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Research: Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region
- Kiana Mohajeri,
- Stuart Cantsilieris,
- John Huddleston,
- Bradley J. Nelson,
- Bradley P. Coe,
- Catarina D. Campbell,
- Carl Baker,
- Lana Harshman,
- Katherine M. Munson,
- Zev N. Kronenberg,
- Milinn Kremitzki,
- Archana Raja,
- Claudia Rita Catacchio,
- Tina A. Graves,
- Richard K. Wilson,
- Mario Ventura,
- and Evan E. Eichler
Genome Res. November 2016 26: 1453-1467; Published in Advance October 7, 2016, doi:10.1101/gr.211284.116
...to distinguish it from the structural haplotype represented by the human reference (H1). We assessed the quality of the Chromosome 8p23.1 H2 haplotype by combining paired-end sequence data, read-depth analysis, and high-quality SMRT sequencing (Supplemental Section 1). Our initial clone-based assemblies...
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Research: Hominoid fission of chromosome 14/15 and the role of segmental duplications
- Giuliana Giannuzzi,
- Michele Pazienza,
- John Huddleston,
- Francesca Antonacci,
- Maika Malig,
- Laura Vives,
- Evan E. Eichler,
- and Mario Ventura
Genome Res. November 2013 23: 1763-1773; Published in Advance September 27, 2013, doi:10.1101/gr.156240.113
...ventricular cardiomyopathy 7: Corroboration and narrowing of the critical region on 10q22.3. Eur J Hum Genet 16: 367–373. Lichter P, Tang CJ, Call K, Hermanson G, Evans GA, Housman D, Ward DC. 1990. High-resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 247: 64...
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METHODS: Optical Mapping of BAC Clones from the Human Y Chromosome DAZ Locus
- Joseph Giacalone,
- Stephanie Delobette,
- Veronica Gibaja,
- Lei Ni,
- Yiannis Skiadas,
- Rong Qi,
- Joanne Edington,
- Zhongwu Lai,
- Damara Gebauer,
- Hongjuan Zhao,
- Thomas Anantharaman,
- Bhubaneswar Mishra,
- Laura G. Brown,
- Richa Saxena,
- David C. Page,
- and David C. Schwartz
Genome Res. September 1, 2000 10: 1421-1429; doi:10.1101/gr.112100
...), the primary emphasis has shifted to the determination of the complete nucleotide sequence of the more than 3000 Mb comprising the 24 different human chromosomes ( Collins et al. 1998 ). The predominant approach to sequence acquisition is the shotgun subcloning of fingerprinted DNA clones, generally BAC, PAC...
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LETTER: Genome Mapping by Fluorescent Fingerprinting
- Simon G. Gregory,
- Gareth R. Howell,
- and David R. Bentley
Genome Res. December 1, 1997 7: 1162-1168; doi:10.1101/gr.7.12.1162
...°C. This protocol resulted in an increased yield and, hence, signal intensity of the fingerprints, and also increased the pass rate from ∼80%–90% to &gt;95% using cosmids, fosmids, P1 or bacterial artificial chromosome [PAC ( Iaonnou et al. 1994 ) or BAC ( Shizuya et al. 1992 ), respectively] clones...
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RESEARCH: Analysis of the 1.1-Mb Human α/δ T-Cell Receptor Locus with Bacterial Artificial Chromosome Clones
- Cecilie Boysen,
- Melvin I. Simon,
- and Leroy Hood
Genome Res. April 1, 1997 7: 330-338; doi:10.1101/gr.7.4.330
...(BAC) clones have been used for physical mapping (Ashworth et al. 1995; Kim et al. 1996). Typically, 2- to 10-fold coverage of the or specific chromosomes has been sought. 2. In the past, sequence-ready maps were prepared by subcloning YACs or BACs, after partial restriction digestion, into cosmid...
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LETTER: High Throughput Fingerprint Analysis of Large-Insert Clones
- Marco A. Marra,
- Tamara A. Kucaba,
- Nicole L. Dietrich,
- Eric D. Green,
- Buddy Brownstein,
- Richard K. Wilson,
- Ken M. McDonald,
- LaDeana W. Hillier,
- John D. McPherson,
- and Robert H. Waterston
Genome Res. November 1, 1997 7: 1072-1084; doi:10.1101/gr.7.11.1072
..., in our experience, more stable than cosmids. Clones identified by STS screening can be characterized by fingerprinting and the fingerprints used to build contigs. Using these contigs, appropriate clones can then be selected for sequencing and to develop probes for chromosome walking. Clones recovered...
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GENOME METHODS: Modification of Bacterial Artificial Chromosome Clones Using Cre Recombinase: Introduction of Selectable Markers for Expression in Eukaryotic Cells
- Su Young Kim,
- Stephen K. Horrigan,
- Janine L. Altenhofen,
- Zarema H. Arbieva,
- Ronald Hoffman,
- and Carol A. Westbrook
Genome Res. April 1, 1998 8: 404-412; doi:10.1101/gr.8.4.404
...of the human have made use of genomic libraries contained in several cloning vectors, including yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), human artificial episomal chromosomes (HAECs), P1 artificial chromosomes (PACs), P1 vectors (P1s), and cosmid clones ( Deaven et al. 1986...
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METHODS: High-Resolution BAC-Based Map of the Central Portion of Mouse Chromosome 5
- Jonathan Crabtree,
- Tim Wiltshire,
- Brian Brunk,
- Shaying Zhao,
- Jonathan Schug,
- Christian J. Stoeckert, Jr.,
- and Maja Bucan
Genome Res. October 1, 2001 11: 1746-1757; doi:10.1101/gr.195101
...; Pennisi 2000 ; Marshall 2000 , 2001 ). Systematic restriction fragment analysis or “fingerprinting” and bacterial artificial chromosome (BAC)-end sequencing of all clones in the selected C57BL/6J (RPCI-23 and RPCI-24) BAC libraries will permit long-range association of sequence contigs. In the second...
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RESOURCE: A Bacterial Artificial Chromosome Library for Sequencing the Complete Human Genome
- Kazutoyo Osoegawa,
- Aaron G. Mammoser,
- Chenyan Wu,
- Eirik Frengen,
- Changjiang Zeng,
- Joseph J. Catanese,
- and Pieter J. de Jong
Genome Res. March 1, 2001 11: 483-496; doi:10.1101/gr.169601
...characterization of the RPCI-11 BAC library has not been reported, although its use in clone end sequencing, fingerprinting, and complete chromosome sequencing has been described ( Dunham et al. 1999 ; Mahairas et al. 1999 ; Hattori et al. 2000 ; Soderlund et al. 2000 ; Zhao et al. 2000 ; McPherson et al. 2001...
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LETTER: Closing the Gaps on Human Chromosome 19 Revealed Genes With a High Density of Repetitive Tandemly Arrayed Elements
- Sun-Hee Leem,
- Natalay Kouprina,
- Jane Grimwood,
- Jung-Hyun Kim,
- Michael Mullokandov,
- Young-Ho Yoon,
- Ji-Youn Chae,
- Jenna Morgan,
- Susan Lucas,
- Paul Richardson,
- Chris Detter,
- Tijana Glavina,
- Eddy Rubin,
- J. Carl Barrett,
- and Vladimir Larionov
Genome Res. February 2004 14: 239-246; Published in Advance January 12, 2004, doi:10.1101/gr.1929904
...), or other fosmid and cosmid libraries. Most of these gaps represent the type 3 gaps that are the most difficult to evaluate, because the sequence flanking these gaps is often not precisely aligned with the fingerprinted clones. The gaps represent ∼30 Mb or 1.0% of the human ( Grimwood and Schmutz 2003...

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