Tissue-specific variation in DNA methylation levels along human chromosome 1 (2009)
De Bustos, Cecilia, Ramos, Edward, Young, Janet M, Tran, Robert K, Menzel, Uwe, Langford, Cordelia F, ...
Abstract Background DNA methylation is a major epigenetic modification important for regulating gene expression and suppressing spurious transcription. Most methods to scan the genome in different...
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data (2009)
Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, S. Cenk Sahinalp, Evan E. Eichler
The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5 % of sequence generated as part of primate genome sequencing projects consists of this material, which is...
A burst of segmental duplications in the genome of the African great ape ancestor (2009)
Marqués-Bonet, Tomàs, Kidd, Jeffrey M., Ventura, Mario, Graves, Tina A., Cheng, Ze, Hillier, LaDeana W., ...
5 pages, 4 figures.-- Supplementary information (3 files) available at: http://www.nature.com/nature/journal/v457/n7231/suppinfo/nature07744.html
Landsverk, Megan L., Ruzzo, Elizabeth K., Mefford, Heather C., Buysse, Karen, Buchan, Jillian G., Eichler, Evan E., ...
Hereditary neuralgic amyotrophy (HNA) is an autosomal dominant disorder associated with recurrent episodes of focal neuropathy primarily affecting the brachial plexus. Point mutations in the SEPT9...
Hormozdiari, Fereydoun, Alkan, Can, Eichler, Evan E., Sahinalp, S. Cenk
Recent studies show that along with single nucleotide polymorphisms and small indels, larger structural variants among human individuals are common. The Human Genome Structural Variation Project aims...
Girirajan, Santhosh, Chen, Lin, Graves, Tina, Marques-Bonet, Tomas, Ventura, Mario, Fronick, Catrina, ...
The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of...
Characterization of six human disease-associated inversion polymorphisms (2009)
Antonacci, Francesca, Kidd, Jeffrey M., Marques-Bonet, Tomas, Ventura, Mario, Siswara, Priscillia, Jiang, Zhaoshi, ...
The human genome is a highly dynamic structure that shows a wide range of genetic polymorphic variation. Unlike other types of structural variation, little is known about inversion variants within...
Nicholas, Thomas J., Cheng, Ze, Ventura, Mario, Mealey, Katrina, Eichler, Evan E., Akey, Joshua M.
Structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of segmental duplications and associated...
Landsverk, Megan L., Ruzzo, Elizabeth K., Mefford, Heather C., Buysse, Karen, Buchan, Jillian G., Eichler, Evan E., ...
Hereditary neuralgic amyotrophy (HNA) is an autosomal dominant disorder associated with recurrent episodes of focal neuropathy primarily affecting the brachial plexus. Point mutations in the SEPT9...
McKernan, Kevin Judd, Peckham, Heather E., Costa, Gina L., McLaughlin, Stephen F., Fu, Yutao, Tsung, Eric F., ...
We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw...
Mefford, Heather C., Cooper, Gregory M., Zerr, Troy, Smith, Joshua D., Baker, Carl, Shafer, Neil, ...
Copy-number variants (CNVs) are substantial contributors to human disease. A central challenge in CNV-disease association studies is to characterize the pathogenicity of rare and possibly...
Dibbens, Leanne M., Mullen, Saul, Helbig, Ingo, Mefford, Heather C., Bayly, Marta A., Bellows, Susannah, ...
Microdeletion at chromosomal position 15q13.3 has been described in intellectual disability, autism spectrum disorders, schizophrenia and recently in idiopathic generalized epilepsy (IGE). Using...
Evolutionary-new centromeres preferentially emerge within gene deserts (2008)
Lomiento, Mariana, Jiang, Zhaoshi, D'Addabbo, Pietro, Eichler, Evan E, Rocchi, Mariano
Abstract Background Evolutionary-new centromeres (ENCs) result from the seeding of a centromere at an ectopic location along the chromosome during evolution. The novel centromere rapidly acquires the...
REVIEW Structural Dynamics of Eukaryotic Chromosome Evolution (2008)
E. W. Brown, J. E. Leclerc, B. Li, W. L. Payne, S. J. Weissman, S. L. Moseley, ...
36. We thank H. Merkert for excellent graphical assistance
Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes (2008)
Sharp, Andrew J, Baker, Carl, Itsara, Andy, Jiang, Zhaoshi, Buysse, Karen, ...
Background: Duplications and deletions in the human genome can cause disease or predispose persons to disease. Advances in technologies to detect these changes allow for the routine identification of...
Marques-Bonet, Tomàs, Cheng, Ze, She, Xinwei, Eichler, Evan E, Navarro, Arcadi
Abstract Background It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the...
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication (2008)
Cardone, Maria, Jiang, Zhaoshi, D'Addabbo, Pietro, Archidiacono, Nicoletta, Rocchi, Mariano, Eichler, Evan E, ...
Abstract Background Chromosomal rearrangements, such as translocations and inversions, are recurrent phenomena during evolution, and both of them are involved in reproductive isolation and...
Analysis ofP/--3[ Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome (2008)
Ge Liu Nis, Eric D. Green, Evan E. Eichler
aterial is available online at www.genome.org.] Initial studie ofprimate gemat variation weR base largeW onindire1 eire1H obtaine from DNA hybridization kineG ics(Sible and Ahlquist 1984; Powe1...
Genome Informatics 13: 93--102 (2002) 93 An Algorithmic Analysis of the Role of Unequal (2008)
Can Alkan, Jeffrey A. Bailey, Evan E. Eichler, S. Cenk, Sahinalp Eray Tuzun
Human DNA consists of a large number of tandem repeat sequences. Such sequences are usually called satellites, with the primary example being the centromeric alpha-satellite DNA. The basic repeat...
Genome analysis of the platypus reveals unique signatures of evolution (2008)
Warren, Wesley C., Hillier, LaDeana W., Marshall Graves, Jennifer A., Birney, Ewan, Ponting, Chris P., Grützner, Frank, ...
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a...
DupMasker: A tool for annotating primate segmental duplications (2008)
Jiang, Zhaoshi, Hubley, Robert, Smit, Arian, Eichler, Evan E.
Segmental duplications (SDs) play an important role in genome rearrangement, evolution, and the copy-number variation (CNV) of primate genomes. Such sequences are difficult to detect, a priori,...
Copy number variation and evolution in humans and chimpanzees (2008)
Perry, George H., Yang, Fengtang, Marques-Bonet, Tomas, Murphy, Carly, Fitzgerald, Tomas, Lee, Arthur S., ...
Copy number variants (CNVs) underlie many aspects of human phenotypic diversity and provide the raw material for gene duplication and gene family expansion. However, our understanding of their...
Haplotype sorting using human fosmid clone end-sequence pairs (2008)
Kidd, Jeffrey M., Cheng, Ze, Graves, Tina, Fulton, Bob, Wilson, Richard K., Eichler, Evan E.
An important goal of human genetics and genomics is to understand the complete spectrum of genetic variation across a specific human haplotype. By combining information from a dense SNP map with...
Kirsch, Stefan, Münch, Claudia, Jiang, Zhaoshi, Cheng, Ze, Chen, Lin, Batz, Christiane, ...
Human chromosomal regions enriched in segmental duplications are subject to extensive genomic reorganization. Such regions are particularly informative for illuminating the evolutionary history of a...
Lyle, Robert, Prandini, Paola, Osoegawa, Kazutoyo, Ten Hallers, Boudewijn, Humphray, Sean, Zhu, Baoli, ...
The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p),...
Optimal design of oligonucleotide microarrays for measurement of DNA copy-number (2007)
Sharp, Andrew J., Itsara, Andy, Cheng, Ze, Alkan, Can, Schwartz, Stuart, Eichler, Evan E.
Copy-number variants (CNVs) occur frequently within the human genome, and may be associated with many human phenotypes. If disease association studies of CNVs are to be performed routinely, it is...
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data (2007)
Can Alkan, Mario Ventura, Nicoletta Archidiacono, Mariano Rocchi, S. Cenk Sahinalp, Evan E. Eichler
The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is...
Population Stratification of a Common APOBEC Gene Deletion Polymorphism (2007)
Jeffrey M. Kidd, Tera L. Newman, Eray Tuzun, Rajinder Kaul, Evan E. Eichler
The APOBEC3 gene family plays a role in innate cellular immunity inhibiting retroviral infection, hepatitis B virus propagation, and the retrotransposition of endogenous elements. We present a...
Characterization of a recurrent 15q24 microdeletion syndrome (2007)
Sharp, Andrew J., Selzer, Rebecca R., Veltman, Joris A., Gimelli, Stefania, Gimelli, Giorgio, Striano, Pasquale, ...
We describe multiple individuals with mental retardation and overlapping de novo submicroscopic deletions of 15q24 (1.7–3.9 Mb in size). High-resolution analysis showed that in three patients both...
Mefford, Heather C., Clauin, Séverine, Sharp, Andrew J., Moller, Rikke S., Ullmann, Reinhard, Kapur, Raj, ...
Most studies of genomic disorders have focused on patients with cognitive disability and/or peripheral nervous system defects. In an effort to broaden the phenotypic spectrum of this disease model,...
Characterization of a recurrent 15q24 microdeletion syndrome (2007)
Sharp, Andrew J, Selzer, Rebecca R, Veltman, Joris A, Gimelli, Stefania, Gimelli, Giorgio, Striano, Pasquale, ...
We describe multiple individuals with mental retardation and overlapping de novo submicroscopic deletions of 15q24 (1.7-3.9 Mb in size). High resolution analysis showed that in three patients both...
Cardone, Maria, Alonso, Alicia, Pazienza, Michele, Ventura, Mario, Montemurro, Gabriella, Carbone, Lucia, ...
Abstract Background Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still...
Recurrent duplication-driven transposition of DNA during hominoid evolution. (2006)
Johnson, Matthew E., Cheng, Ze, Morrison, V. Anne, Scherer, Steven, Ventura, Mario, Gibbs, Richard A., ...
The underlying mechanism by which the interspersed pattern of human segmental duplications has evolved is unknown. Based on a comparative analysis of primate genomes, we show that a particular...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
High-throughput genotyping of intermediate-size structural variation (2006)
Newman, Tera L., Rieder, Mark J., Morrison, V. Anne, Sharp, Andrew J., Smith, Joshua D., Sprague, L. James, ...
The contribution of large-scale and intermediate-size structural variation (ISV) to human genetic disease and disease susceptibility is only beginning to be understood. The development of...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Molecular refinement of gibbon genome rearrangement (2006)
Roberto, Roberta, Capozzi, Oronzo, Wilson, Richard K., Mardis, Elaine R., Lomiento, Mariana, Tuzun, Eray, ...
The gibbon karyotype is known to be extensively rearranged when compared to the human and to the ancestral primate karyotype. By combining a bioinformatics (paired-end sequence analysis) approach and...
High-throughput genotyping of intermediate-size structural variation (2006)
Newman, Tera L., Rieder, Mark J., Morrison, V. Anne, Sharp, Andrew J., Smith, Joshua D., Sprague, L. James, ...
The contribution of large-scale and intermediate-size structural variation to human genetic disease and disease susceptibility is only beginning to be understood. The development of high-throughput...
Chris T. Yohn, Zhaoshi Jiang, Sean D. McGrath, Karen E. Hayden, Philipp Khaitovich, Matthew E. Johnson, ...
Comparison of human and other primate genomes provides evidence for a retroviral infection that bombarded the genomes of chimpanzees and gorillas 3-4 million years ago.
Chris T. Yohn, Zhaoshi Jiang, Sean D. McGrath, Karen E. Hayden, Philipp Khaitovich, Matthew E. Johnson, ...
Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been...
Yohn, Chris T., Jiang, Zhaoshi, McGrath, Sean D., Hayden, Karen E., Khaitovich, Philipp, Johnson, Matthew E., ...
Initial sequence of the chimpanzee genome and comparison with the human genome (2005)
Mikkelsen, Tarjei S., Hillier, LaDeana W., Eichler, Evan E., Zody, Michael C., Jaffe, David B., Yang, Shiaw-Pyng, ...
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences...
Manipulating multiple sequence alignments via MaM and WebMaM. (2005)
Alkan, Can, T Z N, Eray, Buard, Jerome, Lethiec, Franck, Eichler, Evan E., Bailey, Jeffrey A., ...
MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned...
Punctuated duplication seeding events during the evolution of human chromosome 2p11. (2005)
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
A genome-wide survey of structural variation between human and chimpanzee. (2005)
Newman, Tera L., Tuzun, Eray, Morrison, V. Anne, Hayden, Karen E., Ventura, Mario, McGrath, Sean D., ...
Structural changes (deletions, insertions, and inversions) between human and chimpanzee genomes have likely had a significant impact on lineage-specific evolution because of their potential for...
Segmental duplications and copy-number variation in the human genome. (2005)
Sharp, Andrew J., Locke, Devin P., McGrath, Sean D., Cheng, Ze, Bailey, Jeffrey A., Vallente, Rhea U., ...
The human genome contains numerous blocks of highly homologous duplicated sequence. This higher-order architecture provides a substrate for recombination and recurrent chromosomal rearrangement...
Yohn, Chris T, Jiang, Zhaoshi, McGrath, Sean D, Hayden, Karen E, Khaitovich, Philipp, Johnson, Matthew E, ...
Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been...
Manipulating multiple sequence alignments via MaM and (2005)
Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, ...
MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned...
Manipulating multiple sequence alignments via MaM and WebMaM (2005)
Alkan, Can, Tüzün, Eray, Buard, Jerome, Lethiec, Franck, Eichler, Evan E., Bailey, Jeffrey A., ...
MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned...
Punctuated duplication seeding events during the evolution of human chromosome 2p11 (2005)
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
Kirsch, Stefan, Weiß, Birgit, Miner, Tracie L., Waterston, Robert H., Clark, Royden A., Eichler, Evan E., ...
Basic medical research critically depends on the finished human genome sequence. Two types of gaps are known to exist in the human genome: those associated with heterochromatic sequences and those...
Kirsch, Stefan, Weiß, Birgit, Miner, Tracie L., Waterston, Robert H., Clark, Royden A., Eichler, Evan E., ...
Basic medical research critically depends on the finished human genome sequence. Two types of gaps are known to exist in the human genome: those associated with heterochromatic sequences and those...
Punctuated duplication seeding events during the evolution of human chromosome 2p11 (2005)
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
A genome-wide survey of structural variation between human and chimpanzee (2005)
Newman, Tera L., Tuzun, Eray, Morrison, V. Anne, Hayden, Karen E., Ventura, Mario, McGrath, Sean D., ...
Structural changes (deletions, insertions, and inversions) between human and chimpanzee genomes have likely had a significant impact on lineage-specific evolution because of their potential for...
A genome-wide survey of structural variation between human and chimpanzee (2005)
Newman, Tera L., Tuzun, Eray, Morrison, V. Anne, Hayden, Karen E., Ventura, Mario, McGrath, Sean D., ...
Structural changes (deletions, insertions, and inversions) between human and chimpanzee genomes have likely had a significant impact on lineage-specific evolution because of their potential for...
The sequence and analysis of duplication rich human chromosome 16 (2004)
Martin, Joel, Han, Cliff, Gordon, Laurie A., Terry, Astrid, Prabhakar, Shyam, She, Xinwei, ...
We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by...
The complete sequence of human chromosome 5 (2004)
Schmutz, Jeremy, Martin, Joel, Terry, Astrid, Couronne, Olivier, Grimwood, Jane, Lowry, State, ...
Chromosome 5 is one of the largest human chromosomes yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding...
Astbury, Caroline, Christ, Laurie A, Aughton, David J, Cassidy, Suzanne B, Kumar, Arun, Eichler, Evan E, ...
Purpose: The purpose of this study was to test the hypothesis that deletions of varying sizes in de novo apparently balanced chromosome rearrangements are a significant cause of phenotypic...
Astbury, Caroline, Christ, Laurie A, Aughton, David J, Cassidy, Suzanne B, Kumar, Arun, Eichler, Evan E, ...
Purpose: The purpose of this study was to test the hypothesis that deletions of varying sizes in de novo apparently balanced chromosome rearrangements are a significant cause of phenotypic...
The nature, pattern and function of human sequence variation (2004)
Eichler, Evan E, Frazer, Kelly A
Abstract A report on the 2004 Keystone Symposium 'Human Genome Sequence Variation and the Inherited Basis of Common Disease', Breckenridge, USA, 8-13 January 2004.
Hotspots of mammalian chromosomal evolution (2004)
Bailey, Jeffrey A, Baertsch, Robert, Kent, W, Haussler, David, Eichler, Evan E
Abstract Background Chromosomal evolution is thought to occur through a random process of breakage and rearrangement that leads to karyotype differences and disruption of gene order. With the...
Regional Patterns of Gene Expression in Human and Chimpanzee Brains (2004)
Khaitovich, Philipp, Muetzel, Bjoern, She, Xinwei, Lachmann, Michael, Hellmann, Ines, Dietzsch, Janko, ...
Whole-genome shotgun assembly and comparison of human genome assemblies. (2004)
Istrail, Sorin, Sutton, Granger G., Florea, Liliana, Halpern, Aaron L., Mobarry, Clark M., Lippert, Ross, ...
We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in...
Analysis of segmental duplications and genome assembly in the mouse. (2004)
Bailey, Jeffrey A., Church, Deanna M., Ventura, Mario, Rocchi, Mariano, Eichler, Evan E.
Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications. The extent of segmental duplications in other mammalian genomes is unknown and...
Recurrent sites for new centromere seeding. (2004)
Ventura, Mario, Weigl, Stefania, Carbone, Lucia, Cardone, Maria Francesca, Misceo, Doriana, Teti, Mariagrazia, ...
Using comparative FISH and genomics, we have studied and compared the evolution of chromosome 3 in primates and two human neocentromere cases on the long arm of this chromosome. Our results show that...
Segmental duplications flank the multiple sclerosis locus on chromosome 17q. (2004)
Chen, Daniel C., Saarela, Janna, Clark, Royden A., Miettinen, Timo, Chi, Anthony, Eichler, Evan E., ...
Large chromosomal rearrangements, duplications, and inversions are relatively common in mammalian genomes. Here we report interesting features of DNA strands flanking a Multiple Sclerosis (MS)...
Recent segmental duplications in the working draft assembly of the brown Norway rat. (2004)
Tuzun, Eray, Bailey, Jeffrey A., Eichler, Evan E.
We assessed the content, structure, and distribution of segmental duplications (> or =90% sequence identity, > or =5 kb length) within the published version of the Rattus norvegicus genome assembly...
Regional patterns of gene expression in human and chimpanzee brains. (2004)
Khaitovich, Philipp, Muetzel, Bjoern, She, Xinwei, Lachmann, Michael, Hellmann, Ines, Dietzsch, Janko, ...
We have analyzed gene expression in various brain regions of humans and chimpanzees. Within both human and chimpanzee individuals, the transcriptomes of the cerebral cortex are very similar to each...
Hotspots of mammalian chromosomal evolution. (2004)
Bailey, Jeffrey A, Baertsch, Robert, Kent, W James, Haussler, David, Eichler, Evan E
BACKGROUND: Chromosomal evolution is thought to occur through a random process of breakage and rearrangement that leads to karyotype differences and disruption of gene order. With the availability of...
Regional Patterns of Gene Expression in Human and Chimpanzee Brains (2004)
Khaitovich, Philipp, Muetzel, Bjoern, She, Xinwei, Lachmann, Michael, Hellmann, Ines, Dietzsch, Janko, ...
We have analyzed gene expression in various brain regions of humans and chimpanzees. Within both human and chimpanzee individuals, the transcriptomes of the cerebral cortex are very similar to each...
Segmental Duplications Flank the Multiple Sclerosis Locus on Chromosome 17q (2004)
Chen, Daniel C., Saarela, Janna, Clark, Royden A., Miettinen, Timo, Chi, Anthony, Eichler, Evan E., ...
Large chromosomal rearrangements, duplications, and inversions are relatively common in mammalian genomes. Here we report interesting features of DNA strands flanking a Multiple Sclerosis (MS)...
Recent Segmental Duplications in the Working Draft Assembly of the Brown Norway Rat (2004)
Tuzun, Eray, Bailey, Jeffrey A., Eichler, Evan E.
We assessed the content, structure, and distribution of segmental duplications (≥90% sequence identity, ≥5 kb length) within the published version of the Rattus norvegicus genome assembly...
Segmental Duplications Flank the Multiple Sclerosis Locus on Chromosome 17q (2004)
Chen, Daniel C., Saarela, Janna, Clark, Royden A., Miettinen, Timo, Chi, Anthony, Eichler, Evan E., ...
Large chromosomal rearrangements, duplications, and inversions are relatively common in mammalian genomes. Here we report interesting features of DNA strands flanking a Multiple Sclerosis (MS)...
Locke, Devin P, Archidiacono, Nicoletta, Misceo, Doriana, Cardone, Maria, Deschamps, Stephane, Roe, Bruce, ...
Abstract Background Pericentric inversions are the most common euchromatic chromosomal differences among humans and the great apes. The human and chimpanzee karyotype differs by nine such events, in...
Guy, Jane, Hearn, Tom, Crosier, Moira, Mudge, Jonathan, Viggiano, Luigi, Koczan, Dirk, ...
Contiguous finished sequence from highly duplicated pericentromeric regions of human chromosomes is needed if we are to understand the role of pericentromeric instability in disease, and in gene and...
Guy, Jane, Hearn, Tom, Crosier, Moira, Mudge, Jonathan, Viggiano, Luigi, Koczan, Dirk, ...
Contiguous finished sequence from highly duplicated pericentromeric regions of human chromosomes is needed if we are to understand the role of pericentromeric instability in disease, and in gene and...
An Alu transposition model for the origin and expansion of human segmental duplications. (2003)
Bailey, Jeffrey A., Liu, Ge, Eichler, Evan E.
Relative to genomes of other sequenced organisms, the human genome appears particularly enriched for large, highly homologous segmental duplications (> or =90% sequence identity and > or =10 kbp in...
Locke, Devin P, Archidiacono, Nicoletta, Misceo, Doriana, Cardone, Maria Francesca, Deschamps, Stephane, Roe, Bruce, ...
BACKGROUND: Pericentric inversions are the most common euchromatic chromosomal differences among humans and the great apes. The human and chimpanzee karyotype differs by nine such events, in addition...
Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. (2003)
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Locke, Devin P., Segraves, Richard, Carbone, Lucia, Archidiacono, Nicoletta, Albertson, Donna G., Pinkel, Daniel, ...
Large-scale genomic rearrangements are a major force of evolutionary change and the ascertainment of such events between the human and great ape genomes is fundamental to a complete understanding of...
Guy, Jane, Hearn, Tom, Crosier, Moira, Mudge, Jonathan, Viggiano, Luigi, Koczan, Dirk, ...
Contiguous finished sequence from highly duplicated pericentromeric regions of human chromosomes is needed if we are to understand the role of pericentromeric instability in disease, and in gene and...
Guy, Jane, Hearn, Tom, Crosier, Moira, Mudge, Jonathan, Viggiano, Luigi, Koczan, Dirk, ...
Contiguous finished sequence from highly duplicated pericentromeric regions of human chromosomes is needed if we are to understand the role of pericentromeric instability in disease, and in gene and...
Locke, Devin P., Segraves, Richard, Carbone, Lucia, Archidiacono, Nicoletta, Albertson, Donna G., Pinkel, Daniel, ...
Large-scale genomic rearrangements are a major force of evolutionary change and the ascertainment of such events between the human and great ape genomes is fundamental to a complete understanding of...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome (2003)
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Van Geel,Michel, Eichler,Evan E., Beck,Amy F., Shan,Zhihong, Haaf,Thomas, Van Der Maarel,Silvère M., ...
Subtelomeric duplications of an obscure tubulin "genic" segment located near the telomere of human chromosome 4q35 have occurred at different evolutionary time points within the last 25 million years...
Van Geel, Michel, Eichler, Evan E., Beck, Amy F., Shan, Zhihong, Haaf, Thomas, Van Der Maarel, Silvère M., ...
Subtelomeric duplications of an obscure tubulin "genic" segment located near the telomere of human chromosome 4q35 have occurred at different evolutionary time points within the last 25 million years...
Bailey, Jeffrey A., Yavor, Amy M., Viggiano, Luigi, Misceo, Doriana, Horvath, Juliann E., Archidiacono, Nicoletta, ...
In recent decades, comparative chromosomal banding, chromosome painting, and gene-order studies have shown strong conservation of gross chromosome structure and gene order in mammals. However,...
Van Geel, Michel, Eichler, Evan E., Beck, Amy F., Shan, Zhihong, Haaf, Thomas, ...
Subtelomeric duplications of an obscure tubulin "genic" segment located near the telomere of human chromosome 4q35 have occurred at different evolutionary time points within the last 25 million years...
Sequence variation within the fragile X locus. (2001)
Mathews, Debra J., Kashuk, Carl, Brightwell, Gale, Eichler, Evan E., Chakravarti, Aravinda
The human genome provides a reference sequence, which is a template for resequencing studies that aim to discover and interpret the record of common ancestry that exists in extant genomes. To...
Bailey, Jeffrey A., Yavor, Amy M., Massa, Hillary F., Trask, Barbara J., Eichler, Evan E.
Segmental duplications play fundamental roles in both genomic disease and gene evolution. To understand their organization within the human genome, we have developed the computational tools and...
High-throughput variation detection and genotyping using microarrays. (2001)
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
The genetic dissection of complex traits may ultimately require a large number of SNPs to be genotyped in multiple individuals who exhibit phenotypic variation in a trait of interest. Microarray...
Lessons from the human genome: transitions between euchromatin and heterochromatin (2001)
Horvath, Julie E., Bailey, Jeffrey A., Locke, Devin P., Eichler, Evan E.
The publication of the human genome draft sequence provides, for the first time, a global view of the structural properties of the human genome. Initial sequence analysis, in combination with...
High-Throughput Variation Detection and Genotyping Using Microarrays (2001)
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
Sequence Variation Within the Fragile X Locus (2001)
Mathews, Debra J., Kashuk, Carl, Brightwell, Gale, Eichler, Evan E., Chakravarti, Aravinda
High-Throughput Variation Detection and Genotyping Using Microarrays (2001)
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
High-Throughput Variation Detection and Genotyping Using Microarrays (2001)
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
Bailey, Jeffrey A., Carrel, Laura, Chakravarti, Aravinda, Eichler, Evan E.
X inactivation is a chromosome-specific form of genetic regulation in which thousands of genes on one homologue become silenced early in female embryogenesis. Although many aspects of X inactivation...
Horvath, Juliann E., Schwartz, Stuart, Eichler, Evan E.
The pericentromeric regions of human chromosomes pose particular problems for both mapping and sequencing. These difficulties are due, in large part, to the presence of duplicated genomic segments...
Molecular structure and evolution of an alpha satellite/non-alpha satellite junction at 16p11 (2000)
Horvath, Juliann E., Viggiano, Luigi, Loftus, Brendan J., Adams, Mark D., Archidiacono, Nicoletta, Rocchi, Mariano, ...
We have determined the detailed molecular structure and evolution of an alpha satellite junction from human chromosome 16p11. The analysis reveals that the alpha satellite sequence bordering the...
Structure of Chromosomal Duplicons and their Role in Mediating Human Genomic Disorders (2000)
Ji, Yonggang, Eichler, Evan E., Schwartz, Stuart, Nicholls, Robert D.
Eichler, Evan E., Hoffman, Susan M., Adamson, Aaron A., Gordon, Laurie A., McCready, Paula, Lamerdin, Jane E., ...
Evan E. Eichler, Fei Lu, Ying Shen, Rachele Antonacci, Vesna Jurecic, Norman A. Doggett, ...
mechanism for paralogous genome evolution
Thesis (Ph. D.)--Baylor College of Medicine. Dept. of Molecular and Human Genetics, 1995.
Eichler, Evan E., Hammond, Holly A., Macpherson, James N., Ward, Patricia A., Nelson, David L.
Both sequence length and sequence content are important parameters in determining stability of the fragile x syndrome CGG repeat. In order to estimate the incidence of uninterrupted CGG repeats in...
Alternative splicing in the fragile X gene FMR1 (1993)
De Graaff, Esther, De Boulle, Kristel, Eichler, Evan E., Konecki, David S., Reyniers, Edwin, ...
The FMR1 gene, associated with fragile X syndrome, has recently been cloned and the sequence of partial cDNA clones is known. We have determined additional cDNA sequences both at the 5' and 3' end....
Fine structure of the human FMR1 gene (1993)
Eichler, Evan E., Richards, Stephen, Gibbs, Richard A., Nelson, David L.
The fragile X syndrome is due to a CGG triplet expansion in the first exon of FMR1, resulting in hypermethylation and extinction of gene expression. To further our understanding of the gene's...
Bailey, Jeffrey A., Carrel, Laura, Chakravarti, Aravinda, Eichler, Evan E.
X inactivation is a chromosome-specific form of genetic regulation in which thousands of genes on one homologue become silenced early in female embryogenesis. Although many aspects of X inactivation...
Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster
Locke, Devin P, Archidiacono, Nicoletta, Misceo, Doriana, Cardone, Maria Francesca, Deschamps, Stephane, Roe, Bruce, ...
A comparative fluorescence in situ hybridization approach, using probes selected from a combination of physical mapping, genomic sequence, and segmental duplication analyses has been employed to...
Horvath, Juliann E., Schwartz, Stuart, Eichler, Evan E.
The pericentromeric regions of human chromosomes pose particular problems for both mapping and sequencing. These difficulties are due, in large part, to the presence of duplicated genomic segments...
Segmental Duplications: Organization and Impact Within the Current Human Genome Project Assembly
Bailey, Jeffrey A., Yavor, Amy M., Massa, Hillary F., Trask, Barbara J., Eichler, Evan E.
Segmental duplications play fundamental roles in both genomic disease and gene evolution. To understand their organization within the human genome, we have developed the computational tools and...
Sequence Variation Within the Fragile X Locus
Mathews, Debra J., Kashuk, Carl, Brightwell, Gale, Eichler, Evan E., Chakravarti, Aravinda
The human genome provides a reference sequence, which is a template for resequencing studies that aim to discover and interpret the record of common ancestry that exists in extant genomes. To...
High-Throughput Variation Detection and Genotyping Using Microarrays
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
The genetic dissection of complex traits may ultimately require a large number of SNPs to be genotyped in multiple individuals who exhibit phenotypic variation in a trait of interest. Microarray...
Whole-genome shotgun assembly and comparison of human genome assemblies
Istrail, Sorin, Sutton, Granger G., Florea, Liliana, Halpern, Aaron L., Mobarry, Clark M., Lippert, Ross, ...
We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in...
Recent Segmental Duplications in the Working Draft Assembly of the Brown Norway Rat
Tuzun, Eray, Bailey, Jeffrey A., Eichler, Evan E.
We assessed the content, structure, and distribution of segmental duplications (≥90% sequence identity, ≥5 kb length) within the published version of the Rattus norvegicus genome assembly...
The nature, pattern and function of human sequence variation
Eichler, Evan E, Frazer, Kelly A
A report on the 2004 Keystone Symposium 'Human Genome Sequence Variation and the Inherited Basis of Common Disease', Breckenridge, USA, 8-13 January 2004.
Hotspots of mammalian chromosomal evolution
Bailey, Jeffrey A, Baertsch, Robert, Kent, W James, Haussler, David, Eichler, Evan E
This study reports an abundance of primate-specific segmental duplications at the breakpoints of syntenic blocks in the human genome. Segmental duplications are associated with syntenic...
Guy, Jane, Hearn, Tom, Crosier, Moira, Mudge, Jonathan, Viggiano, Luigi, Koczan, Dirk, ...
Contiguous finished sequence from highly duplicated pericentromeric regions of human chromosomes is needed if we are to understand the role of pericentromeric instability in disease, and in gene and...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Locke, Devin P., Segraves, Richard, Carbone, Lucia, Archidiacono, Nicoletta, Albertson, Donna G., Pinkel, Daniel, ...
Large-scale genomic rearrangements are a major force of evolutionary change and the ascertainment of such events between the human and great ape genomes is fundamental to a complete understanding of...
Analysis of Segmental Duplications and Genome Assembly in the Mouse
Bailey, Jeffrey A., Church, Deanna M., Ventura, Mario, Rocchi, Mariano, Eichler, Evan E.
Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications. The extent of segmental duplications in other mammalian genomes is unknown and...
Regional Patterns of Gene Expression in Human and Chimpanzee Brains
Khaitovich, Philipp, Muetzel, Bjoern, She, Xinwei, Lachmann, Michael, Hellmann, Ines, Dietzsch, Janko, ...
We have analyzed gene expression in various brain regions of humans and chimpanzees. Within both human and chimpanzee individuals, the transcriptomes of the cerebral cortex are very similar to each...
Segmental Duplications Flank the Multiple Sclerosis Locus on Chromosome 17q
Chen, Daniel C., Saarela, Janna, Clark, Royden A., Miettinen, Timo, Chi, Anthony, Eichler, Evan E., ...
Large chromosomal rearrangements, duplications, and inversions are relatively common in mammalian genomes. Here we report interesting features of DNA strands flanking a Multiple Sclerosis (MS)...
Recurrent Sites for New Centromere Seeding
Ventura, Mario, Weigl, Stefania, Carbone, Lucia, Cardone, Maria Francesca, Misceo, Doriana, Teti, Mariagrazia, ...
Using comparative FISH and genomics, we have studied and compared the evolution of chromosome 3 in primates and two human neocentromere cases on the long arm of this chromosome. Our results show that...
Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome
Kirsch, Stefan, Weiß, Birgit, Miner, Tracie L., Waterston, Robert H., Clark, Royden A., Eichler, Evan E., ...
Basic medical research critically depends on the finished human genome sequence. Two types of gaps are known to exist in the human genome: those associated with heterochromatic sequences and those...
Yohn, Chris T, Jiang, Zhaoshi, McGrath, Sean D, Hayden, Karen E, Khaitovich, Philipp, Johnson, Matthew E, ...
Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been...
Manipulating multiple sequence alignments via MaM and WebMaM
Alkan, Can, Tüzün, Eray, Buard, Jerome, Lethiec, Franck, Eichler, Evan E., Bailey, Jeffrey A., ...
MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned...
Punctuated duplication seeding events during the evolution of human chromosome 2p11
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
A genome-wide survey of structural variation between human and chimpanzee
Newman, Tera L., Tuzun, Eray, Morrison, V. Anne, Hayden, Karen E., Ventura, Mario, McGrath, Sean D., ...
Structural changes (deletions, insertions, and inversions) between human and chimpanzee genomes have likely had a significant impact on lineage-specific evolution because of their potential for...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Hotspots for copy number variation in chimpanzees and humans
Perry, George H., Tchinda, Joelle, McGrath, Sean D., Zhang, Junjun, Picker, Simon R., Cáceres, Angela M., ...
Copy number variation is surprisingly common among humans and can be involved in phenotypic diversity and variable susceptibility to complex diseases, but little is known of the extent of copy number...
Bailey, Jeffrey A., Carrel, Laura, Chakravarti, Aravinda, Eichler, Evan E.
X inactivation is a chromosome-specific form of genetic regulation in which thousands of genes on one homologue become silenced early in female embryogenesis. Although many aspects of X inactivation...
Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster
Locke, Devin P, Archidiacono, Nicoletta, Misceo, Doriana, Cardone, Maria Francesca, Deschamps, Stephane, Roe, Bruce, ...
A comparative fluorescence in situ hybridization approach, using probes selected from a combination of physical mapping, genomic sequence, and segmental duplication analyses has been employed to...
Horvath, Juliann E., Schwartz, Stuart, Eichler, Evan E.
The pericentromeric regions of human chromosomes pose particular problems for both mapping and sequencing. These difficulties are due, in large part, to the presence of duplicated genomic segments...
Segmental Duplications: Organization and Impact Within the Current Human Genome Project Assembly
Bailey, Jeffrey A., Yavor, Amy M., Massa, Hillary F., Trask, Barbara J., Eichler, Evan E.
Segmental duplications play fundamental roles in both genomic disease and gene evolution. To understand their organization within the human genome, we have developed the computational tools and...
Sequence Variation Within the Fragile X Locus
Mathews, Debra J., Kashuk, Carl, Brightwell, Gale, Eichler, Evan E., Chakravarti, Aravinda
The human genome provides a reference sequence, which is a template for resequencing studies that aim to discover and interpret the record of common ancestry that exists in extant genomes. To...
High-Throughput Variation Detection and Genotyping Using Microarrays
Cutler, David J., Zwick, Michael E., Carrasquillo, Minerva M., Yohn, Christopher T., Tobin, Katherine P., Kashuk, Carl, ...
The genetic dissection of complex traits may ultimately require a large number of SNPs to be genotyped in multiple individuals who exhibit phenotypic variation in a trait of interest. Microarray...
Whole-genome shotgun assembly and comparison of human genome assemblies
Istrail, Sorin, Sutton, Granger G., Florea, Liliana, Halpern, Aaron L., Mobarry, Clark M., Lippert, Ross, ...
We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in...
Recent Segmental Duplications in the Working Draft Assembly of the Brown Norway Rat
Tuzun, Eray, Bailey, Jeffrey A., Eichler, Evan E.
We assessed the content, structure, and distribution of segmental duplications (≥90% sequence identity, ≥5 kb length) within the published version of the Rattus norvegicus genome assembly...
The nature, pattern and function of human sequence variation
Eichler, Evan E, Frazer, Kelly A
A report on the 2004 Keystone Symposium 'Human Genome Sequence Variation and the Inherited Basis of Common Disease', Breckenridge, USA, 8-13 January 2004.
Hotspots of mammalian chromosomal evolution
Bailey, Jeffrey A, Baertsch, Robert, Kent, W James, Haussler, David, Eichler, Evan E
This study reports an abundance of primate-specific segmental duplications at the breakpoints of syntenic blocks in the human genome. Segmental duplications are associated with syntenic...
Van Geel, Michel, Eichler, Evan E., Beck, Amy F., Shan, Zhihong, Haaf, Thomas, Van der Maarel, Silvère M., ...
Subtelomeric duplications of an obscure tubulin “genic” segment located near the telomere of human chromosome 4q35 have occurred at different evolutionary time points within the last 25 million...
Human-Specific Duplication and Mosaic Transcripts: The Recent Paralogous Structure of Chromosome 22
Bailey, Jeffrey A., Yavor, Amy M., Viggiano, Luigi, Misceo, Doriana, Horvath, Juliann E., Archidiacono, Nicoletta, ...
In recent decades, comparative chromosomal banding, chromosome painting, and gene-order studies have shown strong conservation of gross chromosome structure and gene order in mammals. However,...
Guy, Jane, Hearn, Tom, Crosier, Moira, Mudge, Jonathan, Viggiano, Luigi, Koczan, Dirk, ...
Contiguous finished sequence from highly duplicated pericentromeric regions of human chromosomes is needed if we are to understand the role of pericentromeric instability in disease, and in gene and...
Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome
Liu, Ge, Program, NISC Comparative Sequencing, Zhao, Shaying, Bailey, Jeffrey A., Sahinalp, S. Cenk, Alkan, Can, ...
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to...
Locke, Devin P., Segraves, Richard, Carbone, Lucia, Archidiacono, Nicoletta, Albertson, Donna G., Pinkel, Daniel, ...
Large-scale genomic rearrangements are a major force of evolutionary change and the ascertainment of such events between the human and great ape genomes is fundamental to a complete understanding of...
Analysis of Segmental Duplications and Genome Assembly in the Mouse
Bailey, Jeffrey A., Church, Deanna M., Ventura, Mario, Rocchi, Mariano, Eichler, Evan E.
Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications. The extent of segmental duplications in other mammalian genomes is unknown and...
Regional Patterns of Gene Expression in Human and Chimpanzee Brains
Khaitovich, Philipp, Muetzel, Bjoern, She, Xinwei, Lachmann, Michael, Hellmann, Ines, Dietzsch, Janko, ...
We have analyzed gene expression in various brain regions of humans and chimpanzees. Within both human and chimpanzee individuals, the transcriptomes of the cerebral cortex are very similar to each...
Segmental Duplications Flank the Multiple Sclerosis Locus on Chromosome 17q
Chen, Daniel C., Saarela, Janna, Clark, Royden A., Miettinen, Timo, Chi, Anthony, Eichler, Evan E., ...
Large chromosomal rearrangements, duplications, and inversions are relatively common in mammalian genomes. Here we report interesting features of DNA strands flanking a Multiple Sclerosis (MS)...
Recurrent Sites for New Centromere Seeding
Ventura, Mario, Weigl, Stefania, Carbone, Lucia, Cardone, Maria Francesca, Misceo, Doriana, Teti, Mariagrazia, ...
Using comparative FISH and genomics, we have studied and compared the evolution of chromosome 3 in primates and two human neocentromere cases on the long arm of this chromosome. Our results show that...
Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome
Kirsch, Stefan, Weiß, Birgit, Miner, Tracie L., Waterston, Robert H., Clark, Royden A., Eichler, Evan E., ...
Basic medical research critically depends on the finished human genome sequence. Two types of gaps are known to exist in the human genome: those associated with heterochromatic sequences and those...
Yohn, Chris T, Jiang, Zhaoshi, McGrath, Sean D, Hayden, Karen E, Khaitovich, Philipp, Johnson, Matthew E, ...
Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been...
Manipulating multiple sequence alignments via MaM and WebMaM
Alkan, Can, Tüzün, Eray, Buard, Jerome, Lethiec, Franck, Eichler, Evan E., Bailey, Jeffrey A., ...
MaM is a software tool that processes and manipulates multiple alignments of genomic sequence. MaM computes the exact location of common repeat elements, exons and unique regions within aligned...
Punctuated duplication seeding events during the evolution of human chromosome 2p11
Horvath, Julie E., Gulden, Cassandra L., Vallente, Rhea U., Eichler, Marla Y., Ventura, Mario, McPherson, John D., ...
Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within...
An Alu Transposition Model for the Origin and Expansion of Human Segmental Duplications
Bailey, Jeffrey A., Liu, Ge, Eichler, Evan E.
Relative to genomes of other sequenced organisms, the human genome appears particularly enriched for large, highly homologous segmental duplications (⩾90% sequence identity and ⩾10 kbp in...
Segmental Duplications and Copy-Number Variation in the Human Genome
Sharp, Andrew J., Locke, Devin P., McGrath, Sean D., Cheng, Ze, Bailey, Jeffrey A., Vallente, Rhea U., ...
The human genome contains numerous blocks of highly homologous duplicated sequence. This higher-order architecture provides a substrate for recombination and recurrent chromosomal rearrangement...
A genome-wide survey of structural variation between human and chimpanzee
Newman, Tera L., Tuzun, Eray, Morrison, V. Anne, Hayden, Karen E., Ventura, Mario, McGrath, Sean D., ...
Structural changes (deletions, insertions, and inversions) between human and chimpanzee genomes have likely had a significant impact on lineage-specific evolution because of their potential for...
She, Xinwei, Liu, Ge, Ventura, Mario, Zhao, Shaying, Misceo, Doriana, Roberto, Roberta, ...
Compared with other sequenced animal genomes, human segmental duplications appear larger, more interspersed, and disproportionately represented as high-sequence identity alignments. Global sequence...
Hotspots for copy number variation in chimpanzees and humans
Perry, George H., Tchinda, Joelle, McGrath, Sean D., Zhang, Junjun, Picker, Simon R., Cáceres, Angela M., ...
Copy number variation is surprisingly common among humans and can be involved in phenotypic diversity and variable susceptibility to complex diseases, but little is known of the extent of copy number...
Locke, Devin P., Sharp, Andrew J., McCarroll, Steven A., McGrath, Sean D., Newman, Tera L., Cheng, Ze, ...
Studies of copy-number variation and linkage disequilibrium (LD) have typically excluded complex regions of the genome that are rich in duplications and prone to rearrangement. In an attempt to...
Cardone, Maria Francesca, Alonso, Alicia, Pazienza, Michele, Ventura, Mario, Montemurro, Gabriella, Carbone, Lucia, ...
The mammalian evolutionary history of chromosome 13 was characterized and evolutionary-new centromeres compared to two human neocentromeres at 13q21 using chromatin immunoprecipitation and genomic...
Population Stratification of a Common APOBEC Gene Deletion Polymorphism
Kidd, Jeffrey M, Newman, Tera L, Tuzun, Eray, Kaul, Rajinder, Eichler, Evan E
The APOBEC3 gene family plays a role in innate cellular immunity inhibiting retroviral infection, hepatitis B virus propagation, and the retrotransposition of endogenous elements. We present a...
Recurrent duplication-driven transposition of DNA during hominoid evolution
Johnson, Matthew E., Cheng, Ze, Morrison, V. Anne, Scherer, Steven, Ventura, Mario, Gibbs, Richard A., ...
The underlying mechanism by which the interspersed pattern of human segmental duplications has evolved is unknown. Based on a comparative analysis of primate genomes, we show that a particular...
A Comprehensive Analysis of Common Copy-Number Variations in the Human Genome
Wong, Kendy K., DeLeeuw, Ronald J., Dosanjh, Nirpjit S., Kimm, Lindsey R., Cheng, Ze, Horsman, Douglas E., ...
Segmental copy-number variations (CNVs) in the human genome are associated with developmental disorders and susceptibility to diseases. More importantly, CNVs may represent a major genetic component...
Molecular refinement of gibbon genome rearrangements
Roberto, Roberta, Capozzi, Oronzo, Wilson, Richard K., Mardis, Elaine R., Lomiento, Mariana, Tuzun, Eray, ...
The gibbon karyotype is known to be extensively rearranged when compared to the human and to the ancestral primate karyotype. By combining a bioinformatics (paired-end sequence analysis) approach and...
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
Alkan, Can, Ventura, Mario, Archidiacono, Nicoletta, Rocchi, Mariano, Sahinalp, S. Cenk, Eichler, Evan E
The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is...
Lyle, Robert, Prandini, Paola, Osoegawa, Kazutoyo, Ten Hallers, Boudewijn, Humphray, Sean, Zhu, Baoli, ...
The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p),...
Hominoid chromosomal rearrangements on 17q map to complex regions of segmental duplication
Cardone, Maria Francesca, Jiang, Zhaoshi, D'Addabbo, Pietro, Archidiacono, Nicoletta, Rocchi, Mariano, Eichler, Evan E, ...
A FISH analysis of chromosome 17 homologs in primates suggests that genomic architecture has a direct role in karyotype evolution and in the genomic instability associated with human disease.
Kirsch, Stefan, Münch, Claudia, Jiang, Zhaoshi, Cheng, Ze, Chen, Lin, Batz, Christiane, ...
Human chromosomal regions enriched in segmental duplications are subject to extensive genomic reorganization. Such regions are particularly informative for illuminating the evolutionary history of a...
Degenhardt, Jeremiah D., De Candia, Paola, Chabot, Adrien, Schwartz, Stuart, Henderson, Les, Ling, Binhua, ...
Variation in genes underlying host immunity can lead to marked differences in susceptibility to HIV infection among humans. Despite heavy reliance on non-human primates as models for HIV/AIDS, little...
DupMasker: A tool for annotating primate segmental duplications
Jiang, Zhaoshi, Hubley, Robert, Smit, Arian, Eichler, Evan E.
Segmental duplications (SDs) play an important role in genome rearrangement, evolution, and the copy-number variation (CNV) of primate genomes. Such sequences are difficult to detect, a priori,...
Evolutionary-new centromeres preferentially emerge within gene deserts
Lomiento, Mariana, Jiang, Zhaoshi, D'Addabbo, Pietro, Eichler, Evan E, Rocchi, Mariano
A study identifying genomic restructuring and the absence of genes as conditions permissive for the seeding of new centromeres in primates
Death and Resurrection of the Human IRGM Gene
Bekpen, Cemalettin, Marques-Bonet, Tomas, Alkan, Can, Antonacci, Francesca, Leogrande, Maria Bruna, Ventura, Mario, ...
Immunity-related GTPases (IRG) play an important role in defense against intracellular pathogens. One member of this gene family in humans, IRGM, has been recently implicated as a risk factor for...
Copy number variation and evolution in humans and chimpanzees
Perry, George H., Yang, Fengtang, Marques-Bonet, Tomas, Murphy, Carly, Fitzgerald, Tomas, Lee, Arthur S., ...
Copy number variants (CNVs) underlie many aspects of human phenotypic diversity and provide the raw material for gene duplication and gene family expansion. However, our understanding of their...
Zhao, Yongzhong, Marotta, Michael, Eichler, Evan E., Eng, Charis, Tanaka, Hisashi
Copy number variations (CNVs) represent a large source of genetic variation in humans and have been increasingly studied for disease association. A deletion polymorphism of the gene encoding the...
Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse
Church, Deanna M., Goodstadt, Leo, Hillier, LaDeana W., Zody, Michael C., Goldstein, Steve, She, Xinwe, ...
A finished clone-based assembly of the mouse genome reveals extensive recent sequence duplication during recent evolution and rodent-specific expansion of certain gene families. Newly assembled...
Haplotype sorting using human fosmid clone end-sequence pairs
Kidd, Jeffrey M., Cheng, Ze, Graves, Tina, Fulton, Bob, Wilson, Richard K., Eichler, Evan E.
An important goal of human genetics and genomics is to understand the complete spectrum of genetic variation across a specific human haplotype. By combining information from a dense SNP map with...
Characterization of six human disease-associated inversion polymorphisms
Antonacci, Francesca, Kidd, Jeffrey M., Marques-Bonet, Tomas, Ventura, Mario, Siswara, Priscillia, Jiang, Zhaoshi, ...
The human genome is a highly dynamic structure that shows a wide range of genetic polymorphic variation. Unlike other types of structural variation, little is known about inversion variants within...
Tissue-specific variation in DNA methylation levels along human chromosome 1
De Bustos, Cecilia, Ramos, Edward, Young, Janet M, Tran, Robert K, Menzel, Uwe, Langford, Cordelia F, ...
Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites
Girirajan, Santhosh, Chen, Lin, Graves, Tina, Marques-Bonet, Tomas, Ventura, Mario, Fronick, Catrina, ...
The gibbon genome exhibits extensive karyotypic diversity with an increased rate of chromosomal rearrangements during evolution. In an effort to understand the mechanistic origin and implications of...
Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease
Itsara, Andy, Cooper, Gregory M., Baker, Carl, Girirajan, Santhosh, Li, Jun, Absher, Devin, ...
Copy number variants (CNVs) contribute to human genetic and phenotypic diversity. However, the distribution of larger CNVs in the general population remains largely unexplored. We identify large...
The genomic architecture of segmental duplications and associated copy number variants in dogs
Nicholas, Thomas J., Cheng, Ze, Ventura, Mario, Mealey, Katrina, Eichler, Evan E., Akey, Joshua M.
Structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of segmental duplications and associated...
McKernan, Kevin Judd, Peckham, Heather E., Costa, Gina L., McLaughlin, Stephen F., Fu, Yutao, Tsung, Eric F., ...
We describe the genome sequencing of an anonymous individual of African origin using a novel ligation-based sequencing assay that enables a unique form of error correction that improves the raw...
Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease
Itsara, Andy, Cooper, Gregory M., Baker, Carl, Girirajan, Santhosh, Li, Jun, Absher, Devin, ...
Comparative analysis of Alu repeats in primate genomes
Liu, George E., Alkan, Can, Jiang, Lu, Zhao, Shaying, Eichler, Evan E.
Using bacteria artificial chromosome (BAC) end sequences (16.9 Mb) and high-quality alignments of genomic sequences (17.4 Mb), we performed a global assessment of the divergence distributions,...