Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
1997-08-08
2001-04-03
Eyler, Yvonne (Department: 1642)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S007230, C435S810000, C435S975000, C436S064000, C436S813000, C536S024310
Reexamination Certificate
active
06210878
ABSTRACT:
FIELD OF THE INVENTION
This invention pertains to the field of cancer genetics. More particularly this invention pertains to the identification of regions of copy number increase or decrease associated with cancers and other disease.
BACKGROUND OF THE INVENTION
Chromosome abnormalities are often associated with genetic disorders, degenerative diseases, and cancer. In particular, the deletion or multiplication of copies of whole chromosomes or chromosomal segments, and higher level amplifications of specific regions of the genome are common occurrences in cancer. See, for example Smith, et al.,
Breast Cancer Res. Treat.,
18: Suppl. 1: 5-14 (1991, van de Vijer & Nusse,
Biochim. Biophys. Acta.
1072: 33-50 (1991), Sato, et al.,
Cancer. Res.,
50: 7184-7189 (1990). In fact, the amplification and deletion of DNA sequences containing proto-oncogenes and tumor-suppressor genes, respectively, are frequently characteristic of tumorigenesis. Dutrillaux, et al.,
Cancer Genet. Cytogenet.,
49: 203-217 (1990). Clearly, the identification of such regions and the cloning of the genes involved is crucial both to the study of tumorigenesis and to the development of cancer diagnostics.
The detection of chromosomal regions of increased or decreased copy number has traditionally been done by cytogenetics. Because of the complex packing of DNA into the chromosomes, resolution of cytogenetic techniques has been limited to regions larger than about 10 Mb; approximately the width of a band in Giemsa-stained chromosomes. In complex karyotypes with multiple translocations and other genetic changes, traditional cytogenetic analysis is of little utility because karyotype information is lacking or cannot be interpreted. Teyssier, J. R.,
Cancer Genet. Cytogenet.,
37: 103 (1989). Furthermore, conventional cytogenetic banding analysis is time consuming, labor intensive, and frequently difficult or impossible.
More recently, cloned probes have been used to assess the amount of a given DNA sequence in a chromosome by Southern blotting. This method is effective even if the genome is heavily rearranged so as to eliminate useful karyotype information. However, Southern blotting only gives a rough estimate of the copy number of a DNA sequence, and does not give any information about the localization of that sequence within the chromosome.
Comparative genomic hybridization (CGH) is a more recent approach to identify the presence and localization of amplified/deleted sequences. See Kallioniemi, et al.,
Science,
258: 818 (1992). CGH, like Southern blotting, reveals amplifications and deletions irrespective of genome rearrangement. Additionally, CGH provides a more quantitative estimate of copy number than Southern blotting, and moreover also provides information of the localization of the amplified or deleted sequence in the normal chromosome.
SUMMARY OF THE INVENTION
The present invention relates to the identification of new regions of copy number change on chromosome 20. Nucleic acids specific to these regions are useful as probes or as probe targets for monitoring the relative copy number of corresponding sequences from a biological sample such as a tumor cell.
Thus, in one embodiment, this invention provides methods of detecting a chromosome alteration (e.g., copy number increase or decrease) at about the following FLpter positions: 0.603, 0.646, and 0.675 (all decrease), 0.694 and 0.722 (both increase), and 0.867 (increase). The methods involve contacting a nucleic acid sample from a patient with nucleic acid probes each of which binds selectively to a target regions noted above under conditions in which the probe forms a stable hybridization complex with the target sequence; and detecting the hybridization complex. The step of detecting the hybridization complex can involve determining the copy number of the target sequence. The probe preferably comprises a nucleic acid that specifically hybridizes under stringent conditions to a nucleic acid selected from the probes disclosed here. The probe or the sample nucleic acid can be labeled, and is more typically fluorescently labeled. If the sample is labeled, the probes can be attached to a solid surface as an array.
The probes disclosed here can be used in kits for the detection of a chromosomal abnormality at the positions on human chromosome 20 noted above. The kits include a compartment which contains a labeled nucleic acid probe which binds selectively to a target polynucleotide sequence on human chromosome 20. The probe preferably includes at least one nucleic acid that specifically hybridizes under stringent conditions to a nucleic acid selected from the nucleic acids disclosed here. The kit may further include a reference probe specific to a sequence in the centromere of chromosome to 20 or other reference locations.
Definitions A “nucleic acid sample” as used herein refers to a sample comprising DNA in a form suitable for hybridization to a probes of the invention. The nucleic acid may be total genomic DNA, total mRNA, genomic DNA or mRNA from particular chromosomes, or selected sequences (e.g. particular promoters, genes, amplification or restriction fragments, cDNA, etc.) within particular amplicons or deletions disclosed here. The nucleic acid sample may be extracted from particular cells or tissues. The tissue sample from which the nucleic acid sample is prepared is typically taken from a patient suspected of having the disease associated with the amplification or deletion being detected. In some cases, the nucleic acids may be amplified using standard techniques such as PCR, prior to the hybridization. The sample may be isolated nucleic acids immobilized on a solid surface (e.g., nitrocellulose) for use in Southern or dot blot hybridizations and the like. The sample may also be prepared such that individual nucleic acids remain substantially intact and comprises interphase nuclei prepared according to standard techniques. A “nucleic acid sample” as used herein may also refer to a substantially intact condensed chromosome (e.g. a metaphase chromosome). Such a condensed chromosome is suitable for use as a hybridization target in in situ hybridization techniques (e.g. FISH). The particular usage of the term “nucleic acid sample” (whether as extracted nucleic acid or intact metaphase chromosome) will be readily apparent to one of skill in the art from the context in which the term is used. For instance, the nucleic acid sample can be a tissue or cell sample prepared for standard in situ hybridization methods described below. The sample is prepared such that individual chromosomes remain substantially intact and typically comprises metaphase spreads or interphase nuclei prepared according to standard techniques.
A “chromosome sample” as used herein refers to a tissue or cell sample prepared for standard in situ hybridization methods described below. The sample is prepared such that individual chromosomes remain substantially intact and typically comprises metaphase spreads or interphase nuclei prepared according to standard techniques.
As used herein, a “nucleic acid array” is a plurality of target elements, each comprising one or more target nucleic acid molecules immobilized on a solid surface to which probe nucleic acids are hybridized. Target nucleic acids of some target elements typically are from regions of copy number change from chromosome 20. The target nucleic acids of a target element may, for example, contain sequence from specific genes or clones disclosed here. Other target elements will contain, for instance, reference sequences. Target elements of various dimensions can be used in the arrays of the invention. Generally, smaller, target elements are preferred. Typically, a target element will be less than about 1 cm in diameter. Generally element sizes are from 1 &mgr;m to about 3 mm, preferably between about 5 &mgr;m and about 1 mm.
The target elements of the arrays may be arranged on the solid surface at different densities. The target element densities will depend upon a number of factors, such as the nature of the label, the sol
Albertson Donna G.
Gray Joe W.
Pinkel Daniel
Eyler Yvonne
The Regents of the University of California
Townsend and Townsend / and Crew LLP
LandOfFree
Array-based detection of genetic alterations associated with... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Array-based detection of genetic alterations associated with..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Array-based detection of genetic alterations associated with... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-2493669