PCR based targeted genomic and cDNA differential display

Genetic Analysis - Biomolecular Engineering

Volumn 15, Issue 2, 1999, Pages 51-63

  Broude, Natalia E ^a   Storm, Niels ^a   Malpel, Sarah ^a,b   Graber, Joel H ^a   Lukyanov, Sergey ^c   Sverdlov, Eugene ^c   Smith, Cassandra L ^a  

^a Center for Advanced Biotechnology   (United States)

^b UNIVERSITÉ DE STRASBOURG   (France)

^c SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

Author keywords

CDNA differential display; Genomic; PCR based

Indexed keywords

DNA FRAGMENT; MICROSATELLITE DNA; NUCLEIC ACID;

ARTICLE; DNA DETERMINATION; DNA SEQUENCE; GENE AMPLIFICATION; GENOME; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

ALLELES; DNA, COMPLEMENTARY; HUMANS; HUNTINGTON DISEASE; POLYMERASE CHAIN REACTION; TRINUCLEOTIDE REPEATS;

EID: 0032975687     PISSN: 10503862     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1050-3862(98)00038-2     Document Type: Article

References (44)

1. Hill A.V.S., Jeffreys A. Use of minisatellite DNA probes for determination of twin zygosity at birth. Lancet. 2:1985;1394-1395.
2. Jeffreys A., Wilson V., Thein S.L. Individual-specific 'fingerprints' of human DNA. Nature. 316:1985;76-79.
3. Welsh J., McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 18:1990;7213-7218.
4. Williams J.G., Kubelik A.R., Livak K.J., Rafalski J.A., Tingey S.V. DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:1990;6531-6535.
5. Caetano-Anolles G., Bassam B.J., Gresshoff P.M. DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Biotechnology. 6:1991;553-557.
6. Prabhu R.R., Gresshoff P.M. Inheritance of polymorphic markers generated by DNA amplification fingerprinting and their use as genetic markers in soybean. Plant Mol Biol. 26:1994;105-116.
7. Vos P., Hogers R., Bleeker M., Reijans M., van de Lee T., Hornes M., Frijters A., Pot J., Peleman J., Kuiper M., Zabeau M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23:1995;4407-4414.
8. Nelson D.L. Interspersed repetitive sequence polymerase chain reaction (IRS PCR) for generation of human DNA fragments from complex sources. Methods: Companion Meth Enzymol. 2:1991;60-74.
9. Nelson D.L., Ballabio A., Victoria M.F., Pieretti M., Bies R.D., Gibbs R.A., Maley J.A., Chinault A.C., Webster T.D., Caskey C.T. Alu-primed polymerase chain reaction for regional assignment of 110 yeast artificial chromosome clones from the human X chromosome: identification of clones associated with a disease locus. Proc Natl Acad Sci USA. 88:1991;6157-6161.
10. Wooster R., Cleton-Jansen A.-M., Collins N., Mangion J., Cornelis R.S., Cooper C.S., Gusterson B.A., Ponder B.A.J., von Deimling A., Wiestler O.D., Corneliss C.J., Devilee P., Stratton M.R. Instability of short tandem repeats (microsatellites) in human cancers. Nature Genet. 6:1994;152-156.
11. Huddart R.A., Wooster R., Horwich A., Cooper C.S. Microsatellite instability in human testicular germ cell tumors. Br J Cancer. 72:1995;642-645.
12. Edwards A., Civitello A., Hammond H.A., Caskey C.T. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet. 49:1991;746-756.
13. Ostrander E.A., Jong P.M., Rine J., Duyk G. Construction of small-insert genomic DNA libraries highly enriched in microsatellite repeat sequences. Proc Natl Acad Sci USA. 89:1992;3419-3423.
14. Ito T., Kito K., Adati N., Mitsui Y., Hagiwara H., Sakaki Y. Fluorescent differential display: arbitrarily primed RT-PCR fingerprinting on an automated sequencer. FEBS Lett. 351:1994;231-236.
15. Kandpal R.P., Kandpal G., Weissman S.M. Construction of libraries enriched for sequence repeats and jumping clones and hybridization selection for region-specific markers. Proc Natl Acad Sci USA. 91:1994;88-92.
16. Brown J., Hardwick L.J., Wright A.F. A simple method for rapid isolation of microsatellites from yeast artificial chromosomes. Mol Cell Probes. 9:1995;53-58.
17. Feener C.A., Boyce F.M., Kunkel L.M. Rapid detection of CA polymorphism in cloned DNA: application to the 5′ region of the dystrophin gene. Am J Hum Genet. 48:1991;621-627.
18. Ito T., Smith C.L., Cantor C.R. Sequence-specific DNA purification by triplex affinity capture. Proc Natl Acad Sci USA. 89:1992;495-498.
19. Lench N.J., Norris A., Bailey A., Booth A., Markham A.F. Vectorette PCR isolation of microsatellite repeat sequences using anchored dinucleotide repeat primers. Nucleic Acids Res. 24:1996;2190-2191.
20. Travis GH, Milner RJ, Sutcliff JG. Preparation and use of subtractive cDNA hybridization probes for cDNA cloning. In: Boulton AA, Baker GB, Campagnoni AT, editors, Neuromethods, vol. 16, Molecular neurobiological techniques Humana, Clifton, NJ, 1989;49-78.
21. Lisitsyn N., Lisitsyn N., Wigler M. Cloning the differences between two complex genomes. Science. 259:1993;946-951.
22. Diatchenko L., Lau Y.F., Campbell A.P., Chenchik A., Moqadam F., Huang B., Lukyanov S., Lukyanov K., Gurskaya N., Sverdlov E.D., Siebert P.D. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA. 93:1996;6025-6030.
23. Liang P., Pardee A.B. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science. 257:1992;967-971.
24. Broude N.E., Chandra A., Smith C.L. Differential display of genomic subsets containing specific interspersed repeats. Proc Natl Acad Sci USA. 94:1997;4548-4553.
25. Oliveira R., Broude N.E., Macedo A.M., Cantor C.R., Smith C.L., Pena S.D.J. Probing the genetic population structure of Trypanosoma cruzi with polymorphic microsatellites. Proc Natl Acad Sci USA. 95:1998;3776-3780.
26. Lavrentieva I, Broude N, Lebedev Y, Lukyanov SA, Gottesman I, Smith CL, Sverdlov E. High polymorphism level of genomic sequences flanking insertion sites of human endogenous retoviral LTRs. FEBS Lett. 1999; in press.
27. Nguyen Z, Broude NE, Smith CL. Targeted genomic differential display reveals differences in genomes of monozygotic twins. 1999 (in preparation).
28. Siebert P.D.A., Chenchik A., Kellogg D.E., Lukyanov K.A., Lukyanov S.A. An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res. 23:1995;1087-1088.
29. Torrey E.F., Bowler A.E., Taylor E.H., Gottesman I.I. Schizophrenia and Manic-Depressive Disorder. 1994;1-2 Harper Collins, New York. Appendix.
30. Wexler N.S., Young A.B., Tanzi R.E., Travers H., Starosta-Rubinstein S., Penney J.B., Snodgrass S.R., Shoulson I., Gomez F., Ramos Arroyo M.A., Penchazadeh G.D., Moreno H., Gibbons K., Faryniarz A., Hobbs W., Anderson M.A., Bonilla E., Conneally P.M., Gusella J.F. Homozygotes for Huntington's disease. Nature. 326:1987;194-197.
31. Armour J.A.L., Neuman R., Gobert S., Jeffreys A.J. Isolation of human simple repeat loci by hybridization selection. Hum Mol Genet. 3:1994;599-605.
32. Chiba H., Muramatsu M., Nomoto A., Kato H. Two human homologues of Saccharomyces cerevisiae SWI2/SNF2 and Drosophila brahma are transcriptional coactivators cooperating with the estrogen receptor and the retinoic acid receptor. Nucleic Acids Res. 22:1994;1815-1820.
33. Donohue P.J., Hsu D.K.W., Winkles J.A. Differential display using random hexamer-primed cDNA, motif primers and agarose gel electrophoresis. Meth Mol Biol. 85:1997;25-35.
34. Stallings R.L. Distribution of trinucleotide microsatellites in different categories of mammalian genomic sequence: implications for human genetic diseases. Genomics. 21:1994;116-121.
35. n dynamic mutations. Genomics. 32:1996;75-85.
36. Neri C., Albanese V., Lebre A.-S., Holbert S., Saada C., Bougueleret L., Meier-Ewert S., Le Gall I., Millasseau P., Bui H., Giudicelli C., Massart C., Guillou S., Gervy P., Poullier E., Rigaut P., Weissenbach J., Lennon G., Chumakov I., Dausset J., Lehrach H., Cohen D., Cann H.M. Survey of CAG/CTG repeats in human cDNAs representing new genes: candidates for inherited neurological disorders. Hum Mol Genet. 5:1996;1001-1009.
37. Wells R.D. Molecular basis of genetic instability of triplet repeats. J Biol Chem. 271:1996;2875-2878.
38. Demers D.B., Curry E.T., Egholm M., Sozer A.C. Enchanced PCR amplification of VNTR locus D1S80 using peptide nucleic acid (PNA). Nucleic Acids Res. 23:1995;3050-3055.
39. Haddad L.A., Mingroni-Netto R.C., Vianna-Morgante A.M., Pena S.D.J. A PCR-based test suitable for screening for fragile X syndrome among mentally retarded males. Hum Genet. 97:1996;808-812.
40. Storm N, Malpel S, Broude NE, Smith CL. Targeted genomic and cDNA differential display II: Factors influencing the robustness of the method. 1999 (in preparation).
41. Debouck C. Differential display or dismay? Curr Opin Biotechnol. 6:1995;597-599.
42. O'Donnell-Maloney M.J., Smith C.L., Cantor C.R. The development and microfabricated arrays for DNA sequencing and analysis. TIBTECH. 14:1996;401-407.
43. Fu D.J., Broude N.E., Köster H., Smith C.L., Cantor C.R. Efficient preparation of short DNA sequence ladders potentially suitable for MALDI-TOF DNA sequencing. Genet Anal. 12:1996;137-142.
44. Braun A., Little D.P., Reuter D., Müller-Mysok B., Köster H. Improved analysis of microsatellites using mass spectrometry. Genomics. 46:1997;18-23.