Comparative genomic hybridization (CGH)

Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid

Patent

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

435 912, 536 221, 536 231, 536 243, 536 2431, 536 2432, 536 2433, C12Q 168, C12P 1934, C07H 2102, C07H 2104

Patent

active

056655495

ABSTRACT:
Disclosed are new methods comprising the use of in situ hybridization to detect abnormal nucleic acid sequence copy numbers in one or more genomes wherein repetitive sequences that bind to multiple loci in a reference chromosome spread are either substantially removed and/or their hybridization signals suppressed. The invention termed Comparative Genomic Hybridization (CGH) provides for methods of determining the relative number of copies of nucleic acid sequences in one or more subject genomes or portions thereof (for example, a tumor cell) as a function of the location of those sequences in a reference genome (for example, a normal human genome). The intensity(ies) of the signals from each labeled subject nucleic acid and/or the differences in the ratios between different signals from the labeled subject nucleic acid sequences are compared to determine the relative copy numbers of the nucleic acid sequences in the one or more subject genomes as a function of position along the reference chromosome spread. Amplifications, duplications and/or deletions in the subject genome(s) can be detected. Also provided is a method of determining the absolute copy numbers of substantially all RNA or DNA sequences in subject cell(s) or cell population(s).

REFERENCES:
patent: 4358535 (1982-11-01), Falkow et al.
patent: 4647529 (1987-03-01), Rodland et
patent: 4681840 (1987-07-01), Stephenson et al.
patent: 4683195 (1987-07-01), Mullis et al.
patent: 4683202 (1987-07-01), Mullis
patent: 4707440 (1987-11-01), Stavrianopoulos
patent: 4710465 (1987-12-01), Weissman et al.
patent: 4711955 (1987-12-01), Ward et al.
patent: 4721669 (1988-01-01), Barton
patent: 4725536 (1988-02-01), Fritsch et al.
patent: 4770992 (1988-09-01), Van den Engh et al.
patent: 4772691 (1988-09-01), Herman
patent: 4888278 (1989-12-01), Singer et al.
patent: 5085983 (1992-02-01), Scanlon
patent: 5427932 (1995-06-01), Gray et al.
patent: 5447841 (1995-09-01), Gray et al.
patent: 5472842 (1995-12-01), Stokke et al.
Angerer et al, "In Situ Hybridization to Cellular RNAs" Genetic Engineering: Principles and Methods, Setlow and Hollaender, Eds., vol. 7, pp. 43-65, Plenum Press, New York (1985).
Bayer et al, "The Use of the Avidin-Biotin Complex as a Tool in Molecular Biology," Methods of Biochemical Analysis, Vol. 26, pp. 1-45 (1980).
Brigati et al, "Detection of Viral Genomes in Cultured Cells and Paraffin-Embedded Tissue Sections Using Biotin-Labeled Hybridization Probes," Virology, Vol. 126, pp. 32-50 (1983).
Broker et al, "Electron Microscopic Visualization of tRNA Genes with Ferritin-Avidin: Biotin Labels," Nucleic Acids Research, Vol. 5, No. 2, pp 363-384 (1978).
Connolly et al, "Chemical Synthesis of Oligonucleotides Containing A Free Sulphydryl Group and Subsequent Attachment of Thiol Specific Probes," Nucleic Acids Research, Vol. 13, No. 12, pp. 4485-4502 (1985).
Fuscoe et al, "Construction of Fifteen Human Chromosome-Specific DNA Libraries from Flow-Purified Chromosomes," Cytogenetic Cell Genetics, Vol. 43, pp. 79-86 (1986).
Gall et al, "Nucleic Acid Hybridization in Biological Preparations," Methods in Enzymology, Vol. 21, pp. 470-480 (1981).
Henderson, "Cytological Hybridization to Mammalian Chromosomes," International Review of Cytology, Vol. 76, pp. 1-46 (1982).
Kuhlmann, Immuno Enzyme Techniques in Cytochemistry, Verlag Chemie, Weinheim, Basel (1984) (table of contents only).
Lawn et al, "The Isolation and Characterization of Linked .delta.-and .beta.-Globin Genes from a Cloned Library of Human DNA," Cell, Vol. 14, pp. 1157-1174 (1978).
Maniatis et al, "In Vitro Packaging of Bacteriophage .lambda. DNA," Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, pp. 256-307 (1982).
Marmur, "A Procedure for the Isolation of Deoxyribonucleic Acid from Micro-organisms," J. Mol. Biol., Vol. 3, pp. 208-218 (1961).
Richardson et al, "Biotin and Fluorescent Labeling of RNA Using T4 RNA Ligase," Nucleic Acids Research, Vol. 11, No. 18, pp. 6167-6184 (1983).
Smith et al, "The Synthesis of Oligonucleotides Containing an Aliphatic Amino Group at the 5' Terminus: Synthesis of Fluorescent DNA Primers For Use in DNA Sequence Analysis," Nucleic Acids Research, Vol. 13, No. 7, pp. 2399-2412 (1985).
Tchen et al, "Chemically Modified Nucleic Acids as Immunodetectable Probes in Hybridization Experiments," PNAS, Vol. 81, pp. 3466-3470 (1984).
Bufton et al, "A Highly Polymorphic Locus On Chromosome 16q Revealed By A Probe From A Chromosome-Specific Cosmid Library," Human Genetics, Vol. 74, 1986, pp. 425-431.
Bufton et al, "Four Restriction Fragment Length Polymorphisms Revealed By Probes From A Single Cosmid Map To Human Chromosome 19," Am J Hum Genet, Vol. 38, 1986 pp. 447-460.
Burk et al, "Organization and Chromosomal Specificity of Autosomal Homologs of Human Y Chromosome Repeated DNA," Chrmosoma, Vol. 92, 1985, pp. 225-233.
Buroker et al, "Four Restriction Fragment Length Polymorhisms Revealed By Probes From A Single Cosmid Map to Human Chromosome 12q," Human Genetics, Vol. 72, 1986, pp. 86-94.
Cote et al, "Quantitation of in situ Hybridization of Ribosomal Ribonucleic Acids to Human Diploid Cells," Chromosoma, Vol. 80, 1980, pp. 349-367.
Cremer et al, "Preparative Dual-Beam Sorting of the Human Y Chromosome and In Situ Hybridization of Cloned DNA Probes," Cytometry, Vol. 5, 1984, pp. 572-579.
Davies, "The Application of DNA Recombinant Technology to the Analysis of the Human Genome and Genetic Disease," Human Genetics, Vol. 58, 1981, pp. 351-357.
Dennis et al, "Cytogenetics of the Parthenogenetic Grasshopper Warramaba virgo and Its Bisexual Relatives," Chromosoma, Vol. 82, 1981, pp. 453-469.
Gerhard et al, "Localization Of a Unique Gene By Direct Hybridization in situ," PNAS, Vol. 78, 1981, pp. 3755-3759.
Haase et al, "Detection of Two Viral Genomes in Single Cells By Double-Label Hybridization in Situ and Color Microradioautography," Science, Vol. 227, 1985, pp. 189-192.
Holden et al, "Amplified Sequences from Chromosome 15, Including Centromeres, Nucleolar Organizer Regions, and Centromeric Heterochromatin, in Homogeneously Staining Regions in the Human Melanoma Cel Line MeWo," Cancer Genet. & Cytogenet., Vol. 14, 1985, pp. 131-146.
Houldsworth et al, "Comparative Genomic Hybridization: An Overview," Am. J. Pathology, Vol. 145, No. 6, 1994, pp. 1253-1260.
Kallioniemi et al, "Optimizing Comparative Genomic Hybridization for Analysis of DNA Sequence Copy Number Changes in Solid Tumors," Genes Chromosomes & Cancer, Vol. 10, 1994, pp. 231-243.
Krumlauf et al, "Construction and Characterization of Genomic Libraries From Specific Human Chromosomes," PNAS, Vol. 79, 1982, pp. 2971-2975.
Kunkel et al, "Organization and Heterogeneity of Sequences Within A Repeating Unit Of Human Y Chromosome Deoxyribonucleic Acid," Biochem., Vol. 18, 1979, pp. 3343-3353.
Landegent et al, "Fine Mapping Of The Huntington Disease Linked D4S10 Locus By Non-Radioactive In Situ Hybridization," Human Genetics, Vol. 73, 1986, pp. 354-357.
Lichter et al, "Fluorescence in situ Hybridization with Alu and L1 Polymerase Chain Reaction Probes For Rapid Characterization Of Human Chromosomes In Hybrid Cell Lines," PNAS, USA, Vol. 87, 1990, pp. 6634-6638.
Litt et al, "A Highly Polymorphic Locus In Human DNA Revealed By Probes From Cosmid 1-5 Maps To Chromosomes 2q35.fwdarw.37," Am J Hum Genet, Vol. 38, 1986, pp. 288-296.
Litt et al, "A Polymorphic Locus On The Long Arm Of Chromosome 20 Defined By Two Probes From A Single Cosmid," Human Genetics, Vol. 73, 1986, pp. 340-345.
Malcolm et al, "Chromosomal Localization Of A Single Copy Gene By in situ Hybridization -Human .beta. Globin Genes On The Short Arm Of Chromosome 11," Ann. Hum. Genet., Vol. 45, 1981, pp. 134-141.
Nelson et al, "Genomic Mismatch Scanning: A New Approach To Genetic Linkage Mapping," Nature Genetics, Vol. 4, 1993, pp. 11-18.
Pierce et al, "Analysis Of A Dispersed Repetitive DNA Sequence In Isogenic Lines of Drosophila," Chromosoma, Vol. 82, 1981, pp. 471-492.
Rabin, "Mapping Minimally Reiterated Genes On Diploid Chromosomes By In Situ Hybridization," thesis, Dept. of Biochemistry, Univ. Ill.,

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

Comparative genomic hybridization (CGH) does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Comparative genomic hybridization (CGH), we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Comparative genomic hybridization (CGH) will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-68779

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.