Sequencing Center, Washington University, St Louis) and (b) ensure you are using the most up to date version of the sequence possible. (more)
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| Maize Mitochondrial Sequence Available |
| June 6 2002 |
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All sequence available here are from contigs whose length is greater than 1 kb, thus all data available to the blast server may not be contained here. The number/name of the contig within each sequence file may or may not be permanent to that file. With modification and new data, the contig number/name may change with each sequential update. Any data not on the ftp site which is desired can be requested from the webmaster by email. (more)
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| Draft of mouse genome map now publicly available |
| May 10 2002 |
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A draft sequence of the mouse genome -- the genetic blueprint for the mouse -- has been completed and now is available to the public through databases accessible on the Internet. (more)
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| Waterston wins international Gairdner award |
| April 26 2002 |
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Robert H. Waterston, M.D., Ph.D., director of the Genome Sequencing Center in the School of Medicine, is one of eight scientists to receive the 2002 Gairdner International Award, which this year recognizes exceptional achievement in genomics science. The Gairdner Foundation of Toronto, Canada, announced the awards April 23. Each winner receives $30,000. (more)
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| Article link: Human Genome |
| March 19 2002 |
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Two recent papers using different approaches reported draft sequences of the human genome. The international Human Genome Project (HGP) used the hierarchical shotgun approach, whereas Celera Genomics adopted the whole-genome shotgun (WGS) approach. Here, we analyze whether the latter paper provides a meaningful test of the WGS approach on a mammalian genome. In the Celera paper, the authors did not analyze their own WGS data. Instead, they decomposed the HGP's assembled sequence into a "perfect tiling path", combined it with their WGS data, and assembled the merged data set. To study the implications of this approach, we perform computational analysis and find that a perfect tiling path with 2-fold coverage is sufficient to recover virtually the entirety of a genome assembly. We also examine the manner in which the assembly was anchored to the human genome and conclude that the process primarily depended on the HGP's sequence-tagged site maps, BAC maps, and clone-based sequences. Our analysis indicates that the Celera paper provides neither a meaningful test of the WGS approach nor an independent sequence of the human genome. Our analysis does not imply that a WGS approach could not be successfully applied to assemble a draft sequence of a large mammalian genome, but merely that the Celera paper does not provide such evidence. (more)
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| Waterston awarded first Dan David Prize |
| March 15 2002 |
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Robert H. Waterston, M.D., Ph.D., the James S. McDonnell Professor of Genetics, head of the Department of Genetics and director of the School of Medicine's Genome Sequencing Center, has received the first Dan David Prize for achievements that hold great promise for improving the future. (more)
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| Nature: Complete genome sequence of Salmonella enterica serovar Typhimurium LT2 |
| October 15 2001 |
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Salmonella enterica subspecies I, serovar Typhimurium (S. typhimurium), is a leading cause of human gastroenteritis, and is used as a mouse model of human typhoid fever. The incidence of non-typhoid salmonellosis is increasing worldwide, causing millions of infections and many deaths in the human population each year. Here we sequenced the 4,857-kilobase (kb) chromosome and 94-kb virulence plasmid of S. typhimurium strain LT2. The distribution of close homologues of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously completed genomes of three related bacteria, sample sequencing of both S. enterica serovar Paratyphi A (S. paratyphi A) and Klebsiella pneumoniae, and hybridization of three unsequenced genomes to a microarray of S. typhimurium LT2 genes. Lateral transfer of genes is frequent, with 11% of the S. typhimurium LT2 genes missing from S. enterica serovar Typhi (S. typhi), and 29% missing from Escherichia coli K12. The 352 gene homologues of S. typhimurium LT2 confined to subspecies I of S. enterica--containing most mammalian and bird pathogens--are useful for studies of epidemiology, host specificity and pathogenesis. Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets. (more)
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| Genome project conference to bring renowned experts |
| January 25 2002 |
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The Human Genome Project has raised profound legal, ethical, medical and policy issues. "The Human Genome Project: Expanding the Conversation" at the University's schools of Law and Medicine Jan. 28-29 will assemble scholars from widely divergent disciplines to examine the genomics revolution. (more)
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| Mouse BAC Map Available |
| December 13 2001 |
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Two BAC libraries constructed from C57BL/J6 mouse DNA were fingerprinted at the Genome Sequencing Center, Vancouver, B.C.(BCGSC). Using these fingerprints a BAC map is under construction here and is being used to select a tiling path across the genome. BAC based sequencing incorporating the whole genome shotgun reads began in December 2001. Clones that have been selected for sequencing are registered at the NCBI clone registry. (more)
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| C. elegans Single Nucleotide Polymorphism Data |
| December 13 2001 |
Details of the analysis of this data and methodology for mapping has been described in a recent publication: Stephen R. Wicks, Raymond T. Yeh, Warren R. Gish, Robert H. Waterston, Ronald H.A. Plasterk.
Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nature Genetics 28:160-164. (more)
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| Human BAC and Accession Maps |
| November 21 2001 |
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The clone and accession maps of the human genome have been used to assemble the individual sequence entries into a non-redundant sequence path through the genome. The BAC clone map represents the overlap relationships of 393,216 clones, based on shared restriction fragments. These clones fall into 984 sets of overlapping clones or contigs representing an estimated 97-98% of the human genome. Although large repeated sequences (>75kb) can produce local compressions or can cause false joins between clones arising from different parts of the genome, generally the order of clones in contigs appears to reflect the underlying genome. (more)
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| Five yeast genomes sequenced for gene-by-gene comparison |
| November 16 2001 |
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Researchers in the School of Medicine have sequenced the genomes of five yeast species in only three months' time. (more)
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| Salmonella's genetic makeup deciphered by researchers |
| October 26 2001 |
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Scientists at the School of Medicine have mapped and sequenced the genome for a bacterium that is a leading cause of food poisoning worldwide: Salmonella typhimurium. (more)
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| Mouse Sequencing Consortium achieves major DNA milestone |
| May 18 2001 |
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In only six months, the Mouse Sequencing Consortium (MSC), an international public-private effort to accelerate the sequencing of the mouse genome, has generated enough DNA data to cover the mouse genome three times. (more)
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| Arvidson, Waterston receive faculty achievement awards |
| April 27 2001 |
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For their outstanding academic accomplishments, Raymond E. Arvidson, Ph.D., and Robert H. Waterston, M.D., Ph.D., have been named recipients of faculty achievement awards for 2001. (more)
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| Human genome map published by consortium |
| February 16 2001 |
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The Human Genome Project public consortium an- nounced Monday that it has assembled and published a nearly completed physical map of the human genome --the genetic blueprint for a human being. (more)
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| Nature: The Human Genome |
| February 15 01 |
- The Human Genome
- Sequence and analysis of the human genome
- Genome Maps
- Road maps to our genetic landscape
- Analysis
- Mining the genome for information
(more)
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| First complete DNA sequence of a plant generated |
| January 26 2001 |
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School of Medicine research- ers are part of a team that has generated the first complete DNA sequence of a plant. The team sequenced the genome of Arabidopsis thaliana, a flowering mustard. (more)
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| International team looking for genes involved in depression |
| September 8 2000 |
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Theodore Reich, M.D., the Samuel and Mae S. Ludwig Professor of Psychiatry and professor of genetics at the School of Medicine, will help lead an international team of geneticists in a three-year study attempting to uncover the genetic basis of depression. (more)
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| Medical school faculty receive grants totaling $7.4 million for range of studies |
| September 1 2000 |
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Researchers at the School of Medicine recently have received awards that will fund a wide range of studies. (more)
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| Genome Sequencing Center receives $5 million grant |
| August 10 2000 |
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The School of Medicine's Genome Sequencing Center has received a $5 million grant from The National Human Genome Research Institute. The award will fund the final phase of a collaborative effort to identify variations in the DNA sequence between individuals. (more)
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| Milestone: WU geneticists attend celebration at White House |
| July 13 2000 |
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School of Medicine research- ers went to the White House June 26 to help announce the assembly of a working draft of the human genome. Robert H. Waterston, M.D., Ph.D.; Richard K. Wilson, Ph.D.; and Mundeep Sekhon joined scientists from across the nation in celebrating this milestone in the massive effort to decipher the genome --3 billion DNA letters that make the blueprint for the human body. The Genome Sequencing Center at the medical school has contributed approximately one-fourth of the DNA sequence generated by the Human Genome Project, an international public consortium. (more)
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| Public consortium launches final phase of genome sequencing |
| May 18 2000 |
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The Human Genome Project international consortium has announced the official launch of the second and final phase of the human genome sequencing project -- the effort to decipher the 3 billion DNA letters that make the human body. The milestone marks the transition from the initial phase, generating a "working draft" of the human DNA, to the final phase, producing the complete finished sequence. Sixteen genome centers around the world, including the School of Medicine, officially began Phase two May 9. (more)
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| NAS elects Waterston |
| May 11 2000 |
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Robert H. Waterston, M.D., Ph.D., the James S. McDonnell Professor of Genetics and head of the Department of Genetics at the School of Medicine, has been elected to the National Academy of Sciences (NAS), one of 60 new members chosen May 2. Election to the academy is considered one of the highest honors that can be bestowed on an American scientist or engineer. The newly elected members bring the total number of active members to 1,843. (more)
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| Another milestone is reached in race to map human genome |
| April 6 2000 |
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An international consortium that includes Washington University School of Medicine as a major partner announced March 29 that 2 billion of the 3 billion chemical letters making up the human genetic instruction book have been deciphered. The medical school contributed about one-fourth of this DNA sequence and is generating more. (more)
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| Map of human genes belongs to everyone, says Genome Sequencing Center director |
| March 30 2000 |
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"On March 14, President Bill Clinton and British Prime Minister Tony Blair affirmed their support for the Human Genome Project, which is unraveling the human genetic blueprint," Waterston said. "They gave high praise to the policy of making the emerging map of genetic information freely and immediately available to scientists worldwide. (more)
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| Scientists read first 'chapter' unraveling chromosome 22 |
| December 9 1999 |
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An international research team that includes the medical school's Genome Sequencing Center has achieved a scientific milestone: The collaborators have unraveled, for the first time, the genetic code of an entire human chromosome, a chapter of the human genetic instruction book. (more)
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