Research Topics
Genomes and GenesSpecies | Gregory M CooperSummaryAffiliation: University of Washington Country: USA Publications
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Publications
Mapping and sequencing of structural variation from eight human genomesJeffrey M Kidd
Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
Nature 453:56-64. 2008..These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects...- Systematic assessment of copy number variant detection via genome-wide SNP genotypingGregory M Cooper
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Nat Genet 40:1199-203. 2008.... 
Qualifying the relationship between sequence conservation and molecular functionGregory M Cooper
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Genome Res 18:201-5. 2008....
Mutational and selective effects on copy-number variants in the human genomeGregory M Cooper
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Nat Genet 39:S22-9. 2007..Although defining these variants with nucleotide-level precision remains a largely unmet but critical challenge, our understanding of their potential medical impact and evolutionary importance is rapidly emerging...- A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive diseaseHeather C Mefford
Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
Genome Res 19:1579-85. 2009..More generally, this approach offers a previously unavailable balance between customization, cost, and throughput for analysis of CNVs and should prove valuable for targeted CNV detection in both research and diagnostic settings... - A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delaySanthosh Girirajan
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
Nat Genet 42:203-9. 2010..Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease... - Population analysis of large copy number variants and hotspots of human genetic diseaseAndy Itsara
Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
Am J Hum Genet 84:148-61. 2009..g., 3q29, 16p12, and 15q25.2) for further investigation. This study provides one of the first analyses of large, rare (0.1%-1%) CNVs in the general population, with insights relevant to future analyses of genetic disease... - Targeted interrogation of copy number variation using SCIMMkitTroy Zerr
Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
Bioinformatics 26:120-2. 2010..AVAILABILITY: Source code and documentation are available for noncommercial use at http://droog.gs.washington.edu/scimmkit... - Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndromeSarah B Ng
Department of Genome Sciences, University of Washington, Seattle, Washington, USA
Nat Genet 42:790-3. 2010..Our results strongly suggest that mutations in MLL2 are a major cause of Kabuki syndrome... - A copy number variation morbidity map of developmental delayGregory M Cooper
Department of Genome Sciences, University of Washington, Seattle, Washington, USA
Nat Genet 43:838-46. 2011..This evolving CNV morbidity map, combined with exome and genome sequencing, will be critical for deciphering the genetic basis of developmental delay, intellectual disability and autism spectrum disorders... - A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizuresAndrew J Sharp
Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific St, Seattle, Washington 98195, USA
Nat Genet 40:322-8. 2008..The frequency of these microdeletions in mental retardation cases is approximately 0.3% (6/2,082 tested), a prevalence comparable to that of Williams, Angelman and Prader-Willi syndromes... - Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsyHeather C Mefford
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
Am J Hum Genet 81:1057-69. 2007..We also identified the reciprocal duplication, which appears to be enriched in samples from patients with epilepsy. We describe the first example of a recurrent genomic disorder associated with diabetes... - Massively parallel functional dissection of mammalian enhancers in vivoRupali P Patwardhan
Department of Genome Sciences, University of Washington, Seattle, Washington, USA
Nat Biotechnol 30:265-70. 2012.... - A genome-wide scan for common genetic variants with a large influence on warfarin maintenance doseGregory M Cooper
Department of Genome Sciences, University of Washington, Seattle, WA98195, USA
Blood 112:1022-7. 2008..Randomized clinical trials that account for these 2 genes should therefore produce results that are definitive and broadly applicable... - Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive proteinAlexander P Reiner
University of Washington, Department of Epidemiology, Seattle, WA 98195, USA
Am J Hum Genet 82:1193-201. 2008.... - Closing gaps in the human genome with fosmid resources generated from multiple individualsDonald Bovee
Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195, USA
Nat Genet 40:96-101. 2008.... - ABC: software for interactive browsing of genomic multiple sequence alignment dataGregory M Cooper
Department of Genetics, Stanford University, Stanford, CA 94305 9010, USA
BMC Bioinformatics 5:192. 2004..Visualization and browsing of results can be difficult, and there are currently limited software options for performing this task... - Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRichard A Gibbs
Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA <http://www.hgsc.bcm.tmc.edu
Nature 428:493-521. 2004.... - Quantitative estimates of sequence divergence for comparative analyses of mammalian genomesGregory M Cooper
Department of Genetics, Stanford University, Stanford, California 94305, USA
Genome Res 13:813-20. 2003..Estimates of the neutral divergence in these data suggest that a small number of diverse mammalian genomes in addition to human, mouse, and rat would allow single nucleotide resolution in comparative sequence analyses... - Trade-offs in detecting evolutionarily constrained sequence by comparative genomicsEric A Stone
Department of Statistics, Stanford University, Stanford, California 94305, USA
Annu Rev Genomics Hum Genet 6:143-64. 2005..We consider the impact of an expanding diversity of orthologous sequences on our ability to resolve functional elements. This impact is assessed through both recent comparative analyses of deep alignments and mathematical modeling... - Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genomeElliott H Margulies
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
Genome Res 17:760-74. 2007..Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - Functional constraint and small insertions and deletions in the ENCODE regions of the human genomeTaane G Clark
Department of Epidemiology and Public Health, Imperial College, Norfolk Place, London, W2 1PG, UK
Genome Biol 8:R180. 2007..We relate indels to known genomic annotation features and measures of evolutionary constraint... - Characterization of evolutionary rates and constraints in three Mammalian genomesGregory M Cooper
Department of Genetics, Stanford University, Stanford, California 94305, USA
Genome Res 14:539-48. 2004..At least 5% of the human genome is under substantial constraint, most of which is noncoding... - Genomic regulatory regions: insights from comparative sequence analysisGregory M Cooper
Department of Genetics, Stanford University, Stanford, CA 94305-9010, USA
Curr Opin Genet Dev 13:604-10. 2003.... - Automated whole-genome multiple alignment of rat, mouse, and humanMichael Brudno
Department of Computer Science, Stanford University, Stanford, California 94305, USA
Genome Res 14:685-92. 2004..5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present... - Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humansSekar Kathiresan
Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
Nat Genet 40:189-97. 2008..Understanding the molecular, cellular and clinical consequences of the newly identified loci may inform therapy and clinical care... - Distribution and intensity of constraint in mammalian genomic sequenceGregory M Cooper
Department of Genetics, Stanford University, Stanford, California 94305, USA
Genome Res 15:901-13. 2005..We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer... - LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNAMichael Brudno
Department of Computer Science, Stanford University, Stanford, California 94305-9010, USA
Genome Res 13:721-31. 2003..Multi-LAGAN is a practical method for generating multiple alignments of long genomic sequences at any evolutionary distance. Our systems are publicly available at http://lagan.stanford.edu...