http://genome.wustl.edu The news feed of The Genome Institute website at http://genome.wustl.edu/ Sun, 19 May 2013 00:00:00 +0100 en-us hourly 1 http://www.symphony-cms.com http://http://genome.wustl.edu/publications/detail/22-mb-of-contiguous-nucleotide-sequence-from-chromosome-iii-of-c-elegans Thu, 03 Mar 1994 +0100 http://http://genome.wustl.edu/publications/detail/22-mb-of-contiguous-nucleotide-sequence-from-chromosome-iii-of-c-elegans As part of our effort to sequence the 100-megabase (Mb) genome of the nematode Caenorhabditis elegans, we have completed the nucleotide sequence of a contiguous 2,181,032 base pairs in the central gene cluster of chromosome III. Analysis of the finished sequence has indicated an average density of about one gene per five kilobases; comparison with the public sequence databases reveals similarities to previously known genes for about one gene in three. In addition, the genomic sequence contains several intriguing features, including putative gene duplications and a variety of other repeats with potential evolutionary implications. http://wupa.wustl.edu/record_archive/1999/03-18-99/articles/NIH.html Thu, 18 Mar 1999 +0100 http://wupa.wustl.edu/record_archive/1999/03-18-99/articles/NIH.html The National Institutes of Health (NIH) announced Monday, March 15, that Washington University School of Medicine is one of three U.S. sites chosen to begin full-scale sequencing of the human genome -- all of the DNA in our chromosomes. Because it contains genes and regulators of gene function, this DNA choreographs the development of a fertilized egg to an adult, tells every cell in our bodies how to function and can cause disease when faulty. http://http://genome.wustl.edu/publications/detail/a-physical-map-of-the-human-y-chromosome Thu, 15 Feb 2001 +0100 http://http://genome.wustl.edu/publications/detail/a-physical-map-of-the-human-y-chromosome The non-recombining region of the human Y chromosome (NRY), which comprises 95% of the chromosome, does not undergo sexual recombination and is present only in males. An understanding of its biological functions has begun to emerge from DNA studies of individuals with partial Y chromosomes, coupled with molecular characterization of genes implicated in gonadal sex reversal, Turner syndrome, graft rejection and spermatogenic failure. But mapping strategies applied successfully elsewhere in the genome have faltered in the NRY, where there is no meiotic recombination map and intrachromosomal repetitive sequences are abundant. Here we report a high-resolution physical map of the euchromatic, centromeric and heterochromatic regions of the NRY and its construction by unusual methods, including genomic clone subtraction and dissection of sequence family variants. Of the map's 758 DNA markers, 136 have multiple locations in the NRY, reflecting its unusually repetitive sequence composition. The markers anchor 1,038 bacterial artificial chromosome clones, 199 of which form a tiling path for sequencing. http://http://genome.wustl.edu/publications/detail/a-physical-map-of-the-mouse-genome Thu, 15 Aug 2002 +0100 http://http://genome.wustl.edu/publications/detail/a-physical-map-of-the-mouse-genome A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs were aligned to the human genome sequence on the basis of 51,486 homology matches, thus enabling use of the conserved synteny (correspondence between chromosome blocks) of the two genomes to accelerate construction of the mouse map. The map provides a framework for assembly of whole-genome shotgun sequence data, and a tile path of clones for generation of the reference sequence. Definition of the human-mouse alignment at this level of resolution enables identification of a mouse clone that corresponds to almost any position in the human genome. The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy. http://www.nhgri.nih.gov/11509418 Wed, 10 Dec 2003 +0100 http://www.nhgri.nih.gov/11509418 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. http://http://genome.wustl.edu/publications/detail/a-genetic-variation-map-for-chicken-with-28-million-single-nucleotide-polymorphisms Thu, 09 Dec 2004 +0100 http://http://genome.wustl.edu/publications/detail/a-genetic-variation-map-for-chicken-with-28-million-single-nucleotide-polymorphisms We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases. http://www.prnewswire.com/cgi-bin/stories.pl?ACCT=104&STORY=/www/story/12-07-2005/0004229332&EDATE= Wed, 07 Dec 2005 +0100 http://www.prnewswire.com/cgi-bin/stories.pl?ACCT=104&STORY=/www/story/12-07-2005/0004229332&EDATE= 454 Life Sciences Corporation, a majority-owned subsidiary of CuraGen Corporation (Nasdaq: CRGN), and The Genome Center 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 Genome Center. http://http://genome.wustl.edu/publications/detail/a-general-coverage-theory-for-shotgun-dna-sequencing Tue, 08 Aug 2006 +0100 http://http://genome.wustl.edu/publications/detail/a-general-coverage-theory-for-shotgun-dna-sequencing The classical theory of shotgun DNA sequencing accounts for neither the placement dependencies that are a fundamental consequence of the forward-reverse sequencing strategy, nor the edge effect that arises for small to moderate-sized genomic targets. These phenomena are relevant to a number of sequencing scenarios, including large-insert BAC and fosmid clones, filtered genomic libraries, and macro-nuclear chromosomes. Here, we report a model that considers these two effects and provides both the expected value of coverage and its variance. Comparison to methyl-filtered maize data shows significant improvement over classical theory. The model is used to analyze coverage performance over a range of small to moderately-sized genomic targets. We find that the read pairing effect and the edge effect interact in a non-trivial fashion. Shorter reads give superior coverage per unit sequence depth relative to longer ones. In principle, end-sequences can be optimized with respect to template insert length; however, optimal performance is unlikely to be realized in most cases because of inherent size variation in any set of targets. Conversely, single-stranded reads exhibit roughly the same coverage attributes as optimized end-reads. Although linking information is lost, single-stranded data should not pose a significant assembly liability if the target represents predominantly low-copy sequence. We also find that random sequencing should be halted at substantially lower redundancies than those now associated with larger projects. Given the enormous amount of data generated per cycle on pyro-sequencing instruments, this observation suggests devising schemes to split each run cycle between two or more projects. This would prevent over-sequencing and would further leverage the pyrosequencing method. http://http://genome.wustl.edu/publications/detail/a-second-generation-human-haplotype-map-of-over-31-million-snps Thu, 18 Oct 2007 +0100 http://http://genome.wustl.edu/publications/detail/a-second-generation-human-haplotype-map-of-over-31-million-snps We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations. http://http://genome.wustl.edu/articles/detail/a-platypus-genetic-story Mon, 15 Dec 2008 +0100 http://http://genome.wustl.edu/articles/detail/a-platypus-genetic-story With a duckbilled face and a round, furry body, there is arguably no mammalian species with as strange a mixture of characteristics as the platypus. And it has the genes to match its odd appearance. http://http://genome.wustl.edu/articles/detail/studying-the-zebra-finch-genome Wed, 01 Apr 2009 +0100 http://http://genome.wustl.edu/articles/detail/studying-the-zebra-finch-genome Nearly all animals make sounds instinctively, but baby songbirds learn to sing in virtually the same way human infants learn to speak: by imitating a parent. http://news.wustl.edu/news/Pages/14295.aspx Tue, 23 Jun 2009 +0100 http://news.wustl.edu/news/Pages/14295.aspx The National Institutes of Health (NIH) has awarded scientists at Washington University School of Medicine in St. Louis four grants totaling $19 million to explore the trillions of microbes that inhabit the human body and determine how they contribute to good health and disease. http://health.usnews.com/articles/health/cancer/2009/06/30/elaine-mardis-and-richard-wilson-taking-cancers-genetic-measure.html Tue, 30 Jun 2009 +0100 http://health.usnews.com/articles/health/cancer/2009/06/30/elaine-mardis-and-richard-wilson-taking-cancers-genetic-measure.html In 2006, only three years after helping to decode the human genome, Elaine Mardis and Richard Wilson were running out of money. http://www.nytimes.com/2010/04/06/science/06bird.html?ref=science Mon, 05 Apr 2010 +0100 http://www.nytimes.com/2010/04/06/science/06bird.html?ref=science Researchers have gained new insights into the brain by decoding the genome of the zebra finch, a songbird whose males learn a single love song from their fathers that they repeat through life. http://http://genome.wustl.edu/publications/detail/genome-remodelling-in-a-basal-like-breast-cancer-metastasis-and-xenograft Thu, 15 Apr 2010 +0100 http://http://genome.wustl.edu/publications/detail/genome-remodelling-in-a-basal-like-breast-cancer-metastasis-and-xenograft Massively parallel DNA sequencing technologies provide an unprecedented ability to screen entire genomes for genetic changes associated with tumour progression. Here we describe the genomic analyses of four DNA samples from an African-American patient with basal-like breast cancer: peripheral blood, the primary tumour, a brain metastasis and a xenograft derived from the primary tumour. The metastasis contained two de novo mutations and a large deletion not present in the primary tumour, and was significantly enriched for 20 shared mutations. The xenograft retained all primary tumour mutations and displayed a mutation enrichment pattern that resembled the metastasis. Two overlapping large deletions, encompassing CTNNA1, were present in all three tumour samples. The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within the primary tumour. Supplementary information is available here.Following are supplementary tables related to the manuscript titled "Genome remodelling in a basal-like breast cancer metastasis and xenograft." 15 April 2010, Nature.The documents are available in Excel format.Last update: 15 April 2010 Supplementary_Table_3a.xls Supplementary_Table_15.xls Supplementary_Table_3b.xls   http://www.telegraph.co.uk/science/7949651/Human-Microbiome-Project-a-map-of-every-bacterium-in-the-body.html Tue, 17 Aug 2010 +0100 http://www.telegraph.co.uk/science/7949651/Human-Microbiome-Project-a-map-of-every-bacterium-in-the-body.html Scientists suspect that some patients fail to respond to conventional treatment for intestinal infections because they are lacking certain bacteria, which have a protective role, found in the normally functioning gut. http://www.businessweek.com/lifestyle/content/healthday/645763.html Wed, 10 Nov 2010 +0100 http://www.businessweek.com/lifestyle/content/healthday/645763.html Researchers have pinpointed a gene with multiple mutations that seems to separate people who die quickly from acute myeloid leukemia (AML) from those who do not. http://http://genome.wustl.edu/articles/detail/1000-genomes-project-pilot-phase-complete Wed, 10 Nov 2010 +0100 http://http://genome.wustl.edu/articles/detail/1000-genomes-project-pilot-phase-complete Small genetic differences between individuals help explain why some people have a higher risk than others for developing illnesses such as diabetes or cancer. The 1000 Genomes Project, an international public-private consortium that includes the Genome Institute and a number of other research centers, has published the most comprehensive map of these genetic differences, called variations, estimated to contain approximately 95 percent of the genetic variation of any person on Earth. http://http://genome.wustl.edu/articles/detail/trichinosis-parasite-gets-dna-decoded Mon, 21 Feb 2011 +0100 http://http://genome.wustl.edu/articles/detail/trichinosis-parasite-gets-dna-decoded Scientists at the Genome Institute and their collaborators have decoded the DNA of the parasitic worm that causes trichinosis, a disease linked to eating raw or undercooked pork or carnivorous wild game animals, such as bear and walrus. http://www.time.com/time/magazine/article/0,9171,2063851,00.html Mon, 18 Apr 2011 +0100 http://www.time.com/time/magazine/article/0,9171,2063851,00.html Treating cancer is a bit like shooting in the dark. Sometimes it works. Sometimes it doesn't. There's no way to predict. That's because while scientists have some crude ideas about how to disable cancer cells, the inner workings of cancer are a mystery for the most part. http://www.technologyreview.com/biomedicine/37198/ Tue, 19 Apr 2011 +0100 http://www.technologyreview.com/biomedicine/37198/ In the fall of 2006, a new machine arrived at what's now known as the Genome Institute at Washington University in St. Louis. It was capable of reading DNA a thousand times as quickly as the facility's earlier machines, and at far less cost. Elaine Mardis, the center's codirector, immediately began using it to sequence cancer tissues, scouring their DNA for mutations. http://http://genome.wustl.edu/publications/detail/a-dominant-mutation-in-rpe65-identified-by-whole-exome-sequencing-causes-retinitis-pigmentosa-with-choroidal-involvement Wed, 08 Jun 2011 +0100 http://http://genome.wustl.edu/publications/detail/a-dominant-mutation-in-rpe65-identified-by-whole-exome-sequencing-causes-retinitis-pigmentosa-with-choroidal-involvement Linkage testing using Affymetrix 6.0 SNP Arrays mapped the disease locus in TCD-G, an Irish family with autosomal dominant retinitis pigmentosa (adRP), to an 8.8 Mb region on 1p31. Of 50 known genes in the region, 11 candidates, including RPE65 and PDE4B, were sequenced using di-deoxy capillary electrophoresis. Simultaneously, a subset of family members was analyzed using Agilent SureSelect All Exome capture, followed by sequencing on an Illumina GAIIx platform. Candidate gene and exome sequencing resulted in the identification of an Asp477Gly mutation in exon 13 of the RPE65 gene tracking with the disease in TCD-G. All coding exons of genes not sequenced to sufficient depth by next generation sequencing were sequenced by di-deoxy sequencing. No other potential disease-causing variants were found to segregate with disease in TCD-G. The Asp477Gly mutation was not present in Irish controls, but was found in a second Irish family provisionally diagnosed with choroideremia, bringing the combined maximum two-point LOD score to 5.3. Mutations in RPE65 are a known cause of recessive Leber congenital amaurosis (LCA) and recessive RP, but no dominant mutations have been reported. Protein modeling suggests that the Asp477Gly mutation may destabilize protein folding, and mutant RPE65 protein migrates marginally faster on SDS-PAGE, compared with wild type. Gene therapy for LCA patients with RPE65 mutations has shown great promise, raising the possibility of related therapies for dominant-acting mutations in this gene. http://http://genome.wustl.edu/publications/detail/clonal-evolution-in-relapsed-acute-myeloid-leukaemia-revealed-by-whole-genome-sequencing Wed, 11 Jan 2012 +0100 http://http://genome.wustl.edu/publications/detail/clonal-evolution-in-relapsed-acute-myeloid-leukaemia-revealed-by-whole-genome-sequencing Most patients with acute myeloid leukaemia (AML) die from progressive disease after relapse, which is associated with clonal evolution at the cytogenetic level. To determine the mutational spectrum associated with relapse, we sequenced the primary tumour and relapse genomes from eight AML patients, and validated hundreds of somatic mutations using deep sequencing; this allowed us to define clonality and clonal evolution patterns precisely at relapse. In addition to discovering novel, recurrently mutated genes (for example, WAC, SMC3, DIS3, DDX41 and DAXX) in AML, we also found two major clonal evolution patterns during AML relapse: (1) the founding clone in the primary tumour gained mutations and evolved into the relapse clone, or (2) a subclone of the founding clone survived initial therapy, gained additional mutations and expanded at relapse. In all cases, chemotherapy failed to eradicate the founding clone. The comparison of relapse-specific versus primary tumour mutations in all eight cases revealed an increase in transversions, probably due to DNA damage caused by cytotoxic chemotherapy. These data demonstrate that AML relapse is associated with the addition of new mutations and clonal evolution, which is shaped, in part, by the chemotherapy that the patients receive to establish and maintain remissions. http://http://genome.wustl.edu/articles/detail/gene-linked-to-fatal-neuroblastoma-in-adolescents-young-adults Tue, 13 Mar 2012 +0100 http://http://genome.wustl.edu/articles/detail/gene-linked-to-fatal-neuroblastoma-in-adolescents-young-adults Researchers at the Genome Institute and St. Jude Children's Research Hospital have identified the first gene mutation associated with a chronic and often fatal form of neuroblastoma that typically strikes adolescents and young adults. http://http://genome.wustl.edu/publications/detail/metabolic-reconstruction-for-metagenomic-data-and-its-application-to-the-human-microbiome Wed, 13 Jun 2012 +0100 http://http://genome.wustl.edu/publications/detail/metabolic-reconstruction-for-metagenomic-data-and-its-application-to-the-human-microbiome Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/humann. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies. http://http://genome.wustl.edu/articles/detail/defining-the-bodys-microbial-ecosystem-the-human-microbiome Thu, 14 Jun 2012 +0100 http://http://genome.wustl.edu/articles/detail/defining-the-bodys-microbial-ecosystem-the-human-microbiome A consortium of some 200 scientists at the Genome Institute, Washington University School of Medicine in St. Louis and elsewhere report findings from the most comprehensive census of the microbial makeup of healthy humans. http://http://genome.wustl.edu/articles/detail/decoding-dna-finds-breast-tumor-signatures-that-predict-response Thu, 14 Jun 2012 +0100 http://http://genome.wustl.edu/articles/detail/decoding-dna-finds-breast-tumor-signatures-that-predict-response Decoding the DNA of patients with advanced breast cancer has allowed scientists to identify distinct cancer "signatures" that could help predict which women are most likely to benefit from estrogen-lowering therapy, while sparing others from unnecessary treatment http://www.charlierose.com/view/interview/12455 Tue, 17 Jul 2012 +0100 http://www.charlierose.com/view/interview/12455 Frontiers in Cancer Research with Gina Kolata, The New York Times; Dr. John DiPersio, MD, PhD, Washington University School of Medicine; and Dr. Lukas Wartman, MD, Washington University School of Medicine. http://http://genome.wustl.edu/articles/detail/some-deadly-breast-cancers-share-genetic-features-with-ovarian-tumors Mon, 01 Oct 2012 +0100 http://http://genome.wustl.edu/articles/detail/some-deadly-breast-cancers-share-genetic-features-with-ovarian-tumors The most comprehensive analysis yet of breast cancer shows that one of the most deadly subtypes is genetically more similar to ovarian tumors than to other breast cancers. http://www.heraldonline.com/2012/11/12/4408678/gene-sequencing-project-identifies.html Mon, 12 Nov 2012 +0100 http://www.heraldonline.com/2012/11/12/4408678/gene-sequencing-project-identifies.html St. Jude Children's Research Hospital - Washington University Pediatric Cancer Genome Project discovery provides insight into a tough-to-cure form of acute myeloid leukemia that lays the groundwork for clinical care advances. http://http://genome.wustl.edu/articles/detail/abnormal-gene-identified-for-rare-childhood-leukemia Tue, 20 Nov 2012 +0100 http://http://genome.wustl.edu/articles/detail/abnormal-gene-identified-for-rare-childhood-leukemia St. Jude Children's Research Hospital - Washington University Pediatric Cancer Genome Project discovery provides insight into a tough-to-cure form of acute myeloid leukemia that lays the groundwork for clinical care advances. http://http://genome.wustl.edu/articles/detail/a-new-genetic-fingerprint-lives-in-your-belly Wed, 05 Dec 2012 +0100 http://http://genome.wustl.edu/articles/detail/a-new-genetic-fingerprint-lives-in-your-belly Our bodies contain far more microbial genes than human genes. And a new study suggests that just as human DNA varies from person to person, so too does the massive collection of microbial DNA in the intestine.