351
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Abstract
Radiation hybrid mapping is a somatic cell technique for ordering human loci along a chromosome and estimating the physical distance between adjacent loci. The present paper considers a realistic model of fragment generation and retention. This model assumes that fragments are generated in the ancestral cell of a clone according to a Poisson breakage process along the chromosome. Once generated, fragments are independently retained in the clone with a common retention probability. Based on this and less restrictive models, statistical criteria such as minimum obligate breaks, maximum likelihood, and Bayesian posterior probabilities can be used to decide order. Distances can be estimated by either maximum likelihood or Bayesian posterior means. The model also permits rational design of radiation dose for optimal statistical precision. A brief examination of some real data illustrates our criteria and computational algorithms.
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Affiliation(s)
- K Lange
- Department of Biomathematics, School of Medicine, University of California, Los Angeles 90024
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352
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Colman SD, Mellott JK, Almeida AS, Goldman MA, van Tuinen P, Yang TP. Isolation and characterization of radiation-reduced hybrids containing portions of the proximal long arm of the human X chromosome: identification of hybrids containing the Menkes' disease locus. SOMATIC CELL AND MOLECULAR GENETICS 1992; 18:201-13. [PMID: 1496417 DOI: 10.1007/bf01233857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The proximal long arm of the human X chromosome (Xcen----Xq13) encompasses an estimated 23 megabases of DNA and contains numerous identified genetic loci. In order to generate a highly enriched source of DNA from this region, radiation-reduced human-hamster hybrids were constructed and screened to identify those that contained at least part of proximal Xq. Eight such hybrids were identified and characterized by Southern blot and fluorescence in situ hybridization analyses to determine more precisely the human DNA complement in each. One hybrid contains the entire proximal long arm and will be useful for mapping Xcen----Xq13 in its entirety and for localizing genes within this region. Another hybrid contains a smaller portion of the proximal long arm that includes the region reported to contain the gene for Menkes' disease.
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Affiliation(s)
- S D Colman
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville 32610
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353
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Rothschild CB, Noll WW, Gravius TC, Schuster MK, Nutile-McMenemy N, Jones C, Bowden DW. Characterization of radiation/fusion hybrids containing parts of human chromosome 10 and their use in mapping chromosome 10-specific probes. Genomics 1992; 13:25-34. [PMID: 1349579 DOI: 10.1016/0888-7543(92)90197-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have characterized a panel of somatic cell hybrid cell lines which contain different portions of human chromosome 10. Genomic DNA from the somatic cell hybrids was tested for hybridization with each of an ordered set of probes used previously to construct a genetic map of chromosome 10, as well as several additional probes, previously localized by in situ hybridization. Hybridization of an unmapped probe to the cell line DNAs can be used to determine its most likely position on the chromosome relative to the mapped set of probes. Genomic DNA from two of the cell lines has been used to construct region-specific cosmid and bacteriophage libraries, and clones derived from these libraries were localized by hybridization to the panel of hybrid cell lines. Several of these probes reveal restriction fragment length polymorphisms which have been genetically mapped. Three of the probes map near the locus for multiple endocrine neoplasia type 2A, and one of these probes, BG-JC353 (D10S167), maps between RBP3 and TB14.34 (D10S34). Another probe, CRI-J282 (D10S104), is close to the FNRB locus. The panel of hybrid cell lines is thus useful for rapidly localizing unmapped probes and as a source of DNA for the construction of recombinant libraries derived from specific regions of the chromosome.
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Affiliation(s)
- C B Rothschild
- Department of Biochemistry, Bowman Gray School of Medicine, Wake Forest University, Winston-Salem, North Carolina 27157
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354
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Wang D, Fang H, Cantor CR, Smith CL. A contiguous Not I restriction map of band q22.3 of human chromosome 21. Proc Natl Acad Sci U S A 1992; 89:3222-6. [PMID: 1565613 PMCID: PMC48838 DOI: 10.1073/pnas.89.8.3222] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A contiguous high-resolution NotI restriction map of the distal region of the long arm of human chromosome 21 was constructed by three strategies: linking clones to identify adjacent pieces of DNA, partial digestion to identify neighboring fragments, and cell line polymorphisms to prove identity or adjacency of DNA fragments. Twenty-nine single-copy DNA probes and five linking clone probes were used to determine the order of 30 Not I fragments, covering 10 megabases of DNA in band q22.3. Smaller Not I fragments occur preferentially in this region, suggesting that band q22.3 is unusually rich in genes, since Not I sites occur almost exclusively in CpG islands. Comparison of the physical map and genetic maps in this region reveals a 10-fold higher than average recombination frequency.
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Affiliation(s)
- D Wang
- Department of Molecular and Cell Biology, University of California, Berkeley
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355
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Ichikawa H, Shimizu K, Saito A, Wang DN, Oliva R, Kobayashi H, Kaneko Y, Miyoshi H, Smith CL, Cantor CR. Long-distance restriction mapping of the proximal long arm of human chromosome 21 with Not I linking clones. Proc Natl Acad Sci U S A 1992; 89:23-7. [PMID: 1346067 PMCID: PMC48167 DOI: 10.1073/pnas.89.1.23] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human chromosome 21 is the smallest of the 22 autosomes and 2 sex chromosomes. Hybridization of the human repetitive sequence Alu to pulsed-field gel-fractionated Not I-digested genomic DNA from a human-mouse hybrid cell line containing chromosome 21 as the sole human component identified chromosome 21 Not I restriction fragments. A Not I restriction map of regions of the chromosome was constructed, by identifying neighboring Alu bands with Not I linking clones. This approach simplifies the task of physical mapping and avoids ambiguities in Not I fragment assignments that arise from gel-to-gel mobility variations. A contiguous map was constructed with six Not I linking clones that covers at least the proximal one-third of the long arm of chromosome 21 and spans 20 megabases. A more detailed restriction map revealed 11 likely CpG islands in this region and localized 11 additional DNA markers.
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Affiliation(s)
- H Ichikawa
- Department of Immunology and Virology, Saitama Cancer Center Research Institute, Japan
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356
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Benham F, Rowe P. Use of Alu-PCR to characterize hybrids containing multiple fragments and to generate new Xp21.3-p22.2 markers. Genomics 1992; 12:368-76. [PMID: 1740346 DOI: 10.1016/0888-7543(92)90387-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Irradiation fragment hybrids potentially provide highly enriched sources of region-specific human DNA. However, such hybrids often contain multiple human pieces, not all of which can be easily detected. To develop specific resources for rapidly generating markers from Xp21.3-p22.2, we have single cell cloned two previously constructed irradiation hybrids that contain markers in this region and have achieved segregation of the different known fragments originally retained. Alu-PCR products were generated from subclones positive or negative for Xp21.3-p22.2 markers, and comparison of the ethidium bromide patterns between sister subclones facilitated identification of bands likely to map to particular regions; in contrast, subclones that shared markers but were derived from independent lines showed no overlap in ethidium bromide pattern. All Alu-PCR products from one subclone, 50K-19E, in which only three closely linked markers were detected (DXS41, DXS208, DXS274) were mapped back to their region of origin. Of 28 products, 15 mapped to Xp21.2-p22.2, and these make up a new set of regionally assigned markers. However, the mapping data identified four separate Xp fragments in 50K-19E, only one of which had been picked up by marker analysis. Mapping back gel-isolated Alu-PCR products from an irradiation hybrid prior to any cloning or screening generates a comprehensive profile of the human DNA retained and permits rapid selection of sequences derived only from the region of interest.
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Affiliation(s)
- F Benham
- Department of Genetics and Biometry, University College London, United Kingdom
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357
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Ceccherini I, Romeo G, Lawrence S, Breuning MH, Harris PC, Himmelbauer H, Frischauf AM, Sutherland GR, Germino GG, Reeders ST. Construction of a map of chromosome 16 by using radiation hybrids. Proc Natl Acad Sci U S A 1992; 89:104-8. [PMID: 1729675 PMCID: PMC48184 DOI: 10.1073/pnas.89.1.104] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A human-hamster cell hybrid carrying a single copy of chromosome 16 as the only human genetic material was irradiated with a single dose of gamma-rays (7000 rads; 1 rad = 0.01 Gy) and then fused with a thymidine kinase-deficient hamster cell line (RJKM) to generate radiation hybrids retaining unselected fragments of this human chromosome. In two experiments, 223 hybrids were isolated in hypoxanthine/aminopterine/thymidine (HAT) medium and screened with 38 DNA probes, corresponding to anonymous DNA or gene sequences localized on chromosome 16. The most likely order and location of the 38 DNA sequences were established by multiple pairwise analysis and scaled to estimate physical distance in megabases. The order and the distances thus obtained are mostly consistent with available data on genetic and physical mapping of these markers, illustrating the usefulness of radiation hybrids for mapping.
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Affiliation(s)
- I Ceccherini
- Laboratorio di Genetica Molecolare, Istituto G. Gaslini, Genova, Italy
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358
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Affiliation(s)
- L Stubbs
- Biology Division, Oak Ridge National Laboratory, Tennessee 37831
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359
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Butler R, Ogilvie DJ, Elvin P, Riley JH, Finniear RS, Slynn G, Morten JE, Markham AF, Anand R. Walking, cloning, and mapping with yeast artificial chromosomes: a contig encompassing D21S13 and D21S16. Genomics 1992; 12:42-51. [PMID: 1733862 DOI: 10.1016/0888-7543(92)90404-g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Chromosome 21 has often been used as a model system for the development of genome mapping and cloning strategies in humans. In this report methods for systematic chromosome walking, cloning, and mapping are exemplified in the construction of a 1.5-Mb yeast artificial chromosome (YAC) contig encompassing and extending 400 kb beyond each of the genetic loci D21S13 and D21S16. Isolation of insert-terminal sequences from YACs in this contig provides a set of closely spaced physical markers. These have been used to generate a long-range genomic restriction map.
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Affiliation(s)
- R Butler
- Biotechnology Department, ICI Pharmaceuticals, Macclesfield, Cheshire, United Kingdom
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360
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361
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Abstract
A method is presented for the preliminary ordering of loci on a chromosome using pairwise linkage data. The method is based on the biologically reasonable assumption that the "true" order of a set of linked loci will be the one that minimizes the total length of the chromosome segment. Here the "length" is defined as the sum of adjacent recombination fractions. The method searches for the optimal order, represented by a minimum distance map (MDMAP), even when it is not possible to examine the n!/2 possible distinct orders for n loci. A computerized approach, using the simulated annealing algorithm of Kirkpatrick et al. [1983], forms the basis of the method. It can be applied to data from radiation hybrid experiments as well as that from conventional family linkage studies. The technique is applied to several sets of published data to illustrate how it performs in practice. The advantages and the disadvantages of the method are discussed so that it will be clear under what conditions it is likely to work well. When data sets are "complete," in the sense that all possible pairwise recombination fractions have estimates, and when no large clusters of extremely tightly linked loci are present, the method produces ordered sets of loci that agree well with those generated by other, more complex methods. Any discrepancies that occur are likely to be with respect to the orientation of nearest-neighbor loci, where relative order cannot be reliably established by any method. The method thus provides a simple, rapid means of obtaining a preliminary order for a set of loci known to be in the same linkage group.
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Affiliation(s)
- C T Falk
- Lindsley F. Kimball Research Institute, New York Blood Center, New York 10021
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362
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Bowcock AM, Farrer LA, Hebert JM, Bale AE, Cavalli-Sforza L. A contiguous linkage map of chromosome 13q with 39 distinct loci separated on average by 5.1 centimorgans. Genomics 1991; 11:517-29. [PMID: 1685473 DOI: 10.1016/0888-7543(91)90058-m] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A fine-structure linkage map of chromosome 13q is presented. This map contains 39 continuously linked loci defined by genotypes generated from the CEPH family DNAs with 56 probe and enzyme combinations. An alpha-satellite probe for sequences on chromosome 13 was included, resulting in a complete map of 13q with 39 distinct loci. The map spans 1.715 M in males and 2.099 M in females and the mean genetic distance between adjacent loci is 5.1 cM. Although there was generally a several-fold excess of female recombination in the interstitial portion of 13q, an excess of recombination in males was observed at both ends of this chromosomal arm. This map should be useful for the localization of any additional marker, gene, or disease locus of interest on chromosome 13q.
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Affiliation(s)
- A M Bowcock
- Department of Genetics, Stanford University, California 94305
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363
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Green ED, Mohr RM, Idol JR, Jones M, Buckingham JM, Deaven LL, Moyzis RK, Olson MV. Systematic generation of sequence-tagged sites for physical mapping of human chromosomes: application to the mapping of human chromosome 7 using yeast artificial chromosomes. Genomics 1991; 11:548-64. [PMID: 1837788 DOI: 10.1016/0888-7543(91)90062-j] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Basic to the development of long-range physical maps of DNA are the detection and localization of landmarks within recombinant clones. Sequence-tagged sites (STSs), which are short stretches of DNA that can be specifically detected by the polymerase chain reaction (PCR), can be used as such landmarks. Our interest is to construct physical maps of whole human chromosomes by localizing STSs within yeast artificial chromosome (YAC) clones. Here we describe a generalized strategy for the systematic generation of large numbers of STSs specific for human chromosome 7. These STSs can be detected by PCR assays developed following the sequencing of anonymous pieces of chromosome 7 DNA, which was derived from flow-sorted chromosomes or from lambda clones made from DNA of a human-hamster hybrid cell line. Our approach for STS generation is tailored for the development of PCR assays capable of screening a large YAC library. In this study, we report the generation of 100 new STSs specific to human chromosome 7.
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Affiliation(s)
- E D Green
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
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364
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Warrington JA, Hall LV, Hinton LM, Miller JN, Wasmuth JJ, Lovett M. Radiation hybrid map of 13 loci on the long arm of chromosome 5. Genomics 1991; 11:701-8. [PMID: 1663488 DOI: 10.1016/0888-7543(91)90078-s] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Radiation hybrid mapping was used in conjunction with a natural deletion mapping panel to predict the order of and distance between 13 loci in the distal portion of the long arm of human chromosome 5. A panel of irradiation hybrids containing fragments of 5q was generated from an HPRT+ Chinese hamster-human cell hybrid containing a derivative chromosome 5 [der(5)t(4;5)(5qter----5p15.1::4p15.1----4pter)] as its only human DNA. One hundred nine radiation hybrids containing human DNA were screened with polymerase chain reaction primer sets representing nine genes encoding growth factors, growth factor receptors, or hormone receptors (IL3, IL4, IL5, CSF1R, FGFA, ADRB2, GRL, GABRA1, and DRD1) as well as four other loci (FER, SPARC, RPS14, and CD14) to generate a radiation hybrid map of the area 5q21-q35. A physical map predicting the order of and distance between the 13 loci was constructed based on segregation of the 13 loci in hybrid clones. The radiation hybrid panel will be useful as a mapping tool for determining the location and order of other genes and polymorphic loci in this region as well as for generating new DNA probes from specific regions.
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Affiliation(s)
- J A Warrington
- Department of Biological Chemistry, College of Medicine, University of California, Irvine 92717
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365
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Green ED, Green P. Sequence-tagged site (STS) content mapping of human chromosomes: theoretical considerations and early experiences. PCR METHODS AND APPLICATIONS 1991; 1:77-90. [PMID: 1842934 DOI: 10.1101/gr.1.2.77] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The magnitude of the effort required to complete the human genome project will require constant refinements of the tools available for the large-scale study of DNA. Such improvements must include both the development of more powerful technologies and the reformulation of the theoretical strategies that account for the changing experimental capabilities. The two technological advances described here, PCR and YAC cloning, have rapidly become incorporated into the standard armamentarium of genome analysis and represent key examples of how technological developments continue to drive experimental strategies in molecular biology. Because of its high sensitivity, specificity, and potential for automation, PCR is transforming many aspects of DNA mapping. Similarly, by providing the means to isolate and study larger pieces of DNA, YAC cloning has made practical the achievement of megabase-level continuity in physical maps. Taken together, these two technologies can be envisioned as providing a powerful strategy for constructing physical maps of whole chromosomes. Undoubtedly, future technological developments will promote even more effective mapping strategies. Nonetheless, the theoretical projections and practical experience described here suggest that constructing YAC-based STS-content maps of whole human chromosomes is now possible. Random STSs can be efficiently generated and used to screen collections of YAC clones, and contiguous YAC coverage of regions exceeding 2 Mb can be readily obtained. While the predicted laboratory effort required for mapping whole human chromosomes remains daunting, it is clearly feasible.
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Affiliation(s)
- E D Green
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
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366
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MacDonald G, Chu ML, Cox DR. Fine structure physical mapping of the region of mouse chromosome 10 homologous to human chromosome 21. Genomics 1991; 11:317-23. [PMID: 1837533 DOI: 10.1016/0888-7543(91)90138-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Comparative mapping of human and mouse DNA for regions of genetic homology between human Chromosome 21 and the mouse genome is of interest because of the possibility of developing mouse models of human trisomy 21 (Down syndrome), understanding chromosome evolution, and isolating novel sequences conserved between the two species. At least two mouse chromosomes are known to carry sequences homologous to those on human Chromosome 21: mouse Chromosome 16 (D21S16h, D21S13h, D21S52h, App, Sod-1, Mx-1, Ets-2, Prgs,Ifnar) and mouse Chromosome 17 (D21S56h, Crya-1, and Cbs). Recently, five additional genes have been mapped within region 21q22 of human Chromosome 21:PFKL, CD18, COL6A1, COL6A2, and S100B. To assign these sequences to specific mouse chromosomes, we used human cDNA probes for COL6A1, COL6A2, CD18, and PFKL and a rat brain cDNA probe for S100B in conjunction with a panel of seven Chinese hamster-mouse somatic cell hybrids segregating mouse chromosomes. The specific chromosome complements of the hybrid cell lines and the presence or absence of hybridizing mouse sequences in their DNAs allow us to assign all five sequences to mouse Chromosome 10, with the assignment of Pfkl reported here for the first time. Analysis of genomic mouse DNA fragments produced by digestion with rare-cutting restriction enzymes and separated using pulsed-field gel electrophoresis allows us to construct a fine-structure physical map of two segments of the region of Chromosome 10 containing these five markers. The five loci span at least 1900 kb of mouse DNA and are consistent with the human order: Pfkl-Cd-18-Col6a-1-Col6a-2-S100b.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- G MacDonald
- Department of Pediatrics, University of California, San Francisco 94143
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367
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Mares A, Ledbetter SA, Ledbetter DH, Roberts R, Hejtmancik JF. Isolation of a human chromosome 14-only somatic cell hybrid: analysis using Alu and LINE-based PCR. Genomics 1991; 11:215-8. [PMID: 1765380 DOI: 10.1016/0888-7543(91)90122-u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Interspecific somatic cell hybrids containing single human chromosomes are valuable reagents for localization of cloned genes and DNA fragments to specific chromosomes, for the development of chromosome-specific libraries, and for generation of hybrid cell lines containing subchromosomal regions. A CHO somatic cell hybrid containing a single, intact human chromosome 14 (MHR14) was developed and confirmed by LINE PCR amplification gel pattern, by Alu-517 PCR product dot blot hybridization, and by cytogenetic analysis. MHR14 will serve as the chromosome source for the development of a radiation map of human chromosome 14.
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Affiliation(s)
- A Mares
- Department of Medicine, Baylor College of Medicine, Houston, Texas 77030
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368
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Doucette-Stamm LA, Riba L, Handelin B, Difilippantonio M, Ward DC, Wasmuth JJ, Gusella JF, Housman DE. Generation and characterization of irradiation hybrids of human chromosome 4. SOMATIC CELL AND MOLECULAR GENETICS 1991; 17:471-80. [PMID: 1837181 DOI: 10.1007/bf01233171] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In recent years investigators have attempted to develop more rapid and precise methods to isolate specific chromosomal DNA regions. In this paper we demonstrate a modification of the method first developed by Goss and Harris for generation of irradiation hybrids. The gene encoding the dominant selectable marker for resistance to neomycin was introduced into human chromosome 4 using retroviral insertion into human fibroblasts. Transfer of these chromosomes via microcells into the mouse cell line NIH3T6 produced a somatic cell line containing chromosome 4 as the only human chromosome. Irradiation of this cell line followed by fusion with the hamster cell line CHTG49 generated hybrids containing only small portions of chromosome 4p on a hamster background. The use of selection produced stable hybrids that retained chromosome 4 fragments over long periods of tissue culture passage. To obtain new polymorphic markers for Huntington's disease, one of these hybrids was to isolate new genomic fragments. We identified 41 single-copy fragments, of which 27 have been mapped to specific regions of chromosome 4; 52% of these fragments map to the region of chromosome 4 containing the HD gene.
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369
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Abstract
A theory is developed to predict marker retention and conditional retention or loss in radiation hybrids. Applied to multiple pairwise analysis of a human chromosome 21 data set, this theory fits much better than proposed alternatives and gives a physical map consistent with other evidence and robust with respect to errors to typing. Radiation hybrids have great promise to provide order and physical location at two levels of resolution, spanning the techniques of linkage and restriction fragments and not limited to polymorphic loci.
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Affiliation(s)
- S Lawrence
- Department of Community Medicine, University of Southamptom, Southampton General Hospital, United Kingdom
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370
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Abstract
A novel, simultaneous, visual representation of sex-specific genetic maps and physical maps is introduced. Such maps, called Marey maps, provide direct comparisons of multiple genetic maps and elucidate the relationship of recombination frequency to physical distance.
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Affiliation(s)
- A Chakravarti
- Department of Human Genetics, University of Pittsburgh, Pennsylvania 15261
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371
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Florian F, Hornigold N, Griffin DK, Delhanty JD, Sefton L, Abbott C, Jones C, Goodfellow PN, Wolfe J. The use of irradiation and fusion gene transfer (IFGT) hybrids to isolate DNA clones from human chromosome region 9q33-q34. SOMATIC CELL AND MOLECULAR GENETICS 1991; 17:445-53. [PMID: 1763385 DOI: 10.1007/bf01233168] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have generated somatic cell hybrids containing fragments of human chromosome arm 9q by an irradiation and fusion technique. No selection for human material was imposed, but of 23 clones analyzed most contained human DNA sequences and many contained multiple fragments of the human chromosome arm. A hybrid that appears to contain only two small fragments of human DNA from the regions of q33 and q34 has been used as a source from which to clone probes specific to those areas of the chromosome.
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Affiliation(s)
- F Florian
- Department of Genetics and Biometry, University College London, U.K
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372
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Patel K, Cox R, Shipley J, Kiely F, Frazer K, Cox DR, Lehrach H, Sheer D. A novel and rapid method for isolating sequences adjacent to rare cutting sites and their use in physical mapping. Nucleic Acids Res 1991; 19:4371-5. [PMID: 1886764 PMCID: PMC328622 DOI: 10.1093/nar/19.16.4371] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We describe a simple PCR based technique which can be used to isolate sequences adjacent to rare cutter sites and can subsequently be employed for the construction of long range physical maps. The method involves the ligation of an adaptor to rare cutter sequences and its use as a target for forward priming in PCR. Primers to Alu repeat elements initiate synthesis of the reverse strand. Using this technique any rare cutter site which has a repeat element within amplification range can be cloned. We have isolated six unique sequences around NotI sites from an irradiation reduced hybrid containing a fragment of human chromosome 22 and are using these for physical mapping around the Ewing's sarcoma translocation breakpoint on chromosome 22.
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MESH Headings
- Base Sequence
- Cells, Cultured
- Chromosome Mapping/methods
- Chromosomes, Human, Pair 22
- Cloning, Molecular
- DNA, Single-Stranded/genetics
- Deoxyribonucleases, Type II Site-Specific/metabolism
- Humans
- Hybrid Cells
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Polymerase Chain Reaction/methods
- Repetitive Sequences, Nucleic Acid/genetics
- Sarcoma, Ewing/genetics
- Translocation, Genetic/genetics
- Tumor Cells, Cultured
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Affiliation(s)
- K Patel
- Human Cytogenetics Laboratory, ICRF, London, UK
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373
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Abstract
Detailed physical maps of large regions of the human genome are important for locating and cloning genes responsible for human hereditary diseases, as well as for obtaining a more detailed understanding of chromosome structure and evolution. Pulsed field gel electrophoresis provides one method for generating physical maps of non-methylated rare restriction endonuclease sites. This review summarizes recent progress in the isolation of region-specific mapping probes and in their application for the physical mapping of selected regions of the human genome.
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Affiliation(s)
- G A Evans
- Molecular Genetics Laboratory, Salk Institute for Biological Studies, San Diego, California 92138
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374
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Cox RD, Copeland NG, Jenkins NA, Lehrach H. Interspersed repetitive element polymerase chain reaction product mapping using a mouse interspecific backcross. Genomics 1991; 10:375-84. [PMID: 2071145 DOI: 10.1016/0888-7543(91)90322-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have developed a rapid method of generating and simultaneously mapping interrepeat polymerase chain reaction products using DNA from interspecific backcross animals derived from mating C57BL/6J and Mus spretus mice. This method is based on the high degree of B1, B2, and L1 dispersed repeat position polymorphism found between these two species of mouse. We have mapped 13 new loci to 9 different chromosomes and have found no evidence of clustering among these loci. The advantages of this approach are that no prior knowledge of sequence is required, a single PCR reaction generates many markers which can be mapped simultaneously, and only 50 ng of each backcross DNA (a finite resource) is required. We anticipate that many more markers remain to be characterized in this valuable new source of polymorphism.
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Affiliation(s)
- R D Cox
- Genome Analysis Laboratory, Imperial Cancer Research Fund Laboratories, London, United Kingdom
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375
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Abstract
Important new polymerase chain reaction-based techniques have been developed to assist in genome analysis. Applications range from genetic and physical mapping of DNA to sequence analysis. The polymerase chain reaction has played a significant role in increasing the feasibility of many aspects of genome analysis and positional cloning.
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Affiliation(s)
- D L Nelson
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas 77030
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376
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Wilcox AS, Khan AS, Hopkins JA, Sikela JM. Use of 3' untranslated sequences of human cDNAs for rapid chromosome assignment and conversion to STSs: implications for an expression map of the genome. Nucleic Acids Res 1991; 19:1837-43. [PMID: 2030965 PMCID: PMC328113 DOI: 10.1093/nar/19.8.1837] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A general mapping strategy is described in which the 3'untranslated regions of human cDNAs are used to design PCR primers which will selectively amplify human genomic sequences in a rodent background. When applied to panels of human x hamster somatic cell hybrid DNAs, this approach provides a PCR-based method for rapidly assigning genes to specific chromosomes and chromosomal regions. In addition, it follows from the virtual absence of introns in the 3'untranslated region of vertebrate genes that within this region the cDNA sequences almost always will be identical to those of the genomic DNA and can therefore be used to automatically generate gene-specific sequence-tagged sites (STSs). We have applied this strategy to six human cDNAs and demonstrate that 1) the primers selectively amplify human genomic DNA and 2) the PCR product is of the size predicted from the cDNA. To test this approach further we have utilized it to confirm the known chromosomal location of the retinoblastoma gene. Lastly, we describe how this strategy can readily be applied to unknown human cDNAs, and thereby be integrated into efforts to generate a human STS expression map of the genome. A strategy for production of such a map, using human brain cDNAs as a model, is described.
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Affiliation(s)
- A S Wilcox
- Department of Pharmacology, University of Colorado Health Sciences Center, Denver 80262
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377
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Burmeister M, diSibio G, Cox DR, Myers RM. Identification of polymorphisms by genomic denaturing gradient gel electrophoresis: application to the proximal region of human chromosome 21. Nucleic Acids Res 1991; 19:1475-81. [PMID: 1674130 PMCID: PMC333904 DOI: 10.1093/nar/19.7.1475] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Genomic Denaturing Gradient Gel Electrophoresis (gDGGE) provides an alternative to the standard method of restriction fragment length polymorphism (RFLP) analysis for identifying polymorphic sequence variation in genomic DNA. For gDGGE, genomic DNA is cleaved by restriction enzymes, separated in a polyacrylamide gel containing a gradient of DNA denaturants, and then transferred by electroblotting to nylon membranes. Unlike other applications of DGGE, gDGGE is not limited by the size of the probe and does not require probe sequence information. gDGGE can be used in conjunction with any unique DNA probe. Here we use gDGGE with probes from the proximal region of the long arm of human chromosome 21 to identify polymorphic DNA sequence variation in this segment of the chromosome. Our screening panel consisted of DNA from nine individuals, which was cleaved with five restriction enzymes and submitted to electrophoresis in two denaturing gradient conditions. We detected at least one potential polymorphism for nine of eleven probes that were tested. Two polymorphisms, one at D21S4 and one at D21S90, were characterized in detail. Our study demonstrates that gDGGE is a fast and efficient method for identifying polymorphisms that are useful for genetic linkage analysis.
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Affiliation(s)
- M Burmeister
- Department of Physiology, University of California, San Francisco 94143
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378
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Affiliation(s)
- R D Cox
- Genome Analysis Laboratory, Imperial Cancer Research Fund, London, UK
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379
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Hunter K, Housman D, Hopkins N. Isolation and characterization of irradiation fusion hybrids from mouse chromosome 1 for mapping Rmc-1, a gene encoding a cellular receptor for MCF class murine retroviruses. SOMATIC CELL AND MOLECULAR GENETICS 1991; 17:169-83. [PMID: 2011795 DOI: 10.1007/bf01232974] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An irradiation-reduced somatic cell hybrid mapping panel was constructed of BALB/c mouse Chromosome 1. Nineteen hybrids were selected from a pool of 292 clones to generate a fine structure physical map of the distal 40 cM of the chromosome. The hybrids contain mouse DNA fragments only from Chromosome 1, ranging from approximately 5 cM to approximately 20 cM. Utilizing a viral infectibility assay, a cellular receptor gene, Rmc-1, for the MCF class of murine retroviruses was found to be linked to Lamb2, in the region between the Lamb2 and Bxv-1 loci. In addition, analysis of the hybrid mapping panel resulted in the remapping of three loci, Atpb, Ly-5, and Pmv-24, as compared to the mouse linkage map. Two previously unmapped endogenous proviruses are also putatively assigned positions on the chromosome.
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Affiliation(s)
- K Hunter
- Department of Biology, Massachusetts Institute of Technology, Cambridge 01239
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380
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Sefton L, Arnaud D, Goodfellow PN, Simmler MC, Avner P. Characterization of the central region containing the X-inactivation center and terminal region of the mouse X chromosome using irradiation and fusion gene transfer hybrids. Mamm Genome 1991; 2:21-31. [PMID: 1543901 DOI: 10.1007/bf00570437] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The irradiation and fusion gene transfer (IFGT) procedure provides a means of isolating subchromosomal fragments for use in the mapping of loci and for cloning probes from a particular area of a chromosome. Using this procedure, two large panels of somatic cell hybrids that contain mouse X Chromosome (Chr) fragments have been generated. These hybrid panels were generated by irradiating the monochromosomal mouse-hamster hybrid HYBX, which retains the mouse X Chr, with either 10 K or 50 K rads of X-irradiation followed by fusion with a recipient Chinese hamster cell line. IFGT hybrids retaining mouse material were generated at high frequency. These hybrids were used to orient loci in the X-inactivation center region that had not been resolvable in our interspecies backcross panel and also to map, within the terminal region of the X Chr, repeat elements detected by the probe p15-4. These hybrids not only complement existing interspecies meiotic mapping panels for the detailed analysis of specific regions of particular chromosomes, but also provide a potential source of material for chromosome-specific probe isolation.
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Affiliation(s)
- L Sefton
- Human Molecular Genetics Laboratory, Imperial Cancer Research Fund, London, UK
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381
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Abstract
A method is presented for ordering loci on a chromosome based on data generated from radiation hybrids. All loci are tabulated as being present, absent, or not scored in a series of clones. Correlation coefficients are calculated for all pairs of loci indicating how often they are retained or lost together in the clones. On the assumption that a high positive correlation implies closely linked loci, a distance score, d, equal to one minus the correlation coefficient, is obtained for each locus pair and an order is generated that minimizes the sum of the adjacent distances [the MDMAP method of Falk ("Multipoint Mapping and Linkage Analysis Based upon Affected Pedigree Members: Genetic Analysis Workshop 6," pp. 17-22, A. R. Liss, New York, 1989)]. Two sets of data, with information on 13 and 16 loci mapped to chromosome 21q, have been ordered using this method. The results are in very good agreement with other ordering methods used on the same data and with physical mapping data.
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Affiliation(s)
- C T Falk
- Lindsley F. Kimball Research Institute, New York Blood Center, New York 10021
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382
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Burmeister M, Kim S, Price ER, de Lange T, Tantravahi U, Myers RM, Cox DR. A map of the distal region of the long arm of human chromosome 21 constructed by radiation hybrid mapping and pulsed-field gel electrophoresis. Genomics 1991; 9:19-30. [PMID: 2004760 DOI: 10.1016/0888-7543(91)90216-2] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have used radiation hybrid (RH) mapping and pulsed-field gel electrophoresis (PFGE) to determine the order and positions of 28 DNA markers from the distal region of the long arm of human chromosome 21. The maps generated by these two methods are in good agreement. This study, combined with that of D. R. Cox et al. (1990, Science 250:245-250), results in an RH map that covers the long arm of chromosome 21 (21q). We have used a subtelomeric probe to show that our map includes the telomere and have identified single-copy genes and markers within 200 kbp of the telomere. Comparison of the physical and RH maps with genetic linkage maps shows "hot spots" of meiotic recombination in the distal region, one of which is close to the telomere, in agreement with previous cytogenetic observations of increased recombination frequency near telomeres.
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Affiliation(s)
- M Burmeister
- Department of Physiology, University of California, San Francisco 94143
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383
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Affiliation(s)
- G A Evans
- Molecular Genetics Laboratory, Salk Institute, San Diego, CA 92138
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