Research Topics
| Evan EichlerSummaryAffiliation: University of Washington Country: USA Publications
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Detail Information
Publications
Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutansChris 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...- Evolutionary-new centromeres preferentially emerge within gene desertsMariana 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... - Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplicationMaria Francesca Cardone
Department of Genetics and Microbiology, University of Bari, Via Amendola, Bari, 70126, Italy
Genome Biol 9:R28. 2008.... - Independent centromere formation in a capricious, gene-free domain of chromosome 13q21 in Old World monkeys and pigsMaria Francesca Cardone
Department of Genetics and Microbiology, University of Bari, Bari, Italy
Genome Biol 7:R91. 2006..Comparison of the pericentromeric organization of chromosome 13 in four Old World monkey species revealed many differences in sequence organization. The region contains clusters of duplicons showing peculiar features... - Tissue-specific variation in DNA methylation levels along human chromosome 1Cecilia 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... - The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangementsTomas 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.... - Analysis of recent segmental duplications in the bovine genomeGeorge 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... - Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analysesBelen Hurle
Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
BMC Evol Biol 11:23. 2011.... - Missing heritability and strategies for finding the underlying causes of complex diseaseEvan E Eichler
Department of Genome Sciences, University of Washington, Seattle, Washington 98195 5065, USA
Nat Rev Genet 11:446-50. 2010.... - 2005 Curt Stern Award address. Introductory speech for Patrick O. BrownEvan 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 
Fine-scale structural variation of the human genomeEray 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...- Diversity of human copy number variation and multicopy genesPeter 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... - 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... - Personalized copy number and segmental duplication maps using next-generation sequencingCan 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... - Ancestral reconstruction of segmental duplications reveals punctuated cores of human genome evolutionZhaoshi 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.... - A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease riskFrancesca 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... - 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... 
Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophreniaTom 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...- 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... - Optimal design of oligonucleotide microarrays for measurement of DNA copy-numberAndrew J Sharp
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
Hum Mol Genet 16:2770-9. 2007.... - Duplication within the SEPT9 gene associated with a founder effect in North American families with hereditary neuralgic amyotrophyMegan 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... - A genome-wide comparison of recent chimpanzee and human segmental duplicationsZe 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%)... - A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplicationsXinwei 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... - 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... - Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genomeDevin 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... - Discovery of previously unidentified genomic disorders from the duplication architecture of the human genomeAndrew 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... - 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... - Characterization of missing human genome sequences and copy-number polymorphic insertionsJeffrey M Kidd
Department of Genome Sciences, University of Washington School of Medicine, Seattle, USA
Nat Methods 7:365-71. 2010.... - Recurrent duplication-driven transposition of DNA during hominoid evolutionMatthew 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... - Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence dataCan 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... - Duplication hotspots, rare genomic disorders, and common diseaseHeather 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... - 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... - 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.... - The origins and impact of primate segmental duplicationsTomas 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... - 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... - The genomic architecture of segmental duplications and associated copy number variants in dogsThomas 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... - Shotgun sequence assembly and recent segmental duplications within the human genomeXinwei She
Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
Nature 431:927-30. 2004.... - Haplotype sorting using human fosmid clone end-sequence pairsJeffrey M Kidd
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
Genome Res 18:2016-23. 2008.... - 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.... - Genome-wide copy number variation in epilepsy: novel susceptibility loci in idiopathic generalized and focal epilepsiesHeather 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... - Segmental duplications and copy-number variation in the human genomeAndrew 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... - 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.... - Targeted capture and massively parallel sequencing of 12 human exomesSarah 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... - A burst of segmental duplications in the genome of the African great ape ancestorTomas Marques-Bonet
Department of Genome Sciences, University of Washington and the Howard Hughes Medical Institute, Seattle, Washington 98195, USA
Nature 457:877-81. 2009.... - Characterization of six human disease-associated inversion polymorphismsFrancesca 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... - 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... - Mouse segmental duplication and copy number variationXinwei 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... - Completing the map of human genetic variationEvan E Eichler
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
Nature 447:161-5. 2007 - Population stratification of a common APOBEC gene deletion polymorphismJeffrey 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... - A genome-wide survey of structural variation between human and chimpanzeeTera 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... - Programmed loss of millions of base pairs from a vertebrate genomeJeramiah 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... - Characterization of a recurrent 15q24 microdeletion syndromeAndrew 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... - Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypesHeather 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... - DupMasker: a tool for annotating primate segmental duplicationsZhaoshi 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... - 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.... - High-throughput genotyping of intermediate-size structural variationTera 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... - Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sitesSanthosh 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.... - Structural variation of the human genomeAndrew 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... - Death and resurrection of the human IRGM geneCemalettin 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... - A human genome structural variation sequencing resource reveals insights into mutational mechanismsJeffrey M Kidd
Department of Genome Sciences, University of Washington School of Medicine, Seattle, 98195, USA
Cell 143:837-47. 2010.... - Copy number variation analysis in single-suture craniosynostosis: multiple rare variants including RUNX2 duplication in two cousins with metopic craniosynostosisHeather 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... - SPANX gene variation in fertile and infertile malesSierra 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... - Recent segmental duplications in the human genomeJeffrey 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... - An assessment of the sequence gaps: unfinished business in a finished human genomeEvan 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 - Analysis of segmental duplications and genome assembly in the mouseJeffrey 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... - A cascade of complex subtelomeric duplications during the evolution of the hominoid and Old World monkey genomesMichel 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... - The DNA sequence and biology of human chromosome 19Jane 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.... - Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10pJane 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... - An Alu transposition model for the origin and expansion of human segmental duplicationsJeffrey 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.... - 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.... - Large-scale variation among human and great ape genomes determined by array comparative genomic hybridizationDevin 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... - The DNA sequence of human chromosome 7Ladeana 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... - Structural dynamics of eukaryotic chromosome evolutionEvan 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... - Segmental duplications and the evolution of the primate genomeRhea 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... - Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22Jeffrey 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.... - Complex SNP-related sequence variation in segmental genome duplicationsDavid Fredman
Center for Genomics and Bioinformatics, Karolinska Institute, , 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... - Evolutionary and biomedical insights from the rhesus macaque genomeRichard 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... - Generation and annotation of the DNA sequences of human chromosomes 2 and 4Ladeana 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... - Punctuated duplication seeding events during the evolution of human chromosome 2p11Julie 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... - Evolutionary dynamics of segmental duplications from human Y-chromosomal euchromatin/heterochromatin transition regionsStefan Kirsch
Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany
Genome Res 18:1030-42. 2008.... - Analysis of the DNA sequence and duplication history of human chromosome 15Michael 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... - Hotspots for copy number variation in chimpanzees and humansGeorge 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... - A comprehensive analysis of common copy-number variations in the human genomeKendy 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... - Molecular refinement of gibbon genome rearrangementsRoberta 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... - Hotspots of mammalian chromosomal evolutionJeffrey 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.... - The sequence and analysis of duplication-rich human chromosome 16Joel Martin
DOE Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA
Nature 432:988-94. 2004.... - Segmental duplications flank the multiple sclerosis locus on chromosome 17qDaniel 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.... - The DNA sequence and comparative analysis of human chromosome 5Jeremy 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... - Regional patterns of gene expression in human and chimpanzee brainsPhilipp 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... - The structure and evolution of centromeric transition regions within the human genomeXinwei 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... - Challenges and standards in integrating surveys of structural variationStephen 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... - Recent segmental duplications in the working draft assembly of the brown Norway ratEray Tuzun
Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
Genome Res 14:493-506. 2004..2 Mb), indicating that segmental duplications have been problematic for sequence and assembly of the rat genome. Further targeted efforts are required to resolve the organization and complexity of these regions... - Explaining human uniqueness: genome interactions with environment, behaviour and cultureAjit 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.... - Widening the spectrum of human genetic variationEvan E Eichler
Nat Genet 38:9-11. 2006 - Evolutionary formation of new centromeres in macaqueMario 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... - Whole-genome shotgun assembly and comparison of human genome assembliesSorin Istrail
Applied Biosystems, 45 West Gude Drive, Rockville, MD 20850, USA
Proc Natl Acad Sci U S A 101:1916-21. 2004..The Celera results provide more order and orientation, and the consortium sequence provides better coverage of exact and nearly exact repeats... - Genomes and evolution. From sequence to organismEvan E Eichler
Curr Opin Genet Dev 13:559-61. 2003 - Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication clusterDevin P Locke
Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine, University Hospitals of Cleveland, Cleveland, OH 44106, USA
Genome Biol 4:R50. 2003..Reproductive isolation and subsequent speciation are thought to be the potential result of pericentric inversions, as reproductive boundaries form as a result of hybrid sterility...
Research Grants
- MECHANISM AND INSTABILITY OF SEGMENTAL DUPLICATIONSEvan 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. ..
- Sequence and Assembly of Pericentromeric DuplicationEvan Eichler; Fiscal Year: 2006..The resolution of these exceptional regions is, therefore, critical for accurate assembly and annotation of genomes. ..
- SEGMENTAL ANEUSOMY BETWEEN BLOCKS OF DUPLICATED DNAEvan Eichler; Fiscal Year: 2007..RESEARCH GRANT TABLE OF CONTENTS Page Numbers Face Page .................................................................................................................................................. 1 Description, ..
- MECHANISM AND INSTABILITY OF SEGMENTAL DUPLICATIONSEvan Eichler; Fiscal Year: 2007....
- Sequence and Assembly of Segmental DuplicationsEvan Eichler; Fiscal Year: 2007..Such targeted studies are essential to complete our understanding of the evolution of the human genome. ..
- Sequence and Assembly of Segmental DuplicationsEvan Eichler; Fiscal Year: 2009..Such targeted studies are essential to complete our understanding of the evolution of the human genome. ..
- Genomic Identification of Autism LociEvan Eichler; Fiscal Year: 2009..Such subcategorizations of autism will significantly enhance phenotypic characterization leading to future downstream treatments and interventions for autism. ..
- MECHANISM AND INSTABILITY OF SEGMENTAL DUPLICATIONSEvan E Eichler; Fiscal Year: 2010....
- Genomic Identification of Autism LociEvan E Eichler; Fiscal Year: 2010..Such subcategorizations of autism will significantly enhance phenotypic characterization leading to future downstream treatments and interventions for autism. ..
- SEGMENTAL ANEUSOMY BETWEEN BLOCKS OF DUPLICATED DNAEvan 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? ..
- MECHANISM & INSTABILITY OF PERICENTROMERIC DUPLICATIONSEvan Eichler; Fiscal Year: 2002....
- SEGMENTAL ANEUSOMY BETWEEN BLOCKS OF DUPLICATED DNAEvan 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? ..
- SEQUENCE AND ASSEMBLY OF PERICENTROMERIC DUPLICATIONSEvan 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. ..
- Sequence and Assembly of Segmental DuplicationsEvan E Eichler; Fiscal Year: 2010....