Primate segmental duplications: crucibles of evolution, diversity and disease

[1]  Junjun Zhang,et al.  Hotspots for copy number variation in chimpanzees and humans. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[2]  E. Eichler,et al.  A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications. , 2006, Genome research.

[3]  Sinead B. O'Leary,et al.  Analysis of the DNA sequence and duplication history of human chromosome 15 , 2006, Nature.

[4]  Enrico Petretto,et al.  Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans , 2006, Nature.

[5]  J. Lupski,et al.  Spastic paraplegia type 2 associated with axonal neuropathy and apparent PLP1 position effect , 2006, Annals of neurology.

[6]  L. Feuk,et al.  Structural variation in the human genome , 2006, Nature Reviews Genetics.

[7]  Evan E Eichler,et al.  Widening the spectrum of human genetic variation , 2006, Nature Genetics.

[8]  S. Scherer,et al.  Murine segmental duplications are hot spots for chromosome and gene evolution. , 2005, Genomics.

[9]  N. Carter,et al.  Heterogeneous duplications in patients with Pelizaeus-Merzbacher disease suggest a mechanism of coupled homologous and nonhomologous recombination. , 2005, American journal of human genetics.

[10]  J. Souciet,et al.  Duplication processes in Saccharomyces cerevisiae haploid strains , 2005, Nucleic acids research.

[11]  A. Gentles,et al.  Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome. , 2005, Genome research.

[12]  M. Hurles,et al.  Evidence for widespread reticulate evolution within human duplicons. , 2005, American journal of human genetics.

[13]  M. Laan,et al.  Segmental duplications and gene conversion: Human luteinizing hormone/chorionic gonadotropin beta gene cluster. , 2005, Genome research.

[14]  E. Eichler,et al.  A genome-wide survey of structural variation between human and chimpanzee. , 2005, Genome research.

[15]  L. Feuk,et al.  Discovery of Human Inversion Polymorphisms by Comparative Analysis of Human and Chimpanzee DNA Sequence Assemblies , 2005, PLoS genetics.

[16]  C. Ponting,et al.  Duplication and positive selection among hominin-specific PRAME genes , 2005, BMC Genomics.

[17]  L. Pérez-Jurado,et al.  Evolutionary mechanisms shaping the genomic structure of the Williams-Beuren syndrome chromosomal region at human 7q11.23. , 2005, Genome research.

[18]  P. D. de Jong,et al.  Independent intrachromosomal recombination events underlie the pericentric inversions of chimpanzee and gorilla chromosomes homologous to human chromosome 16. , 2005, Genome research.

[19]  Barbara J. Trask,et al.  Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication , 2005, Nature.

[20]  Jean L. Chang,et al.  Initial sequence of the chimpanzee genome and comparison with the human genome , 2005, Nature.

[21]  E. Eichler,et al.  A genome-wide comparison of recent chimpanzee and human segmental duplications , 2005, Nature.

[22]  A. Jeffreys,et al.  Factors influencing recombination frequency and distribution in a human meiotic crossover hotspot. , 2005, Human molecular genetics.

[23]  P. Pevzner,et al.  Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps , 2005, Science.

[24]  E. Eichler,et al.  Segmental duplications and copy-number variation in the human genome. , 2005, American journal of human genetics.

[25]  E. Eichler,et al.  Punctuated duplication seeding events during the evolution of human chromosome 2p11. , 2005, Genome research.

[26]  E. Eichler,et al.  Fine-scale structural variation of the human genome , 2005, Nature Genetics.

[27]  D. Cooper,et al.  Molecular characterisation of the pericentric inversion that distinguishes human chromosome 5 from the homologous chimpanzee chromosome , 2005, Human Genetics.

[28]  S. Deeb,et al.  The molecular basis of variation in human color vision , 2005, Clinical genetics.

[29]  M. Ehrlich,et al.  Frequent DNA hypomethylation of human juxtacentromeric BAGE loci in cancer , 2005, Genes, chromosomes & cancer.

[30]  M. Platzer,et al.  Molecular characterization of the pericentric inversion of chimpanzee chromosome 11 homologous to human chromosome 9. , 2005, Genomics.

[31]  P. Stankiewicz,et al.  Position effects due to chromosome breakpoints that map ∼900 Kb upstream and ∼1.3 Mb downstream of SOX9 in two patients with campomelic dysplasia , 2005 .

[32]  B. Mishra,et al.  Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[33]  B. Rovin,et al.  The Influence of CCL 3 L 1 Gene – Containing Segmental Duplications on HIV-1 / AIDS Susceptibility , 2009 .

[34]  M. Suyama,et al.  Complex genomic rearrangements lead to novel primate gene function. , 2005, Genome research.

[35]  E. Eichler,et al.  Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome. , 2005, Genome research.

[36]  H. Stefánsson,et al.  A common inversion under selection in Europeans , 2005, Nature Genetics.

[37]  Matthias Platzer,et al.  Breakpoint analysis of the pericentric inversion distinguishing human chromosome 4 from the homologous chromosome in the chimpanzee (Pan troglodytes) , 2005, Human mutation.

[38]  Wen-Hsiung Li,et al.  Patterns of segmental duplication in the human genome. , 2004, Molecular biology and evolution.

[39]  P. Stankiewicz,et al.  Position effects due to chromosome breakpoints that map approximately 900 Kb upstream and approximately 1.3 Mb downstream of SOX9 in two patients with campomelic dysplasia. , 2005, American journal of human genetics.

[40]  Naomichi Matsumoto,et al.  Identification of a 3.0-kb major recombination hotspot in patients with Sotos syndrome who carry a common 1.9-Mb microdeletion. , 2005, American journal of human genetics.

[41]  D. Kleinjan,et al.  Long-range control of gene expression: emerging mechanisms and disruption in disease. , 2005, American journal of human genetics.

[42]  S. Benner,et al.  Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: The sulfotransferase 1A gene family example , 2005, BMC Evolutionary Biology.

[43]  J. Selfe,et al.  Structural evolution of the BRCA1 genomic region in primates. , 2004, Genomics.

[44]  Jeroen Raes,et al.  Duplication and divergence: the evolution of new genes and old ideas. , 2004, Annual review of genetics.

[45]  Fengtang Yang,et al.  Genomic structure and paralogous regions of the inversion breakpoint occurring between human chromosome 3p12.3 and orangutan chromosome 2 , 2004, Cytogenetic and Genome Research.

[46]  H. Hameister,et al.  Breakpoint analysis of the pericentric inversion between chimpanzee chromosome 10 and the homologous chromosome 12 in humans , 2004, Cytogenetic and Genome Research.

[47]  J. Mudge,et al.  Evolutionary implications of pericentromeric gene expression in humans , 2004, Cytogenetic and Genome Research.

[48]  N. Saitou,et al.  Nucleotide sequence comparison of a chromosome rearrangement on human chromosome 12 and the corresponding ape chromosomes , 2004, Cytogenetic and Genome Research.

[49]  P. Stankiewicz,et al.  Serial segmental duplications during primate evolution result in complex human genome architecture. , 2004, Genome research.

[50]  E. Lander,et al.  Finishing the euchromatic sequence of the human genome , 2004 .

[51]  E. Eichler,et al.  Shotgun sequence assembly and recent segmental duplications within the human genome , 2004, Nature.

[52]  J. Bonfield,et al.  Finishing the euchromatic sequence of the human genome , 2004, Nature.

[53]  Sarah A Tishkoff,et al.  Signatures of selection and gene conversion associated with human color vision variation. , 2004, American journal of human genetics.

[54]  L. Feuk,et al.  Detection of large-scale variation in the human genome , 2004, Nature Genetics.

[55]  D. Haussler,et al.  The structure and evolution of centromeric transition regions within the human genome , 2004, Nature.

[56]  D. Ledbetter,et al.  Diverse fates of paralogs following segmental duplication of telomeric genes. , 2004, Genomics.

[57]  E. Eichler,et al.  Regional patterns of gene expression in human and chimpanzee brains. , 2004, Genome research.

[58]  Kenny Q. Ye,et al.  Large-Scale Copy Number Polymorphism in the Human Genome , 2004, Science.

[59]  M. Hurles,et al.  Origins of chromosomal rearrangement hotspots in the human genome: evidence from the AZFa deletion hotspots , 2004, Genome Biology.

[60]  J. Sikela,et al.  Lineage-Specific Gene Duplication and Loss in Human and Great Ape Evolution , 2004, PLoS biology.

[61]  Anthony J Brookes,et al.  Complex SNP-related sequence variation in segmental genome duplications , 2004, Nature Genetics.

[62]  M. Hurles,et al.  Dynamics of a human interparalog gene conversion hotspot. , 2004, Genome research.

[63]  E. Eichler,et al.  Analysis of segmental duplications and genome assembly in the mouse. , 2004, Genome research.

[64]  Evan E. Eichler,et al.  An assessment of the sequence gaps: Unfinished business in a finished human genome , 2004, Nature Reviews Genetics.

[65]  E. Eichler,et al.  Recent segmental duplications in the working draft assembly of the brown Norway rat. , 2004, Genome research.

[66]  A. Jeffreys,et al.  Intense and highly localized gene conversion activity in human meiotic crossover hot spots , 2004, Nature Genetics.

[67]  P. Pevzner,et al.  Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. , 2004, Genome research.

[68]  J. Lupski,et al.  Implications of human genome architecture for rearrangement-based disorders: the genomic basis of disease. , 2004, Human molecular genetics.

[69]  E. McConkey,et al.  Inversion, duplication, and changes in gene context are associated with human chromosome 18 evolution. , 2004, Genomics.

[70]  J. Jurka,et al.  Duplication, coclustering, and selection of human Alu retrotransposons. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[71]  B. Dujon,et al.  Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments , 2004, The EMBO journal.

[72]  W. Flegel,et al.  Review: the molecular basis of the Rh blood group phenotypes , 2004, Immunohematology.

[73]  I. Dunham,et al.  DNA sequence and analysis of human chromosome 9 , 2003, Nature.

[74]  D. Haussler,et al.  Hotspots of mammalian chromosomal evolution , 2004, Genome Biology.

[75]  J. Lupski,et al.  Reciprocal crossovers and a positional preference for strand exchange in recombination events resulting in deletion or duplication of chromosome 17p11.2. , 2003, American journal of human genetics.

[76]  L. Shaffer,et al.  Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution. , 2003, Genome research.

[77]  E. Eichler,et al.  An Alu transposition model for the origin and expansion of human segmental duplications. , 2003, American journal of human genetics.

[78]  D. Haussler,et al.  Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[79]  J. Wienberg,et al.  Chromosomal phylogeny and evolution of gibbons (Hylobatidae) , 2003, Human Genetics.

[80]  J. Barber,et al.  Extensive normal copy number variation of a beta-defensin antimicrobial-gene cluster. , 2003, American journal of human genetics.

[81]  S. Scherer,et al.  Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements. , 2003, Human molecular genetics.

[82]  M. Ventura,et al.  Juxtacentromeric region of human chromosome 21: a boundary between centromeric heterochromatin and euchromatic chromosome arms. , 2003, Gene.

[83]  B. Roe,et al.  Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster , 2003, Genome Biology.

[84]  Junjun Zhang,et al.  Recent segmental and gene duplications in the mouse genome , 2003, Genome Biology.

[85]  M. Bayés,et al.  Mutational mechanisms of Williams-Beuren syndrome deletions. , 2003, American journal of human genetics.

[86]  Steve Rozen,et al.  Abundant gene conversion between arms of palindromes in human and ape Y chromosomes , 2003, Nature.

[87]  P. Pevzner,et al.  Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[88]  R. Schiffmann,et al.  Gaucher disease with parkinsonian manifestations: does glucocerebrosidase deficiency contribute to a vulnerability to parkinsonism? , 2003, Molecular genetics and metabolism.

[89]  C. Semple,et al.  Duplication and selection in the evolution of primate β-defensin genes , 2003, Genome Biology.

[90]  Patrick Gaudray,et al.  Segmental duplications in euchromatic regions of human chromosome 5: a source of evolutionary instability and transcriptional innovation. , 2003, Genome research.

[91]  D. Haber,et al.  The Tre2 (USP6) oncogene is a hominoid-specific gene , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[92]  Jonathan M. Mudge,et al.  Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p. , 2003, Genome research.

[93]  P. Pevzner,et al.  Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. , 2003, Genome research.

[94]  J. R. MacDonald,et al.  Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence , 2003, Genome Biology.

[95]  B. Trask,et al.  Genomic structure and evolution of the ancestral chromosome fusion site in 2q13-2q14.1 and paralogous regions on other human chromosomes. , 2002, Genome research.

[96]  Xavier Estivill,et al.  Chromosomal regions containing high-density and ambiguously mapped putative single nucleotide polymorphisms (SNPs) correlate with segmental duplications in the human genome. , 2002, Human molecular genetics.

[97]  M. Adams,et al.  Recent Segmental Duplications in the Human Genome , 2002, Science.

[98]  S. Fucharoen,et al.  Thalassemia and abnormal hemoglobin , 2002, International journal of hematology.

[99]  Matthias Platzer,et al.  Molecular characterization of the pericentric inversion that causes differences between chimpanzee chromosome 19 and human chromosome 17. , 2002, American journal of human genetics.

[100]  P. Stankiewicz,et al.  Genome architecture, rearrangements and genomic disorders. , 2002, Trends in genetics : TIG.

[101]  Stuart Schwartz,et al.  Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22. , 2002, American journal of human genetics.

[102]  Evan E. Eichler,et al.  Positive selection of a gene family during the emergence of humans and African apes , 2001, Nature.

[103]  M. Dorschner,et al.  Recombination hotspot in NF1 microdeletion patients. , 2001, Human molecular genetics.

[104]  B. Trask,et al.  Segmental duplications: organization and impact within the current human genome project assembly. , 2001, Genome research.

[105]  J. Nahon,et al.  Birth of Two Chimeric Genes in the Hominidae Lineage , 2001, Science.

[106]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[107]  R. Moyzis,et al.  Integration of telomere sequences with the draft human genome sequence , 2001, Nature.

[108]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[109]  J. Sulston,et al.  Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10q. , 2000, Human molecular genetics.

[110]  E. Eichler,et al.  The mosaic structure of human pericentromeric DNA: a strategy for characterizing complex regions of the human genome. , 2000, Genome research.

[111]  J. Spivak,et al.  Commentary on and reprint of Cooley TB, Lee PA, A series of cases of splenomegaly in children with anemia and peculiar bone changes, in Transactions of the American Pediatric Society (1925) 37:29–30, 1925 , 2000 .

[112]  E. Eichler,et al.  CAGGG repeats and the pericentromeric duplication of the hominoid genome. , 1999, Genome research.

[113]  B. Roe,et al.  Two novel human RAB genes with near identical sequence each map to a telomere-associated region: the subtelomeric region of 22q13.3 and the ancestral telomere band 2q13. , 1999, Genomics.

[114]  B. Trask,et al.  A genomic region encompassing a cluster of olfactory receptor genes and a myosin light chain kinase (MYLK) gene is duplicated on human chromosome regions 3q13-q21 and 3p13. , 1999, Genomics.

[115]  J. Lupski.  Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. , 1998, Trends in genetics : TIG.

[116]  J. Lupski,et al.  Human meiotic recombination products revealed by sequencing a hotspot for homologous strand exchange in multiple HNPP deletion patients. , 1998, American journal of human genetics.

[117]  B. Trask,et al.  Members of the olfactory receptor gene family are contained in large blocks of DNA duplicated polymorphically near the ends of human chromosomes. , 1998, Human molecular genetics.

[118]  J. Lupski,et al.  A recombination hotspot responsible for two inherited peripheral neuropathies is located near a mariner transposon-like element , 1998, Nature Genetics.

[119]  E. Eichler,et al.  Interchromosomal duplications of the adrenoleukodystrophy locus: a phenomenon of pericentromeric plasticity. , 1997, Human molecular genetics.

[120]  A. C. Chinault,et al.  Charcot–Marie–Tooth type 1A duplication appears to arise from recombination at repeat sequences flanking the 1.5 Mb monomer unit , 1992, Nature Genetics.

[121]  J. Erickson,et al.  Variation among human 28S ribosomal RNA genes. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[122]  J. Nadeau,et al.  Lengths of chromosomal segments conserved since divergence of man and mouse. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[123]  J. Sawyer,et al.  The striking resemblance of high-resolution G-banded chromosomes of man and chimpanzee. , 1980, Science.

[124]  S. Ohno,et al.  Evolution from fish to mammals by gene duplication. , 2009, Hereditas.

[125]  P. Barlow.  Sex Chromosomes , 1967, Nature.

[126]  P. Levine,et al.  ISOIMMUNIZATION IN PREGNANCY: ITS POSSIBLE BEARING ON THE ETIOLOGY OF ERYTHROBLASTOSIS FOETALIS , 1941 .

[127]  J. Sprague,et al.  THIOUREA AS A KEY REAGENT FOR THE PREPARATION OF ALIPHATIC SULPHONYL CHLORIDES AND BROMIDES. , 1936, Science.

[128]  H J Muller,et al.  BAR DUPLICATION. , 1936, Science.

[129]  T. Cooley,et al.  A series of cases of splenomegaly in children with anemia and peculiar bone changes , 1925 .

[130]  E. Wilson.  The sex chromosomes , 1911 .

[131]  W. Willis,et al.  The Origin of Man : A Chromosomal Pictorial Legacy , 2014 .