DNA probe pooling for rapid delineation of chromosomal breakpoints

Journal of Histochemistry and Cytochemistry

Volumn 57, Issue 6, 2009, Pages 587-597

  Lu, Chun Mei ^a   Kwan, Johnson ^b   Baumgartner, Adolf ^c   Weier, Jingly F ^c   Wang, Mei ^e   Escudero, Tomas ^d   Munné, Santiago ^d   Zitzelsberger, Horst F ^f   Weier, Heinz Ulrich G ^b  

^a NATIONAL CHIN YI UNIVERSITY OF TECHNOLOGY   (Taiwan)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Reprogenetics LLC   (United States)

^e CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^f INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

Bacterial artificial chromosome; Chromosome aberration; Cytogenetics; DNA probes; Fluorescence in situ hybridization; IVF; PGD; Thyroid cancer; Translocation

Indexed keywords

CONTIG;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BACTERIAL GENE; CANCER RESEARCH; CHROMOSOME BREAKAGE; CHROMOSOME MAP; CONTROLLED STUDY; DNA PROBE; FERTILIZATION IN VITRO; HUMAN; HUMAN CELL; KARYOTYPE; MALE; MOLECULAR CLONING; PRENATAL DIAGNOSIS; PRIORITY JOURNAL; RECIPROCAL CHROMOSOME TRANSLOCATION; THYROID CANCER; TURNAROUND TIME; ADULT; CELL LINE; CHROMOSOME 1; CHROMOSOME 13; CHROMOSOME 4; CONTIG MAPPING; FEMALE; GENE TRANSLOCATION; GENETICS; METAPHASE; PREGNANCY; THYROID TUMOR;

BACTERIA (MICROORGANISMS);

CELL LINE; CHROMOSOME BREAKAGE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, HUMAN, PAIR 1; CHROMOSOMES, HUMAN, PAIR 13; CHROMOSOMES, HUMAN, PAIR 4; CLONING, MOLECULAR; CONTIG MAPPING; DNA PROBES; FEMALE; HUMANS; MALE; METAPHASE; PREGNANCY; PREIMPLANTATION DIAGNOSIS; THYROID NEOPLASMS; TRANSLOCATION, GENETIC; YOUNG ADULT;

EID: 67649210241     PISSN: 00221554     EISSN: None     Source Type: Journal    
DOI: 10.1369/jhc.2009.953638     Document Type: Article

References (55)

1. Baldwin EL, May LF, Justice AN, Martin CL, Ledbetter DH (2008) Mechanisms and consequences of small supernumerary marker chromosomes: from Barbara McClintock to modern genetic-counseling issues. Am J Hum Genet 82:398-410
2. Baumgartner A, Weier JF, Weier H-UG (2006) Chromosome-specific DNA repeat probes. J Histochem Cytochem 54:1363-1370
3. Bayani J, Squire JA (2004) Preparation of cytogenetic specimens from tissue samples. In Bonifacino JS, ed. Current Protocols in Cell Biology, Suppl 23. New York, JohnWiley & Sons, Inc., 22.2.1-22.2.15
4. Beimfohr C, Klugbauer S, Demidchik EP, Lengfelder E, Rabes HM (1999) NTRK1 re-arrangement in papillary thyroid carcinomas of children after the Chernobyl reactor accident. Int J Cancer 80:842-847
5. Birnboim HC, Doly J (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA.NucleicAcids Res 7:1513-1523 Braude P, Pickering S, Flinter F, Ogilvie CM (2002) Preimplantation genetic diagnosis. Nat Rev Genet 3:941-953
6. Carreira IM, Mascarenhas A, Matoso E, Couceiro AB, Ramos L, Dufke A, Mazauric M, et al. (2007) Three unusual but cytogenetically similar cases with up to five different cell lines involving structural and numerical abnormalities of chromosome 18. J Histochem Cytochem 55:1123-1128
7. Cassel MJ, Munné S, Fung J, Weier H-UG (1997) Carrier-specific breakpoint-spanning DNA probes for pre-implantation genetic diagnosis [PGD] in interphase cells. Hum Reprod 12:101-109
8. D'Alton ME, Malone FD, Chelmow D, Ward BE, Bianchi DW (1997) Defining the role of fluorescence in situ hybridization on uncultured amniocytes for prenatal diagnosis of aneuploidies. Am J Obstet Gynecol 176:769-776
9. Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE, Smith J, et al. (2003) DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 36:361-374
10. Forus A, Berner JM, Meza-Zepeda LA, Saeter G, Mischke D, Fodstad O, Myklebost O (1998) Molecular characterization of a novel amplicon at 1q21-q22 frequently observed in human sarcomas. Br J Cancer 78:495-503
11. Fung J, Munné S, Duell T, Weier H-UG (1998) Rapid cloning of translocation breakpoints: from blood to YAC in 50 days. J Biochem Mol Biol Biophys 1:181-192
12. Fung J, Munné S, Garcia J, Kim U-J, Weier H-UG (1999) Reciprocal translocations and infertility: molecular cloning of breakpoints in a case of constitutional translocation t(11;22)(q23;q11) and preparation of probes for preimplantation genetic diagnosis (PGD). Reprod Fertil Dev 11:17-23
13. Fung J, Munné S,Weier H-UG (2001) Detection of chromosome translocation products in single interphase cell nuclei. In Darzynkiewicz Z, Chrissman HA, Robinson JP, eds.Methods in Cell Biology, vol. 64, part B, Cytometry. 3rd ed. San Diego, Academic Press, 98-117
14. Fung J, Weier H-UG, Goldberg JD, Pedersen RA (2000) Multilocus genetic analysis of single interphase cells by spectral imaging. Hum Genet 107:615-622
15. Fung J, Weier H-UG, Pedersen RA, Zitzelsberger HF (2002) Spectral imaging analysis ofmetaphase and interphase cells. In Rautenstrauss B, Liehr T, eds. FISH Technology. Heidelberg, Springer Verlag, 363-387
16. Greco A, Roccato E, Pierotti MA (2004) TRK oncogenes in papillary thyroid carcinomas. In Farid NR, ed. Molecular Basis of Thyroid Cancer, Cancer Treatment and Research. Boston, Kluwer Academic Publishers, 207-219
17. Herrmann MA, Hay ID, Bartelt DH, Ritland SR, Dahl RJ, Grant CS, Jenkins RB (1991) Cytogenetic and molecular genetic studies of follicular and papillary thyroid cancers. J Clin Invest 88:1596-1604
18. Iourov IY, Liehr T, Vorsanova SG, Yurov YB (2007) Interphase chromosome-specific multicolor banding (ICS-MCB): a new tool for analysis of interphase chromosomes in their integrity. Biomol Eng 24:415-417
19. Jossart GH, Greulich KM, Siperstein AE, Duh Q, Clark OH, Weier H-UG (1995) Molecular and cytogenetic characterization of a t(1;10;21) translocation in the human papillary thyroid cancer cell line TPC-1 expressing the ret/H4 chimeric transcript. Surgery 118:1018-1023
20. Jossart GH, O'Brien B, Cheng J-F, Tong Q, Jhiang SM, Duh Q, Clark OH, et al. (1996) A novel multicolor hybridization scheme applied to localization of a transcribed sequence (D10S170/H4) and deletion mapping in the thyroid cancer cell line TPC-1. Cytogenet Cell Genet 75:254-257
21. Kalousek DK (2000) Pathogenesis of chromosomal mosaicism and its effect on early human development. Am JMed Genet 91:39-45
22. Kim UJ, Shizuya H, Kang HL, Choi SS, Garrett CL, Smink LJ, Birren BW, et al. (1996) A bacterial artificial chromosome-based frame-work contig map of human chromosome 22q. Proc Natl Acad Sci USA 93:6297-6301
23. Kozma SC, Redmond SMS, Fu XC, Saurer SM, Groner B, Hynes NE (1988) Activation of the receptor kinase domain of the trk oncogene by recombination with two different cellular sequences. EMBO J 7:147-154
24. Lehmann L, Zitzelsberger H, Kellerer AM, Braselmann H, Kulka U, Georgiadou-Schumacher V, Negele T, et al. (1996) Chromosome translocations in thyroid tissues from Belarussian children exposed to radioiodine from the Chernobyl accident, measured by FISH-painting. Int J Radiat Biol 70:513-516
25. Liehr T, Weise A, Heller A, Starke H, Mrasek K, Kuechler A, Weier H-UG, et al. (2002) Multicolor chromosome banding (MCB) with YAC/BAC-based probes and region-specific microdissection DNA libraries. Cytogenet Genome Res 97:43-50
26. Lu CM, Wang M, Greulich-Bode K, Weier JF, Weier HUG (2008) Quantitative DNA fiber mapping. In Liehr T, ed. Springer FISH Lab Manual. Heidelberg, Springer Verlag, 269-291
27. Meza-Zepeda LA, Forus A, Lygren B, Dahlberg AB, Godager LH, South AP, Marenholz I, et al. (2002) Positional cloning identifies a novel cyclophilin as a candidate amplified oncogene in 1q21. Oncogene 21:2261-2269
28. Munné S (2002) Preimplantation genetic diagnosis of numerical and structural chromosome abnormalities. Reprod Biomed Online 4:183-196
29. Munné S, Fung J, Cassel MJ, Márquez C, Weier H-UG (1998) Preimplantation genetic analysis of translocations: case-specific probes for interphase cell analysis. Hum Genet 102:663-674
30. Munné S, Grifo J, Cohen J,Weier H-UG (1994) Mosaicism and aneuploidy in arrested human preimplantation embryos: a multiple probe fluorescence in situ hybridization (FISH) study. Am J Hum Genet 55:150-159
31. Munné S, Sandalinas M, Escudero T, Fung J, Gianaroli L, Cohen J (2000) Outcome of preimplantation genetic diagnosis of translocations. Fertil Steril 73:1209-1218
32. Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ (2001) A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res 11:483-496
33. Pehlivan T, Rubio C, Rodrigo L, Remohi J, Pellicer A, Simon C (2003) Preimplantation genetic diagnosis by fluorescence in situ hybridization: clinical possibilities and pitfalls. J Soc Gynecol Investig 10:315-322
34. Peng HH, Chao AS, Wang TH, Chang YL, Chang SD (2006) Prenatally diagnosed balanced chromosome rearrangements: eight years' experience. J Reprod Med 51:699-703
35. Pierotti MA, Santoro M, Jenkins RB, Sozzi G, Bongarzone I, Grieco M, Monzini N, et al. (1992) Characterization of an inversion on the long arm of chromosome 10 juxtaposing D10S170 and RET and creating the oncogenic sequence RET/TPC. Proc Natl Acad Sci USA 89:1616-1620
36. Plastira K, Maher E, Fantes J, Ramsay J, Angelopoulou R (2006) Using BAC clones to characterize unbalanced chromosome abnormalities in interphase cells. Eur J Med Genet 49:235-246
37. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual. 2nd ed. Cold Spring Harbor, NY, Cold Spring Harbor Laboratory Press
38. Sampson JE, Ouhibi N, Lawce H, Patton PE, Battaglia DE, Burry KA, Olsen SB (2004) The role of preimplantation genetic diagnosis in balanced translocation carriers. Am J Obstet Gynecol 190: 1707-1713
39. Scriven PN, Handyside AH, Ogilvie CM (1998) Chromosome translocation: segregation modes and strategies for preimplantation genetic diagnosis. Prenat Diagn 18:1437-1449
40. Selleri L, Eubanks JH, Giovannini M, Hermanson GG, Romo A, Djabali M, Maurer S, et al. (1992) Detection and characterization of "chimeric" yeast artificial chromosome clones by fluorescent in situ suppression hybridization. Genomics 14:536-541
41. Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794-8797
42. Srb AM, Owen RD, Edgar RS (1965) General Genetics. 2nd ed. San Francisco, W.H. Freeman and Co
43. Stern C, Pertile M, Norris H (1999) Chromosome translocations in couples with in vitro fertilisation implantation failure. Hum Reprod 14:2097-2101
44. Stumm M, Wegner R-D, Bloechle M, Eckel H (2006) Interphase M-FISH applications using commercial probes in prenatal and PGD diagnostics. Cytogenet Genome Res 114:296-301
45. Subrt I (1980) Reciprocal translocation with special reference to reproductive failure. Hum Genet 55:303-307
46. Thorsen J, Zhu B, Frengen E, Osoegawa K, de Jong PJ, Koop BF, Davidson WS, et al. (2005) A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects. BMC Genomics 6:50
47. Tönnies H, Pietrzak J, Bocian E, MacDermont K, Kuechler A, Belitz B, Trautmann U, et al. (2007) New immortalized cell lines of patients with small supernumerary marker chromosome: towards the etablishment of a cell bank. J Histochem Cytochem 55:651-660
48. Verlinsky Y, Cohen J, Munné S, Gianaroli L, Simpson JL, Ferraretti AP, Kuliev A (2004) Over a decade of experience with preimplantation genetic diagnosis: a multicenter report. Fertil Steril 82:292-294
49. Waye JS, Durfy SJ, Pinkel D, Kenwrick S, Patterson M, Davies KE, Willard HF (1987) Chromosome-specific alpha satellite DNA from human chromosome 1: hierarchical structure and genomic organization of a polymorphic domain spanning several hundred kilobase pairs of centromeric DNA. Genomics 1:43-51
50. Weier HU, Rhein AP, Shadravan F, Collins C, Polikoff D (1995) Rapid physical mapping of the human trk protooncogene (NTRK1) to human chromosome 1q21-q22 by P1 clone selection, fluorescence in situ hybridization (FISH), and computer-assisted microscopy. Genomics 26:390-393
51. Weier HUG, Munné S, Fung J (1999) Patient-specific probes for preimplantation genetic diagnosis (PGD) of structural and numerical aberrations in interphase cells. J Assist Reprod Genet 16:182-189
52. Weier HUG, Tuton TB, Chu LW, Ito Y, Lu C-M, Baumgartner A, Zitzelsberger HF, et al. (2006) Molecular cytogenetic characterization of a human thyroid cancer cell line. Cytogenet Genome Res 114:284-291
53. Weier JF, Weier H-UG, Jung CJ, Gormley M, Yan Zhou Y, Chu LW, Genbacev O, et al. (2005) Human cytotrophoblasts acquire aneuploidies as they differentiate to an invasive phenotype. Dev Biol 279:420-432
54. Zitzelsberger H, Lehmann L, Hieber L, Weier H-UG, Janish C, Fung J, Negele T, et al. (1999) Cytogenetic changes in radiation-induced tumors of the thyroid. Cancer Res 59:135-140
55. Zitzelsberger HF, O'Brien B, Weier H-UG (2002) Multicolor FISH techniques for the detection of inter- and intrachromosomal rearrangements. In Rautenstrauss B, Liehr T, eds. FISH Technology. Heidelberg, Springer Verlag, 408-424