Gregory M Cooper

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. pmc Mapping and sequencing of structural variation from eight human genomes
    Jeffrey M Kidd
    Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
    Nature 453:56-64. 2008
  2. pmc Systematic assessment of copy number variant detection via genome-wide SNP genotyping
    Gregory M Cooper
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nat Genet 40:1199-203. 2008
  3. pmc A copy number variation morbidity map of developmental delay
    Gregory M Cooper
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Genet 43:838-46. 2011
  4. ncbi request reprint Mutational and selective effects on copy-number variants in the human genome
    Gregory M Cooper
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nat Genet 39:S22-9. 2007
  5. doi request reprint Qualifying the relationship between sequence conservation and molecular function
    Gregory M Cooper
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 18:201-5. 2008
  6. pmc A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease
    Heather C Mefford
    Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
    Genome Res 19:1579-85. 2009
  7. pmc Population analysis of large copy number variants and hotspots of human genetic disease
    Andy Itsara
    Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
    Am J Hum Genet 84:148-61. 2009
  8. pmc A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay
    Santhosh Girirajan
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
    Nat Genet 42:203-9. 2010
  9. pmc Targeted interrogation of copy number variation using SCIMMkit
    Troy Zerr
    Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 26:120-2. 2010
  10. pmc Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome
    Sarah B Ng
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Genet 42:790-3. 2010

Detail Information

Publications30

  1. pmc Mapping and sequencing of structural variation from eight human genomes
    Jeffrey 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...
  2. pmc Systematic assessment of copy number variant detection via genome-wide SNP genotyping
    Gregory M Cooper
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nat Genet 40:1199-203. 2008
    ....
  3. pmc A copy number variation morbidity map of developmental delay
    Gregory 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...
  4. ncbi request reprint Mutational and selective effects on copy-number variants in the human genome
    Gregory 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...
  5. doi request reprint Qualifying the relationship between sequence conservation and molecular function
    Gregory M Cooper
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 18:201-5. 2008
    ..This hypothesis does not lead to the conclusion that huge amounts of vertebrate genomes are functionally important, but rather that such "functionality" represents molecular noise that has weak or no effect on organismal phenotypes...
  6. pmc A method for rapid, targeted CNV genotyping identifies rare variants associated with neurocognitive disease
    Heather 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...
  7. pmc Population analysis of large copy number variants and hotspots of human genetic disease
    Andy 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...
  8. pmc A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay
    Santhosh 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...
  9. pmc Targeted interrogation of copy number variation using SCIMMkit
    Troy Zerr
    Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 26:120-2. 2010
    ..SCIMMkit is applicable to standardized genome-wide SNP arrays and customized multiplexed SNP panels, providing economy, efficiency and flexibility in experimental design...
  10. pmc Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome
    Sarah 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...
  11. pmc A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures
    Andrew 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...
  12. pmc Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy
    Heather 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...
  13. pmc A general framework for estimating the relative pathogenicity of human genetic variants
    Martin Kircher
    1 Department of Genome Sciences, University of Washington, Seattle, Washington, USA 2
    Nat Genet 46:310-5. 2014
    ..The ability of CADD to prioritize functional, deleterious and pathogenic variants across many functional categories, effect sizes and genetic architectures is unmatched by any current single-annotation method. ..
  14. pmc Massively parallel functional dissection of mammalian enhancers in vivo
    Rupali P Patwardhan
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Biotechnol 30:265-70. 2012
    ....
  15. ncbi request reprint Closing gaps in the human genome with fosmid resources generated from multiple individuals
    Donald Bovee
    Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195, USA
    Nat Genet 40:96-101. 2008
    ....
  16. pmc Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein
    Alexander P Reiner
    University of Washington, Department of Epidemiology, Seattle, WA 98195, USA
    Am J Hum Genet 82:1193-201. 2008
    ....
  17. pmc A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose
    Gregory 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...
  18. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  19. pmc Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes
    Gregory 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...
  20. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard 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 lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  21. pmc Characterization of evolutionary rates and constraints in three Mammalian genomes
    Gregory 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...
  22. pmc ABC: software for interactive browsing of genomic multiple sequence alignment data
    Gregory 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...
  23. ncbi request reprint Trade-offs in detecting evolutionarily constrained sequence by comparative genomics
    Eric 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...
  24. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott 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...
  25. pmc Functional constraint and small insertions and deletions in the ENCODE regions of the human genome
    Taane 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...
  26. pmc Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans
    Sekar 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...
  27. pmc Distribution and intensity of constraint in mammalian genomic sequence
    Gregory 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...
  28. pmc Automated whole-genome multiple alignment of rat, mouse, and human
    Michael 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...
  29. ncbi request reprint Genomic regulatory regions: insights from comparative sequence analysis
    Gregory M Cooper
    Department of Genetics, Stanford University, Stanford, CA 94305 9010, USA
    Curr Opin Genet Dev 13:604-10. 2003
    ....
  30. pmc LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA
    Michael 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...