Image analysis – Applications – Biomedical applications
Reexamination Certificate
2000-12-14
2004-11-30
Mehta, Bhavesh M. (Department: 2625)
Image analysis
Applications
Biomedical applications
30, C435S006120, C707S793000
Reexamination Certificate
active
06826296
ABSTRACT:
BACKGROUND OF THE INVENTION
The present invention relates to the collection and storage of information pertaining to chips for processing samples.
Devices and computer systems for forming and using arrays of materials on a substrate are known. For example, PCT application WO92/10588, incorporated herein by reference for all purposes, describes techniques for sequencing or sequence checking nucleic acids and other materials. Arrays for performing these operations may be formed in arrays according to the methods of, for example, the pioneering techniques disclosed in U.S. Pat. No. 5,143,854 and U.S. Pat. No. 5,571,639, both incorporated herein by reference for all purposes.
According to one aspect of the techniques described therein, an array of nucleic acid probes is fabricated at known locations on a chip or substrate. A fluorescently labeled nucleic acid is then brought into contact with the chip and a scanner generates an image file indicating the locations where the labeled nucleic acids bound to the chip. Based upon the identities of the probes at these locations, it becomes possible to extract information such as the monomer sequence of DNA or RNA. Such systems have been used to form, for example, arrays of DNA that may be used to study and detect mutations relevant to cystic fibrosis, the P53 gene (relevant to certain cancers), HIV, and other genetic characteristics.
Computer-aided techniques for monitoring gene expression using such arrays of probes have also been developed as disclosed in U.S. patent application Ser. No. 08/828,952 and PCT publication No. WO 97/10365, the contents of which are herein incorporated by reference. Many disease states are characterized by differences in the expression levels of various genes either through changes in the copy number of the genetic DNA or through changes in levels of transcription (e.g., through control of initiation, provision of RNA precursors, RNA processing, etc.) of particular genes. For example, losses and gains of genetic material play an important role in malignant transformation and progression. Furthermore, changes in the expression (transcription) levels of particular genes (e.g., oncogenes or tumor suppressors), serve as signposts for the presence and progression of various cancers.
As can be seen, the probe array chips are designed to answer questions about genomic items, herein defined to include genes, expressed sequence tags (EST's), gene clusters, and EST clusters. Associated with information about genomic items is genetic sequence information concerning the base sequences of genomic items. Probes are designed and selected for inclusion on a chip based on: 1) the identity of the genomic items to be investigated by the chip, 2) the sequence information associated with those genomic information, and 3) the type of information sought, e.g., expression analysis, polymorphism analysis, etc. The interrelationships, however, among probes, genomic items, and sequence information are, however, extremely complex, greatly complicating the tasks of designing chips, effectively exploiting chips that have already been designed, and efficiently interpreting the information generated by application of the chips.
Moreover, it is contemplated that the operations of chip design, construction, and application will occur on a very large scale. The quantity of information related to chip design to store and correlate is vast. What is needed is a system and method suitable for storing and organizing large quantities of information used in conjunction with the design of probe array chips.
SUMMARY OF THE INVENTION
The present invention provides systems and method for organizing information relating to the design of polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of chips having complex designs.
According to one aspect of the present invention, a computer-readable storage medium is provided. A relational database is stored on this medium. The relational database includes: a probe table including a plurality of probe records, each of the probe records specifying a polymer probe for use in one or more polymer probe arrays, a sequence item table including a plurality of sequence item records, each of the sequence item records specifying a nucleotide sequence to be investigated in the one or more polymer probe arrays, wherein there is a many-to-many relationship between the probe records and the sequence item records.
A further understanding of the nature and advantages of the inventions herein may be realized by reference to the remaining portions of the specification and the attached drawings.
REFERENCES:
patent: 4683202 (1987-07-01), Mullis
patent: 5143854 (1992-09-01), Pirrung et al.
patent: 5206137 (1993-04-01), Ip et al.
patent: 5445934 (1995-08-01), Fodor et al.
patent: 5492806 (1996-02-01), Drmanac et al.
patent: 5525464 (1996-06-01), Drmanac et al.
patent: 5571639 (1996-11-01), Hubbell et al.
patent: 5593839 (1997-01-01), Hubbell et al.
patent: 5667972 (1997-09-01), Drmanac et al.
patent: 5695940 (1997-12-01), Drmanac et al.
patent: 5700637 (1997-12-01), Southern
patent: 5707806 (1998-01-01), Shuber
patent: 5777888 (1998-07-01), Rine et al.
patent: 5800992 (1998-09-01), Fodor et al.
patent: 5819282 (1998-10-01), Hooper et al.
patent: 5843669 (1998-12-01), Kaiser et al.
patent: 5843767 (1998-12-01), Beattie
patent: 5856101 (1999-01-01), Hubbell et al.
patent: 5871697 (1999-02-01), Rothberg et al.
patent: 5871928 (1999-02-01), Fodor et al.
patent: 5925525 (1999-07-01), Fodor et al.
patent: 5961923 (1999-10-01), Nova et al.
patent: 5974164 (1999-10-01), Chee
patent: 5991766 (1999-11-01), Sadiq et al.
patent: 6032151 (2000-02-01), Arnold et al.
patent: 6040138 (2000-03-01), Lockhart et al.
patent: 6140054 (2000-10-01), Wittwer et al.
patent: 6185561 (2001-02-01), Balaban et al.
patent: 6188783 (2001-02-01), Balaban et al.
patent: WO 0 307 476 (1989-03-01), None
patent: WO 0 235 726 (1989-05-01), None
patent: WO 90/11548 (1989-11-01), None
patent: WO 0 392 546 (1990-10-01), None
patent: WO 90/15070 (1990-12-01), None
patent: WO 92/10588 (1992-06-01), None
patent: WO 93/22456 (1993-11-01), None
patent: WO 95/11995 (1995-05-01), None
patent: WO 0 717 113 (1996-07-01), None
patent: WO 96/23078 (1996-08-01), None
patent: WO 97/10365 (1997-03-01), None
patent: WO 97/17317 (1997-05-01), None
patent: WO 97/19410 (1997-05-01), None
patent: WO 97/27317 (1997-07-01), None
patent: WO 97/29212 (1997-08-01), None
Mattila et al., “Fidelity of DNA Synthesis by theThermococcus LitoralisDNS Polymerase—An Extremely Heat Stable Enzyme with Proofreading Activity”,Nucleic Acids Res., vol. 19, No. 18, 1991, pp. 4967-4973.
Matsubara et al., “Identification of New Genes by Systematic Analysis of cDNAs and Database Construction”,Curr. Opin. Biotechnol., vol. 4, No. 6, 1993, pp. 672-677.
Orita et al., “Detection of polymorphisms of human DNA by gel electrophoresis was wingle-strand conformation polymorphisms”,Proc. Natl. Acad. Sci. USA, vol. 86, Apr. 1989, pp. 2766-2770.
Okubo et al., “Large Scale cDNA Sequencing for Analysis of Quantitative and Qualitative Aspects of Gene Expresssion”,Nature Genetics, vol. 2, 1993, pp. 173-179.
PR Newswire, “Gene Logic to Use Affymetrix GeneChip Arrays to Build Gene Expession Database Products”, Jan. 11, 1999.
Saiki et al., “Analysis of Enzymatically Amplified Beta-Globin and HLA-DQ Aplha DNA with Allele-Specific Oligonucleotide Probes”,Nature, vol. 324, No. 6093, 1986, pp. 163-166.
Hara et al., “Subtractive cDNA cloning using oligo(dT)30-latex and PCR: isolation of cDNA clones specific to undifferentiated human embryonal carcinoma cells”,Nucleic Acids Res.,vol. 19. No. 25, 1991. pp. 7097-7104.
IntelliGenetics Suite ™, Release 5.4, Advanced Training Manual, Jan. 1993
Balaban David J.
Cheung Gloria
Dai Josie
Hubbell Earl
Mittmann Michael P.
Affymetrix Inc.
Choobin Barry
Mehta Bhavesh M.
Townsend and Townsend / and Crew LLP
LandOfFree
Method and system for providing a probe array chip design... does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Method and system for providing a probe array chip design..., we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method and system for providing a probe array chip design... will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-3314013