Evan Eichler

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. pmc A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk
    Francesca Antonacci
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Genet 42:745-50. 2010
  2. pmc Personalized copy number and segmental duplication maps using next-generation sequencing
    Can Alkan
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
    Nat Genet 41:1061-7. 2009
  3. 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
  4. pmc Characterization of missing human genome sequences and copy-number polymorphic insertions
    Jeffrey M Kidd
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, USA
    Nat Methods 7:365-71. 2010
  5. pmc Detection of structural variants and indels within exome data
    Emre Karakoc
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
    Nat Methods 9:176-8. 2012
  6. pmc Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
    Brian J O'Roak
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Nature 485:246-50. 2012
  7. pmc Structural diversity and African origin of the 17q21.31 inversion polymorphism
    Karyn Meltz Steinberg
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Genet 44:872-80. 2012
  8. pmc Estimating the human mutation rate using autozygosity in a founder population
    Catarina D Campbell
    Department of Genome Sciences, University of Washington, Seattle, USA
    Nat Genet 44:1277-81. 2012
  9. pmc Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
    Fereydoun Hormozdiari
    School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
    Bioinformatics 26:i350-7. 2010
  10. pmc Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations
    Brian J O'Roak
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
    Nat Genet 43:585-9. 2011

Detail Information

Publications106 found, 100 shown here

  1. pmc A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk
    Francesca Antonacci
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Genet 42:745-50. 2010
    ..Notably, we show that the S2 configuration harbors directly oriented duplications, specifically predisposing this chromosome to disease-associated rearrangement...
  2. pmc Personalized copy number and segmental duplication maps using next-generation sequencing
    Can Alkan
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
    Nat Genet 41:1061-7. 2009
    ..2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology...
  3. 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...
  4. pmc Characterization of missing human genome sequences and copy-number polymorphic insertions
    Jeffrey M Kidd
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, USA
    Nat Methods 7:365-71. 2010
    ....
  5. pmc Detection of structural variants and indels within exome data
    Emre Karakoc
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
    Nat Methods 9:176-8. 2012
    ..The algorithm discovers indels, structural variants, de novo events and copy number-polymorphic processed pseudogenes missed by other methods...
  6. pmc Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
    Brian J O'Roak
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Nature 485:246-50. 2012
    ..Combined with copy number variant (CNV) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics...
  7. pmc Structural diversity and African origin of the 17q21.31 inversion polymorphism
    Karyn Meltz Steinberg
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    Nat Genet 44:872-80. 2012
    ..Whereas H1 and H2 segmental duplications arose independently and before human migration out of Africa, they have reached high frequencies recently among Europeans, either because of extraordinary genetic drift or selective sweeps...
  8. pmc Estimating the human mutation rate using autozygosity in a founder population
    Catarina D Campbell
    Department of Genome Sciences, University of Washington, Seattle, USA
    Nat Genet 44:1277-81. 2012
    ..We observed a non-uniform distribution of heterozygous SNVs (both newly identified and known) in the autozygous segments (P = 0.001), which is suggestive of mutational hotspots or sites of long-range gene conversion...
  9. pmc Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
    Fereydoun Hormozdiari
    School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
    Bioinformatics 26:i350-7. 2010
    ....
  10. pmc Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations
    Brian J O'Roak
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
    Nat Genet 43:585-9. 2011
    ..Our results show that trio-based exome sequencing is a powerful approach for identifying new candidate genes for ASDs and suggest that de novo mutations may contribute substantially to the genetic etiology of ASDs...
  11. pmc Relative burden of large CNVs on a range of neurodevelopmental phenotypes
    Santhosh Girirajan
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, United States of America
    PLoS Genet 7:e1002334. 2011
    ..When autism without ID was considered separately, the increase in CNV burden was modest compared to controls (p = 0.07, odds ratio = 2.33)...
  12. pmc The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild
    Javier Prado-Martinez
    Institut de Biologia Evolutiva, CSIC Universitat Pompeu Fabra, PRBB, Barcelona 08003, Spain
    BMC Genomics 14:363. 2013
    ..Here, we study the genetic cause of his albinism and making use of whole genome sequencing data we find a higher inbreeding coefficient compared to other gorillas...
  13. pmc Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans
    Chris T Yohn
    Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
    PLoS Biol 3:e110. 2005
    ..We speculate on the potential impact of such recent events on the evolution of humans and great apes...
  14. pmc Evolutionary-new centromeres preferentially emerge within gene deserts
    Mariana Lomiento
    Department of Genetics and Microbiology, University of Bari, Via Amendola 165 A, Bari 70126, Italy
    Genome Biol 9:R173. 2008
    ..We hypothesized that these two observations were not merely coincidental and that the absence of genes in the seeding area constituted a crucial condition for the evolutionary-new centromere fixation in the population...
  15. pmc Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication
    Maria Francesca Cardone
    Department of Genetics and Microbiology, University of Bari, Via Amendola, Bari, 70126, Italy
    Genome Biol 9:R28. 2008
    ....
  16. pmc Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigs
    Maria Francesca Cardone
    Department of Genetics and Microbiology, University of Bari, Bari, Italy
    Genome Biol 7:R91. 2006
    ....
  17. pmc Tissue-specific variation in DNA methylation levels along human chromosome 1
    Cecilia De Bustos
    Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    Epigenetics Chromatin 2:7. 2009
    ..CONCLUSION: The varied patterns of methylation differences detected between tissues by our methylation profiling method reinforce the potential functional significance of regional differences in methylation levels outside of CpG islands...
  18. pmc The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
    Tomas Marques-Bonet
    Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
    BMC Genomics 9:384. 2008
    ....
  19. pmc Analysis of recent segmental duplications in the bovine genome
    George E Liu
    USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland 20705, USA
    BMC Genomics 10:571. 2009
    ..Similar to other mammalian draft assemblies, almost half (47% of 94.4 Mb) of these sequences have not been assigned to cattle chromosomes...
  20. pmc Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses
    Belen Hurle
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Evol Biol 11:23. 2011
    ....
  21. pmc 2005 Curt Stern Award address. Introductory speech for Patrick O. Brown
    Evan Eichler
    Department of Genome Sciences and the Howard Hughes Medical Institute, University of Washington School of Medicine, Health Sciences, Seattle, WA 98195, USA
    Am J Hum Genet 79:427-8. 2006
  22. ncbi request reprint Fine-scale structural variation of the human genome
    Eray Tuzun
    Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
    Nat Genet 37:727-32. 2005
    ..These data provide a fine-scale structural variation map of the human genome and the requisite sequence precision for subsequent genetic studies of human disease...
  23. pmc Missing heritability and strategies for finding the underlying causes of complex disease
    Evan E Eichler
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195 5065, USA
    Nat Rev Genet 11:446-50. 2010
    ....
  24. pmc Diversity of human copy number variation and multicopy genes
    Peter H Sudmant
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
    Science 330:641-6. 2010
    ..Our approach makes ~1000 genes accessible to genetic studies of disease association...
  25. 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...
  26. 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...
  27. ncbi request reprint Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolution
    Zhaoshi Jiang
    Department of Genome Sciences, University of Washington School of Medicine and the Howard Hughes Medical Institute, 1705 NE Pacific Street, Seattle, Washington 98195, USA
    Nat Genet 39:1361-8. 2007
    ....
  28. 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...
  29. ncbi request reprint Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia
    Tom Walsh
    Department of Medicine, University of Washington, Seattle, WA 98195, USA
    Science 320:539-43. 2008
    ..These results suggest that multiple, individually rare mutations altering genes in neurodevelopmental pathways contribute to schizophrenia...
  30. pmc A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications
    Xinwei She
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Genome Res 16:576-83. 2006
    ..These architectural shifts in genomic structure and elevated substitution rates have important implications for the emergence of new genes, gene-expression differences, and structural variation among humans and great apes...
  31. ncbi request reprint Optimal design of oligonucleotide microarrays for measurement of DNA copy-number
    Andrew J Sharp
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
    Hum Mol Genet 16:2770-9. 2007
    ....
  32. ncbi request reprint A genome-wide comparison of recent chimpanzee and human segmental duplications
    Ze Cheng
    Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
    Nature 437:88-93. 2005
    ..Nevertheless, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species than single-base-pair substitution (1.2%)...
  33. pmc Duplication within the SEPT9 gene associated with a founder effect in North American families with hereditary neuralgic amyotrophy
    Megan L Landsverk
    Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
    Hum Mol Genet 18:1200-8. 2009
    ..This exon also encodes for a majority of the SEPT9 N-terminal proline rich region suggesting that this region plays a role in the pathogenesis of HNA...
  34. 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
    ....
  35. doi request reprint Human IRGM gene "to be or not to be"
    Cemaletin Bekpen
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    Semin Immunopathol 32:437-44. 2010
    ....
  36. pmc Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data
    Can Alkan
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
    PLoS Comput Biol 3:1807-18. 2007
    ..Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution...
  37. pmc Genome-wide copy number variation in epilepsy: novel susceptibility loci in idiopathic generalized and focal epilepsies
    Heather C Mefford
    Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
    PLoS Genet 6:e1000962. 2010
    ..2, 15q13.3, or 16p13.11, genomic hotspots previously associated with ID, autism, or schizophrenia. In summary, our findings suggest common etiological factors for seemingly diverse diseases such as ID, autism, schizophrenia, and epilepsy...
  38. 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...
  39. pmc Targeted capture and massively parallel sequencing of 12 human exomes
    Sarah B Ng
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 461:272-6. 2009
    ..This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of non-synonymous variants by predicted functional impact...
  40. doi request reprint Sequencing primate genomes: what have we learned?
    Tomas Marques-Bonet
    Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98105, USA
    Annu Rev Genomics Hum Genet 10:355-86. 2009
    ....
  41. pmc Haplotype sorting using human fosmid clone end-sequence pairs
    Jeffrey M Kidd
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Genome Res 18:2016-23. 2008
    ....
  42. pmc Duplication hotspots, rare genomic disorders, and common disease
    Heather C Mefford
    Department of Pediatrics, University of Washington, Seattle, WA 98195, United States
    Curr Opin Genet Dev 19:196-204. 2009
    ..The genomic hotspot model may provide a powerful approach for understanding the role of rare variants in common disease...
  43. 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...
  44. pmc The origins and impact of primate segmental duplications
    Tomas Marques-Bonet
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
    Trends Genet 25:443-54. 2009
    ..Although many genomes will be sequenced in the future, resolution of this aspect of genomic architecture still requires high quality sequences and detailed analyses...
  45. pmc The genomic architecture of segmental duplications and associated copy number variants in dogs
    Thomas J Nicholas
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 19:491-9. 2009
    ..Our results provide insight into mechanisms of canine genome evolution and generate a valuable resource for future evolutionary and phenotypic studies...
  46. 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...
  47. ncbi request reprint Shotgun sequence assembly and recent segmental duplications within the human genome
    Xinwei She
    Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
    Nature 431:927-30. 2004
    ....
  48. pmc Segmental duplications and copy-number variation in the human genome
    Andrew J Sharp
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
    Am J Hum Genet 77:78-88. 2005
    ..Our specialized segmental duplication BAC microarray and associated database of structural polymorphisms will provide an important resource for the future characterization of human genomic disorders...
  49. pmc Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome
    Devin P Locke
    Department of Genome Sciences, University of Washington and Howard Hughes Medical Institute, Seattle, WA 98195, USA
    Am J Hum Genet 79:275-90. 2006
    ..Our results underscore the need for complete maps of genetic variation in duplication-rich regions of the genome...
  50. ncbi request reprint Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome
    Andrew J Sharp
    Department of Genome Sciences and the Howard Hughes Medical Institute, University of Washington School of Medicine, 1705 NE Pacific St, Seattle, Washington 98195, USA
    Nat Genet 38:1038-42. 2006
    ..In common with the 17q21.31 deletion, these breakpoint regions are sites of copy number polymorphism in controls, indicating that these may be inherently unstable genomic regions...
  51. pmc Recurrent duplication-driven transposition of DNA during hominoid evolution
    Matthew E Johnson
    Department of Genome Sciences and the Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 103:17626-31. 2006
    ..Our data support a model of duplication where the probability that a segment of DNA becomes duplicated is determined by its proximity to core duplicons, such as LCR16a...
  52. 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...
  53. pmc Mouse segmental duplication and copy number variation
    Xinwei She
    Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195, USA
    Nat Genet 40:909-14. 2008
    ..We show large and complex patterns of interstrain copy number variation restricted to large gene families associated with spermatogenesis, pregnancy, viviparity, pheromone signaling and immune response...
  54. pmc A burst of segmental duplications in the genome of the African great ape ancestor
    Tomas Marques-Bonet
    Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98195, USA
    Nature 457:877-81. 2009
    ....
  55. pmc Characterization of six human disease-associated inversion polymorphisms
    Francesca Antonacci
    Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
    Hum Mol Genet 18:2555-66. 2009
    ..In these cases, discovery and genotyping methods based on SNPs may be confounded and molecular cytogenetics remains the only method to genotype these inversions...
  56. pmc Completing the map of human genetic variation
    Evan E Eichler
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Nature 447:161-5. 2007
  57. pmc Population stratification of a common APOBEC gene deletion polymorphism
    Jeffrey M Kidd
    Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
    PLoS Genet 3:e63. 2007
    ..These data emphasize the importance of directly genotyping structural variation in association studies and of accurately resolving variant breakpoints before proceeding with more detailed population-genetic analysis...
  58. pmc Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes
    Heather C Mefford
    University of Washington School of Medicine, Seattle 98195, USA
    N Engl J Med 359:1685-99. 2008
    ..Advances in technologies to detect these changes allow for the routine identification of submicroscopic imbalances in large numbers of patients...
  59. pmc A genome-wide survey of structural variation between human and chimpanzee
    Tera L Newman
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Genome Res 15:1344-56. 2005
    ..Furthermore, this work prioritizes regions for further finishing in the chimpanzee genome and provides a resource for interrogating functional differences between humans and chimpanzees...
  60. pmc DupMasker: a tool for annotating primate segmental duplications
    Zhaoshi Jiang
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
    Genome Res 18:1362-8. 2008
    ..We predict this tool will be valuable in the annotation of large-insert sequence clones, allowing putative unique and duplicated regions of the genomes to be annotated prior to whole genome assembly comparisons...
  61. ncbi request reprint High-throughput genotyping of intermediate-size structural variation
    Tera L Newman
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
    Hum Mol Genet 15:1159-67. 2006
    ..The approach we describe may be used to characterize a large number of individuals in a cost-effective manner once the sequence organization of ISVs is known...
  62. 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
    ....
  63. ncbi request reprint Characterization of a recurrent 15q24 microdeletion syndrome
    Andrew J Sharp
    Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street Seattle, WA 98195, USA
    Hum Mol Genet 16:567-72. 2007
    ..Our results define microdeletion of 15q24 as a novel recurrent genomic disorder...
  64. pmc Programmed loss of millions of base pairs from a vertebrate genome
    Jeramiah J Smith
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 106:11212-7. 2009
    ..Understanding the mechanisms by which this vertebrate species regulates such extensive remodeling of its genome will provide invaluable insight into factors that can promote stability and change in vertebrate genomes...
  65. ncbi request reprint Structural variation of the human genome
    Andrew J Sharp
    Department of Genome Sciences, University of Washington, Howard Hughes Medical Institute, Seattle, Washington 98195, USA
    Annu Rev Genomics Hum Genet 7:407-42. 2006
    ..Our current knowledge of the extent of human structural variation shows that the human genome is a highly dynamic structure that shows significant large-scale variation from the currently published genome reference sequence...
  66. pmc Death and resurrection of the human IRGM gene
    Cemalettin Bekpen
    Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
    PLoS Genet 5:e1000403. 2009
    ..Such dynamism in structure and evolution may be critical for a gene family locked in an arms race with an ever-changing repertoire of intracellular parasites...
  67. pmc A human genome structural variation sequencing resource reveals insights into mutational mechanisms
    Jeffrey M Kidd
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, 98195, USA
    Cell 143:837-47. 2010
    ....
  68. pmc Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites
    Santhosh Girirajan
    Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington 98195, USA
    Genome Res 19:178-90. 2009
    ....
  69. doi request reprint SPANX gene variation in fertile and infertile males
    Sierra Hansen
    Institute of Public Health Genetics, University of Washington, Seattle, WA, USA
    Syst Biol Reprod Med 55:18-26. 2010
    ..As this was a targeted assay, it was limited in scope to detect further CNV at a genome-wide level which is an area of increasing interest in the field of genomics...
  70. pmc Copy number variation analysis in single-suture craniosynostosis: multiple rare variants including RUNX2 duplication in two cousins with metopic craniosynostosis
    Heather C Mefford
    Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
    Am J Med Genet A 152:2203-10. 2010
    ..The genes within and disrupted by CNVs in this cohort are potential novel candidate genes for craniosynostosis...
  71. pmc A cascade of complex subtelomeric duplications during the evolution of the hominoid and Old World monkey genomes
    Michel van Geel
    Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY, USA
    Am J Hum Genet 70:269-78. 2002
    ..Our analysis emphasizes the dynamic nature of duplication-mediated genome evolution and the delicate balance between gene acquisition and silencing...
  72. 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
    ....
  73. pmc Analysis of segmental duplications and genome assembly in the mouse
    Jeffrey A Bailey
    Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 4410, USA
    Genome Res 14:789-801. 2004
    ..In addition, our unique method provides the means for improving whole-genome shotgun sequence assembly of mouse and future mammalian genomes...
  74. pmc Hotspots of mammalian chromosomal evolution
    Jeffrey A Bailey
    Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA
    Genome Biol 5:R23. 2004
    ..With the availability of both the human and mouse genomic sequences, detailed analysis of the sequence properties underlying these breakpoints is now possible...
  75. ncbi request reprint The DNA sequence and biology of human chromosome 19
    Jane Grimwood
    Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Avenue, Palo Alto, California 94304, USA
    Nature 428:529-35. 2004
    ....
  76. ncbi request reprint Segmental duplications and the evolution of the primate genome
    Rhea Vallente Samonte
    Department of Genetics and Center for Human Genetics, School of Medicine and University Hospitals of Cleveland, Case Western Reserve University, Cleveland, Ohio 44106, USA
    Nat Rev Genet 3:65-72. 2002
    ..Although the precise fraction is unknown, some of these duplicated segments have recently been shown to be associated with rapid gene innovation and chromosomal rearrangement in the genomes of man and the great apes...
  77. ncbi request reprint Recent segmental duplications in the human genome
    Jeffrey A Bailey
    Department of Genetics, Center for Computational Genomics, and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA
    Science 297:1003-7. 2002
    ..Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity...
  78. pmc Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p
    Jane Guy
    The Institute of Human Genetics, The International Centre For Life, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 3BZ, UK
    Genome Res 13:159-72. 2003
    ..This suggests that any novel gene structures formed by these interchromosomal events would require relocation to a more open chromatin environment to be expressed...
  79. pmc Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization
    Devin P Locke
    Department of Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
    Genome Res 13:347-57. 2003
    ..In contrast to previous cytogenetic and comparative mapping studies, these results indicate extensive local repatterning of hominoid chromosomes in euchromatic regions through a duplication-driven mechanism of genome evolution...
  80. ncbi request reprint The DNA sequence of human chromosome 7
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 424:157-64. 2003
    ..Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame...
  81. ncbi request reprint Structural dynamics of eukaryotic chromosome evolution
    Evan E Eichler
    Department of Genetics, Center for Human Genetics and Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA
    Science 301:793-7. 2003
    ..Computational algorithms that take into account these dynamic forces along with traditional models of chromosomal rearrangement show promise for reconstructing the natural history of eukaryotic chromosomes...
  82. pmc Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22
    Jeffrey A Bailey
    Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, OH, USA
    Am J Hum Genet 70:83-100. 2002
    ....
  83. pmc An Alu transposition model for the origin and expansion of human segmental duplications
    Jeffrey A Bailey
    Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH, 44106, USA
    Am J Hum Genet 73:823-34. 2003
    ....
  84. ncbi request reprint An assessment of the sequence gaps: unfinished business in a finished human genome
    Evan E Eichler
    Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, BRB720, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
    Nat Rev Genet 5:345-54. 2004
  85. ncbi request reprint Complex SNP-related sequence variation in segmental genome duplications
    David Fredman
    Center for Genomics and Bioinformatics, Karolinska Institute, Berzelius vag 35, S 171 77 Stockholm, Sweden
    Nat Genet 36:861-6. 2004
    ..Given that duplicons comprise at least 5% of the genome and many are yet to be annotated in the genome draft, effective strategies to identify multisite variation must be established and deployed...
  86. pmc Segmental duplications flank the multiple sclerosis locus on chromosome 17q
    Daniel C Chen
    Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California 90095, USA
    Genome Res 14:1483-92. 2004
    ....
  87. ncbi request reprint Analysis of the DNA sequence and duplication history of human chromosome 15
    Michael C Zody
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 440:671-5. 2006
    ..Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome...
  88. pmc Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regions
    Stefan Kirsch
    Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany
    Genome Res 18:1030-42. 2008
    ....
  89. pmc Molecular refinement of gibbon genome rearrangements
    Roberta Roberto
    Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
    Genome Res 17:249-57. 2007
    ..Our data emphasize the synergistic effect of combining computational genomics and cytogenetics and provide a framework for ultimate sequence and assembly of the gibbon genome...
  90. pmc Punctuated duplication seeding events during the evolution of human chromosome 2p11
    Julie E Horvath
    Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
    Genome Res 15:914-27. 2005
    ..The data further indicate that factors other than sequence are important determinants for such bursts of duplicative transposition from the euchromatin to pericentromeric regions...
  91. ncbi request reprint Generation and annotation of the DNA sequences of human chromosomes 2 and 4
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 434:724-31. 2005
    ..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...
  92. pmc A comprehensive analysis of common copy-number variations in the human genome
    Kendy K Wong
    Department of Cancer Genetics and Developmental Biology, University of British Columbia, Vancouver, BC, Canada
    Am J Hum Genet 80:91-104. 2007
    ..This in-depth survey of CNVs across the human genome provides a valuable baseline for studies involving human genetics...
  93. ncbi request reprint The sequence and analysis of duplication-rich human chromosome 16
    Joel Martin
    DOE Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA
    Nature 432:988-94. 2004
    ....
  94. ncbi request reprint The DNA sequence and comparative analysis of human chromosome 5
    Jeremy Schmutz
    Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Ave, Palo Alto, California 94304, USA
    Nature 431:268-74. 2004
    ..These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy...
  95. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  96. ncbi request reprint The structure and evolution of centromeric transition regions within the human genome
    Xinwei She
    Department of Genetics, Center for Computational Genomics and the Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
    Nature 430:857-64. 2004
    ..The distribution of these duplicated segments is nonrandom among pericentromeric regions, suggesting that some regions have served as preferential acceptors of euchromatic DNA...
  97. pmc Regional patterns of gene expression in human and chimpanzee brains
    Philipp Khaitovich
    Max Planck Institute for Evolutionary Anthropology, D 04103 Leipzig, Germany
    Genome Res 14:1462-73. 2004
    ..Furthermore, genes that show an elevated expression level in humans are statistically significantly enriched in regions that are recently duplicated in humans...
  98. pmc Hotspots for copy number variation in chimpanzees and humans
    George H Perry
    School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA
    Proc Natl Acad Sci U S A 103:8006-11. 2006
    ..Therefore, some of these regions may be unstable "hotspots" for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species...
  99. ncbi request reprint Evolutionary formation of new centromeres in macaque
    Mario Ventura
    Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
    Science 316:243-6. 2007
    ..Our results suggest that novel centromeres may trigger only local duplication activity and that the absence of genes in the seeding region may have been important in ENC maintenance and progression...
  100. pmc Challenges and standards in integrating surveys of structural variation
    Stephen W Scherer
    The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, 101 College Street, Room 14 701, Ontario M5G 1L7, Canada
    Nat Genet 39:S7-15. 2007
    ..From this, we derive recommendations for standards to be adopted, with the aim of ensuring the accurate presentation of this form of genetic variation to facilitate ongoing research...
  101. pmc Explaining human uniqueness: genome interactions with environment, behaviour and culture
    Ajit Varki
    Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California 92093, USA
    Nat Rev Genet 9:749-63. 2008
    ....

Research Grants34

  1. MECHANISM & INSTABILITY OF PERICENTROMERIC DUPLICATIONS
    Evan Eichler; Fiscal Year: 1999
    ....
  2. MECHANISM AND INSTABILITY OF SEGMENTAL DUPLICATIONS
    Evan Eichler; Fiscal Year: 2006
    ..Furthermore, these detailed studies should provide framework for a more global understanding of the impact of segmental duplications on large-scale genomic variation and disease. ..
  3. Sequence and Assembly of Pericentromeric Duplication
    Evan Eichler; Fiscal Year: 2005
    ..The resolution of these exceptional regions is, therefore, critical for accurate assembly and annotation of genomes. ..
  4. Sequence and Assembly of Pericentromeric Duplication
    Evan Eichler; Fiscal Year: 2006
    ..The resolution of these exceptional regions is, therefore, critical for accurate assembly and annotation of genomes. ..
  5. SEGMENTAL ANEUSOMY BETWEEN BLOCKS OF DUPLICATED DNA
    Evan Eichler; Fiscal Year: 2007
    ..RESEARCH GRANT TABLE OF CONTENTS Page Numbers Face Page .................................................................................................................................................. 1 Description, ..
  6. MECHANISM AND INSTABILITY OF SEGMENTAL DUPLICATIONS
    Evan Eichler; Fiscal Year: 2007
    ....
  7. Sequence and Assembly of Segmental Duplications
    Evan Eichler; Fiscal Year: 2007
    ..Such targeted studies are essential to complete our understanding of the evolution of the human genome. ..
  8. MECHANISM AND INSTABILITY OF SEGMENTAL DUPLICATIONS
    Evan Eichler; Fiscal Year: 2009
    ....
  9. Sequence and Assembly of Segmental Duplications
    Evan Eichler; Fiscal Year: 2009
    ..Such targeted studies are essential to complete our understanding of the evolution of the human genome. ..
  10. Genomic Identification of Autism Loci
    Evan Eichler; Fiscal Year: 2009
    ..Such subcategorizations of autism will significantly enhance phenotypic characterization leading to future downstream treatments and interventions for autism. ..
  11. MECHANISM AND INSTABILITY OF SEGMENTAL DUPLICATIONS
    Evan E Eichler; Fiscal Year: 2010
    ....
  12. Genomic Identification of Autism Loci
    Evan E Eichler; Fiscal Year: 2010
    ..Such subcategorizations of autism will significantly enhance phenotypic characterization leading to future downstream treatments and interventions for autism. ..
  13. SEGMENTAL ANEUSOMY BETWEEN BLOCKS OF DUPLICATED DNA
    Evan Eichler; Fiscal Year: 2006
    ..what is the nature and frequency of duplication-mediated structural polymorphisms within the human genome? Are there an excess of de novo events among children with mental retardation and congenital birth defects? ..
  14. Sequence and Assembly of Pericentromeric Duplication
    Evan Eichler; Fiscal Year: 2005
    ..The resolution of these exceptional regions is, therefore, critical for accurate assembly and annotation of genomes. ..
  15. MECHANISM & INSTABILITY OF PERICENTROMERIC DUPLICATIONS
    Evan Eichler; Fiscal Year: 2000
    ....
  16. SEQUENCE AND ASSEMBLY OF PERICENTROMERIC DUPLICATIONS
    Evan Eichler; Fiscal Year: 2001
    ..These results should provide the framework for understanding the peculiar genomic architecture of pericentromeric DNA and for defining the instability of these regions with respect to genetic disease. ..
  17. MECHANISM & INSTABILITY OF PERICENTROMERIC DUPLICATIONS
    Evan Eichler; Fiscal Year: 2001
    ....
  18. MECHANISM & INSTABILITY OF PERICENTROMERIC DUPLICATIONS
    Evan Eichler; Fiscal Year: 2002
    ....
  19. SEQUENCE AND ASSEMBLY OF PERICENTROMERIC DUPLICATIONS
    Evan Eichler; Fiscal Year: 2002
    ..These results should provide the framework for understanding the peculiar genomic architecture of pericentromeric DNA and for defining the instability of these regions with respect to genetic disease. ..
  20. SEGMENTAL ANEUSOMY BETWEEN BLOCKS OF DUPLICATED DNA
    Evan Eichler; Fiscal Year: 2003
    ..fundamental questions; what is the nature and frequency of duplication-mediated structural polymorphisms within the human genome? Are there an excess of de novo events among children with mental retardation and congenital birth defects? ..
  21. MECHANISM AND INSTABILITY OF SEGMENTAL DUPLICATIONS
    Evan Eichler; Fiscal Year: 2003
    ..Furthermore, these detailed studies should provide framework for a more global understanding of the impact of segmental duplications on large-scale genomic variation and disease. ..
  22. SEQUENCE AND ASSEMBLY OF PERICENTROMERIC DUPLICATIONS
    Evan Eichler; Fiscal Year: 2003
    ..These results should provide the framework for understanding the peculiar genomic architecture of pericentromeric DNA and for defining the instability of these regions with respect to genetic disease. ..
  23. MECHANISM AND INSTABILITY OF SEGMENTAL DUPLICATIONS
    Evan Eichler; Fiscal Year: 2004
    ..Furthermore, these detailed studies should provide framework for a more global understanding of the impact of segmental duplications on large-scale genomic variation and disease. ..
  24. Sequence and Assembly of Pericentromeric Duplication
    Evan Eichler; Fiscal Year: 2004
    ..The resolution of these exceptional regions is, therefore, critical for accurate assembly and annotation of genomes. ..
  25. MECHANISM AND INSTABILITY OF SEGMENTAL DUPLICATIONS
    Evan Eichler; Fiscal Year: 2005
    ..Furthermore, these detailed studies should provide framework for a more global understanding of the impact of segmental duplications on large-scale genomic variation and disease. ..
  26. MECHANISM AND INSTABILITY OF SEGMENTAL DUPLICATIONS
    Evan Eichler; Fiscal Year: 2004
    ..Furthermore, these detailed studies should provide framework for a more global understanding of the impact of segmental duplications on large-scale genomic variation and disease. ..
  27. Sequence and Assembly of Segmental Duplications
    Evan E Eichler; Fiscal Year: 2010
    ....