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Doggett NA, Xie G, Meincke LJ, Sutherland RD, Mundt MO, Berbari NS, Davy BE, Robinson ML, Rudd MK, Weber JL, Stallings RL, Han C. A 360-kb interchromosomal duplication of the human HYDIN locus. Genomics 2006; 88:762-771. [PMID: 16938426 DOI: 10.1016/j.ygeno.2006.07.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Revised: 07/06/2006] [Accepted: 07/19/2006] [Indexed: 11/16/2022]
Abstract
The HYDIN gene located in human chromosome band 16q22.2 is a large gene encompassing 423 kb of genomic DNA that has been suggested as a candidate for an autosomal recessive form of congenital hydrocephalus. We have found that the human HYDIN locus has been very recently duplicated, with a nearly identical 360-kb paralogous segment inserted on chromosome 1q21.1. The duplication, among the largest interchromosomal segmental duplications described in humans, is not accounted for in the current human genome assembly and appears to be part of a greater than 550-kb contig that must lie within 1 of the 11 sequence gaps currently remaining in 1q21.1. Both copies of the HYDIN gene are expressed in alternatively spliced transcripts. Elucidation of the role of HYDIN in human disease susceptibility will require careful discrimination among the paralogous copies.
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Affiliation(s)
- Norman A Doggett
- DOE Joint Genome Institute and Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Gary Xie
- DOE Joint Genome Institute and Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Linda J Meincke
- DOE Joint Genome Institute and Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Robert D Sutherland
- DOE Joint Genome Institute and Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Mark O Mundt
- DOE Joint Genome Institute and Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nicolas S Berbari
- Division of Molecular and Human Genetics, Children's Research Institute, Ohio State University, 700 Children's Drive, Columbus, OH 43205, USA
| | - Brian E Davy
- Division of Molecular and Human Genetics, Children's Research Institute, Ohio State University, 700 Children's Drive, Columbus, OH 43205, USA
| | - Michael L Robinson
- Division of Molecular and Human Genetics, Children's Research Institute, Ohio State University, 700 Children's Drive, Columbus, OH 43205, USA
| | - M Katharine Rudd
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, C3-168, Seattle, WA 98109, USA
| | - James L Weber
- Center for Medical Genetics, Marshfield Medical Research Foundation, 1000 North Oak Avenue, Marshfield, WI 54449, USA
| | - Raymond L Stallings
- Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Cliff Han
- DOE Joint Genome Institute and Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM, Altherr M, Couronne O, Aerts A, Bajorek E, Black S, Blumer H, Branscomb E, Brown NC, Bruno WJ, Buckingham JM, Callen DF, Campbell CS, Campbell ML, Campbell EW, Caoile C, Challacombe JF, Chasteen LA, Chertkov O, Chi HC, Christensen M, Clark LM, Cohn JD, Denys M, Detter JC, Dickson M, Dimitrijevic-Bussod M, Escobar J, Fawcett JJ, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Goodwin LA, Grady DL, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Hildebrand CE, Huang W, Israni S, Jett J, Jewett PB, Kadner K, Kimball H, Kobayashi A, Krawczyk MC, Leyba T, Longmire JL, Lopez F, Lou Y, Lowry S, Ludeman T, Manohar CF, Mark GA, McMurray KL, Meincke LJ, Morgan J, Moyzis RK, Mundt MO, Munk AC, Nandkeshwar RD, Pitluck S, Pollard M, Predki P, Parson-Quintana B, Ramirez L, Rash S, Retterer J, Ricke DO, Robinson DL, Rodriguez A, Salamov A, Saunders EH, Scott D, Shough T, Stallings RL, Stalvey M, Sutherland RD, Tapia R, Tesmer JG, Thayer N, Thompson LS, Tice H, Torney DC, Tran-Gyamfi M, Tsai M, Ulanovsky LE, Ustaszewska A, Vo N, White PS, Williams AL, Wills PL, Wu JR, Wu K, Yang J, Dejong P, Bruce D, Doggett NA, Deaven L, Schmutz J, Grimwood J, Richardson P, Rokhsar DS, Eichler EE, Gilna P, Lucas SM, Myers RM, Rubin EM, Pennacchio LA. The sequence and analysis of duplication-rich human chromosome 16. Nature 2004; 432:988-94. [PMID: 15616553 DOI: 10.1038/nature03187] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2004] [Accepted: 11/15/2004] [Indexed: 01/30/2023]
Abstract
Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.
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Affiliation(s)
- Joel Martin
- DOE Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA
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Han CS, Sutherland RD, Jewett PB, Campbell ML, Meincke LJ, Tesmer JG, Mundt MO, Fawcett JJ, Kim UJ, Deaven LL, Doggett NA. Construction of a BAC contig map of chromosome 16q by two-dimensional overgo hybridization. Genome Res 2000; 10:714-21. [PMID: 10810094 PMCID: PMC310869 DOI: 10.1101/gr.10.5.714] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have used sequence-based markers from an integrated YAC STS-content/somatic cell hybrid breakpoint physical map and radiation hybrid maps of human chromosome 16 to construct a new sequence-ready BAC map of the long arm of this chromosome. The integrated physical map was generated previously in our laboratory and contains 1150 STSs, providing a marker on average every 78 kb on the euchromatic arms of chromosome 16. The other two maps used for this effort were the radiation hybrid maps of chromosome 16 from Whitehead Institute and Stanford University. To create large sequenceable targets of this chromosome, we used a systematic approach to screen high-density BAC filters with probes generated from overlapping oligonucleotides (overgos). We first identified all available sequences in the three maps. These include sequences from genes, ESTs, STSs, and cosmid end sequences. We then used BLASTto identify 36-bp unique fragments of DNA for overgo probes. A total of 906 overgos were selected from the long arm of chromosome 16. Hybridizations occurred in three stages: (1) superpool hybridizations against the 12x coverage human BAC library (RPCI-11); (2) two-dimensional hybridizations against rearrayed positive BACs identified in the superpool hybridizations; and (3) pooled tertiary hybridizations for those overgos that had ambiguous positives remaining after the two-dimensional hybridization. For the superpool hybridizations, up to 236 overgos have been pooled in a single hybridization against the 12x BAC library. A total of 5187 positive BACs from chromosome 16q were identified as a result of five superpool hybridizations. These positive clones were rearrayed on membranes and hybridized with 161 two-dimensional subpools of overgos to determine which BAC clones were positive for individual overgos. An additional 46 tertiary hybridizations were required to resolve ambiguous overgo-BAC relationships. Thus, after a total of 212 hybridizations, we have constructed an initial probe-content BAC map of chromosome 16q consisting of 828 overgo markers and 3363 BACs providing >85% coverage of the long arm of this chromosome. The map has been confirmed by the fingerprinting data and BAC end PCR screening.
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Affiliation(s)
- C S Han
- DOE Joint Genome Institute, Bioscience Division and Center for Human Genome Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.
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