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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
...segment.In 3421/3436 humans, AGAP1, AGAP2, and AGAP3, which map outside Chromosome 10, are in single copy. Conversely, the other 10 AGAP genes, which map on Chromosome 10, have a WSSD diploid copy number ranging from 15 to 32, with the mean value equal to 19 or 20 (representative AGAP4 copynumber plot...
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RESOURCE: Construction of a BAC Contig Map of Chromosome 16q by Two-Dimensional Overgo Hybridization
- Cliff S. Han,
- Robert D. Sutherland,
- Phillip B. Jewett,
- Mary L. Campbell,
- Linda J. Meincke,
- Judy G. Tesmer,
- Mark O. Mundt,
- John J. Fawcett,
- Ung-Jin Kim,
- Larry L. Deaven,
- and Norman A. Doggett
Genome Res. May 1, 2000 10: 714-721; doi:10.1101/gr.10.5.714
....L. , Xu X. , Wang M. , Dho S.H. , RyulHuh J. , Lee B.-J. , Kalush F. , Bocska D. , Ding Y. , et al. ( 1999 ) A 12 Mbp complete coverage BAC contig map in human chromosome 16p13.1–11.2. Genome Res. 9 : 763 – 774 . ↵ Chumakov I.M. , Rigault P. , Le Gall I. , Bellanné-Chantelot C. , Billault A. , Guillou S...
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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
...by the contig (chr7:81552000–83132000, rheMac2). In particular, gap and STS locations, BAC clones, FISH mapping data, chained alignments with hg18 reference, WSSD (whole- shotgun sequence detection) depth-of-coverage data (the green color corresponds to single copy; the red color to duplication; Marques...
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RESEARCH: A Physical Map of Human Chromosome 7: An Integrated YAC Contig Map with Average STS Spacing of 79 kb
- Gerard G. Bouffard,
- Jacquelyn R. Idol,
- Valerie V. Braden,
- Leslie M. Iyer,
- Aimee F. Cunningham,
- Lauren A. Weintraub,
- Jeffrey W. Touchman,
- Rose M. Mohr-Tidwell,
- Dale C. Peluso,
- Robert S. Fulton,
- Melinda S. Ueltzen,
- Jean Weissenbach,
- Charles L. Magness,
- and Eric D. Green
Genome Res. July 1, 1997 7: 673-692; doi:10.1101/gr.7.7.673
...(G.G. Bouffard and E.D. Green, unpubl.). Furthermore, STSs developed from the insert ends of several of these BACs have been found to map to orphan YAC contigs, further suggesting that some of the gaps and orphan contigs correspond to regions difficult to clone in YACs. Apparent False...
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Methods: Mapping segmental and sequence variations among laboratory mice using BAC array CGH
- Antoine M. Snijders,
- Norma J. Nowak,
- Bing Huey,
- Jane Fridlyand,
- Sindy Law,
- Jeffrey Conroy,
- Taku Tokuyasu,
- Kubilay Demir,
- Readman Chiu,
- Jian-Hua Mao,
- Ajay N. Jain,
- Steven J.M. Jones,
- Allan Balmain,
- Daniel Pinkel,
- and Donna G. Albertson
Genome Res. February 2005 15: 302-311; doi:10.1101/gr.2902505
...). Some of the other BACs that map to single sites by FISH are also likely to identify regions that contain gene families and/or low copy number repeats. For example, Akr1b3, Akr1b8 , and Akr1b7 map within the region spanned by the contig of three polymorphic BACs on Chromosome 6. Similarly, several BAC...
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LETTER: Integrated YAC Contig Map of the Prader–Willi/Angelman Region on Chromosome 15q11–q13 with Average STS Spacing of 35 kb
- Susan L. Christian,
- Nehal K. Bhatt,
- Scott A. Martin,
- James S. Sutcliffe,
- Takeo Kubota,
- Bing Huang,
- Apiwat Mutirangura,
- A. Craig Chinault,
- Arthur L. Beaudet,
- and David H. Ledbetter
Genome Res. February 1, 1998 8: 146-157; doi:10.1101/gr.8.2.146
...proximal markers failed to identify any additional YACs. It is possible that this region, which resides near the centromere of chromosome 15, may be under-represented in the YAC libraries. Screening of PAC, BAC, and cosmid libraries may be necessary to complete the physical map of this region. Weak...
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LETTER: Bacterial Contig Map of the 21q11 Region Associated with Alzheimer’s Disease and Abnormal Myelopoiesis in Down Syndrome
- Jürgen Groet,
- Jane H. Ives,
- Andrew P. South,
- Pedro R. Baptista,
- Tania A. Jones,
- Marie-Laure Yaspo,
- Hans Lehrach,
- Marie-Claude Potier,
- Christine Van Broeckhoven,
- and Dean Nižetić
Genome Res. April 1, 1998 8: 385-398; doi:10.1101/gr.8.4.385
.... , de Jong P.J. , Korenberg J.R. ( 1997 ) BAC and PAC contigs covering 3.5Mb of the Down syndrome congenital heart disease region between D21S55 and MX1 on chromosome 21. Genomics 41 : 218 – 226 . ↵ Ichikawa, H., F. Hosoda, Y. Arai, K. Shimizu, M. Ohira, and M. Ohki. 1993. A Not I restriction map...
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LETTER: Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla
- Gary M. Wilson,
- Stephane Flibotte,
- Perseus I. Missirlis,
- Marco A. Marra,
- Steven Jones,
- Kevin Thornton,
- Andrew G. Clark,
- and Robert A. Holt
Genome Res. February 2006 16: 173-181; Published in Advance December 19, 2005, doi:10.1101/gr.4456006
...duplicated segments ( She et al. 2004 ). Thus, to achieve a complete survey of DNA copy number in human versus chimpanzee, we have performed comparative hybridization (CGH) using the first full-coverage bacterial artificial chromosome (BAC) array of the human , which consists of 32,855 overlapping clones...
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LETTER: Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions
- Laurie Gordon,
- Shan Yang,
- Mary Tran-Gyamfi,
- Dan Baggott,
- Mari Christensen,
- Aaron Hamilton,
- Richard Crooijmans,
- Martien Groenen,
- Susan Lucas,
- Ivan Ovcharenko,
- and Lisa Stubbs
Genome Res. November 2007 17: 1603-1613; Published in Advance October 5, 2007, doi:10.1101/gr.6775107
...from conserved HSA19 genes (see Methods). We focused on generating complete JF BAC contigs but also generated WL contigs for most regions. The BACs were selected to provide maximum coverage and sequenced to &gt;10× depth. Automated JF sequence assembly was curated manually and checked against parallel...
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LETTER: Perfect Conserved Linkage Across the Entire Mouse Chromosome 10 Region Homologous to Human Chromosome 21
- Tim Wiltshire,
- Mathew Pletcher,
- Susan E. Cole,
- Melissa Villanueva,
- Bruce Birren,
- Jessica Lehoczky,
- Ken Dewar,
- and Roger H. Reeves
Genome Res. December 1, 1999 9: 1214-1222; doi:10.1101/gr.9.12.1214
...to this region were also mapped on the contig. PAC clones were underrepresented in the mouse RPCI-21 library for the region just distal to Pfkl . The mouse RPCI-22 BAC library was screened to provide additional depth of coverage for this region. The final contig spans 2.8 Mb and includes the entire HSA21 region...

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