WO2002033123A1 - Jeux ordonnes d'echantillons d'oligonucleotides pour reconnaissance numerique par ordinateur - Google Patents

Jeux ordonnes d'echantillons d'oligonucleotides pour reconnaissance numerique par ordinateur Download PDF

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Publication number
WO2002033123A1
WO2002033123A1 PCT/KR2000/001166 KR0001166W WO0233123A1 WO 2002033123 A1 WO2002033123 A1 WO 2002033123A1 KR 0001166 W KR0001166 W KR 0001166W WO 0233123 A1 WO0233123 A1 WO 0233123A1
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WO
WIPO (PCT)
Prior art keywords
computer
arrays
probes
oligonucleotide probes
dna
Prior art date
Application number
PCT/KR2000/001166
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English (en)
Inventor
Dong Kyu Jin
Original Assignee
Cosmogenome Co., Ltd
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Cosmogenome Co., Ltd filed Critical Cosmogenome Co., Ltd
Priority to AU2000279678A priority Critical patent/AU2000279678A1/en
Priority to PCT/KR2000/001166 priority patent/WO2002033123A1/fr
Publication of WO2002033123A1 publication Critical patent/WO2002033123A1/fr

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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/30—Microarray design

Definitions

  • the present invention provides arrays of oligonucleotide probes immobilized in microfabricated patterns on chips to detect specific nucleic acid sequences contained in a target nucleic acid in a sample for digital recognition by computers.
  • the invention therefore relates to diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine, and medical diagnostics.
  • DNA chip is usually defined as a micro-array technique using the DNA probes for the detection of gene expression or DNA sequence difference.
  • the probe molecule can be replaced by protein or oligosaccharides.
  • the microarray can be called a biochip.
  • a biochip involves more broad terminology for the detection of bio-molecules in very concentrated ways.
  • the DNA chip can be classified into i ) c-DNA chip and ⁇ ) oligonucleotide-chip according to the usage and the probes used. Our technique is on the oligonucleotide-chip.
  • DNA chip Focused on the DNA chip in general, during recent several years, there has been a big progress in the field of biotechnology, especially, in the field of genomics.
  • the human genome project which reveals the sequence of human genome has almost finished, and there is now abundant sources of information for the sequence of human genes.
  • DNA chip is now emerging as novel technology for the detection of the sequence information in a large scale, because the probes can be spotted in a very tiny space and the detection seems readily adaptable to the highly parallel implementation, i,e, a large number of data can be generated simultaneously.
  • the DNA chip has been constructed by robotic machine which transfers the hundred or thousand probes into the tiny space, or by other ways like photolithography or electronic array.
  • the end product is always same whatever methods they use.
  • the object of the present invention is to provide an array of oligonucleotide probes on a solid support for detecting the point mutation of testee's DNA sample which comprises i ) a labelling part of arrays including catalog number, gene sequence number, ID number, command and IP address, which indicates the information for sample DNA identification to be read by computer; and ii ) a logic part of arrays including arrays of probes in 4 columns in at least 100 up to 100,000 rows, wherein each column consists of 2 symbols, that are, a control symbol having detectible marker for digital recognition by computer and a hybridization symbol comprising oligonucleotide probes in the 5—30 nucleotides length occupying known sites by substituting target oligonucleotide into A C G T in each column.
  • the array of oligonucleotide probes on a solid support for detecting the point mutation of testee's DNA sample can be fabricated in a form of round diskette, eg. a form of CD-ROM for convenient recognition by computer.
  • the labelling part of arrays can be constructed in a form of bar code for digital recognition by computer.
  • labelling part and logic part of the present invention can be stored by computer, or transmitted to other researchers through internet.
  • FIG 1 shows the schematic diagram indicating the developmental strategy of the present invention.
  • FIG 2 shows an example of construction of digital DNA chip in the present invention.
  • FIG 3 shows another example of bar code type of labelling part including catalog number, gene sequence number, ID number, command and IP address in the present invention.
  • FIG 4 shows an example of gene number and logic part of the present invention.
  • FIG 5 shows an embodiment of DNA chip of the present invention.
  • FIG 6 shows a photo of DNA chip of the present invention before hybridization.
  • FIG 7 shows a photo of DNA chip of the present invention after hybridization.
  • FIG 8 shows a round form of DNA chip as another embodiment of the present invention.
  • FIG 9 shows Region 1, Region 2 and Region 3 in the round form of DNA chip of the present invention.
  • FIG 10 shows the data analysis and interpretation of DNA chip by computer of the present invention.
  • some symbols like bar codes or simple logical calculators are designed and constructed by the assembly of the probe dots to be read by computer or to be interpreted into digital information.
  • the chip is composed of 2 parts, that are, labelling part and logic part.
  • Labelling part is represented by bar codes which is interpreted as numbers or digital informations
  • logic part is represented by the bar code type of probes, which can be represented by only two symbols (+) or (-).
  • Each row consists of 8 symbols (8 bits), having 2 symbols in one column.
  • the first symbol in one column is a control symbol which determines or controls the following calculator symbol.
  • the first symbol plays a role for the fixed (+) or (-) before hybridization, because this symbol is designed just for controlling the next symbol.
  • the next symbol (calculator) is also designed for indicating (+) or (-) after hybridization. This fact reminds us that the DRAM used in memory consists of one CMOS (1st symbol) and one capacitance (2nd symbol).
  • the genetic information of the target (usually patient's DNA sequence) becomes apparent on the chip. Since the information in this chip is represented as discrete digital information, the information can be read and translated by mechanical device into digital information without analog to digital conversion.
  • the read information can be transmitted to any computer in the world as a small memory, neither as a photo file nor as an image file. We believe that our way of storing information as a digital method dramatically reduces the capacity of memory.
  • bar codes which include catalog number, gene sequence number, ID number, commands and IP address.
  • Catalog number represents a kind of chip which we constructed. Gene sequence number explains the name of the gene with the accession number. The accession number is important because the same sequence can be reported by several researchers. Therefore, different accession numbers may exist in the same gene. Further, each accession number has different starting number even though it is the same gene. ID number is written to identify the person who is tested. Because we do not know who will use the chip before hybridization, the information of ID number will be sent to the server nowadays and the information will be merged.
  • Command directs the short program which shows the urgent information. Because of the limited space of chip, the symbol in the chip is a short message to recruit the main program in the server or nearby detecting device. We include one example of the order.
  • IP address There is also an information for the IP address where the ultimate genetic information is stored. Because all the information is digitalized and readily sent to the main computer, there will be no loss of genetic information if the digital chip is used for the genetic analysis.
  • the embodiment of the present invention can be explained as follows.
  • FIG 1 the develpomental strategy of DNA chip of the present invention is illustrated.
  • the genomic DNA preparation is made as testing material.
  • said DNA fragments are amplified by fluorescein labelled primers.
  • amplified DNA fragments are laid on the chip to be hybridized.
  • the hybridized and fluorescent DNA fragments are detected using con-focal laser scanner.
  • the digital DNA chip of the present invention comprises i ) labelling part including catalog number, gene sequence number, ID number, commands and IP address; and ii ) logic part including 4 columns.
  • FIG 3 also shows an example of bar code type of labelling part. Therefore, the information regarding catalog number, gene sequence number, ID number, commands and IP address can be represented by bar codes, which makes it possible for computer to read it automatically.
  • FIG 4 shows an example of gene number and logic part.
  • Logic part comprises arrays of probes in 4 columns in at least 100 up to 100,000 rows, wherein each column consists of 2 symbols, that are, a control symbol having detectible marker for digital recognition by computer and a hybridization symbol comprising oligonucleotide probes in the 5 — 30 nucleotides length occupying known sites by substituting target oligonucleotide into A C G T in each column.
  • the gene number it shows the number of oligonucleotide where we want to detect if the point mutation is occurred or not.
  • FIG 5 shows another embodiment of DNA chip of the present invention.
  • This figure illustrates the bar code type of labelling part and the logic part for hybridization.
  • FIG 6 shows a photo of DNA chip of the present invention before hybridization.
  • FIG 7 shows a photo of DNA chip of the present invention after hybridization.
  • FIG 8 shows a round form of DNA chip as another embodiment of the present invention
  • FIG 8 illustrates that a round form of DNA chip consists of 8 sectors in a fan shape.
  • Region 1, 2 and 3 are included, which comprises head part, data part and tail part.
  • the labelling part shall correspond with Region 1 and Region 2.
  • the information regarding catalog number, gene sequence number, ID number, commands and IP address shall be constructed for digital recognition by computer.
  • Region 1 comprises index and extra space
  • Region 2 comprises operation code and code information
  • Region 3 comprises header and logic part for hybridization.
  • FIG 10 shows the data analysis and interpretation of DNA chip by computer of the present invention.
  • Such DNA chips are readable by computer and such information read by computer can be stored in hard disc of the computer. Further, such information can be transmitted to anybody who wants to access the information by internet system.

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  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

L'invention concerne un jeu ordonné d'échantillons d'oligonucléotides sur un support solide pour détecter la mutation ponctuelle de l'échantillon d'ADN d'essai, qui comprend i) une partie de marquage de jeux ordonnés d'échantillons comprenant un numéro de lot, un numéro de séquence de gènes, un numéro d'identification, une adresse de commande et une adresse IP, qui indique l'information pour l'identification de l'échantillon d'ADN que l'ordinateur doit lire ; ii) une partie logique de jeux ordonnés comprenant des jeux ordonnés d'échantillons en 4 colonnes en au moins 100 à 100.000 rangées au plus. Chaque colonne comprend 2 symboles, à savoir un symbole de commande à marqueur détectable pour la reconnaissance numérique par ordinateur et un symbole d'hybridation comprenant des échantillons d'oligonucléotides dans des sites connus occupant une longueur de 5 à 30 nucléotides, par substitution de l'oligonucléotide cible en A C G T dans chaque colonne.
PCT/KR2000/001166 2000-10-18 2000-10-18 Jeux ordonnes d'echantillons d'oligonucleotides pour reconnaissance numerique par ordinateur WO2002033123A1 (fr)

Priority Applications (2)

Application Number Priority Date Filing Date Title
AU2000279678A AU2000279678A1 (en) 2000-10-18 2000-10-18 Arrays of oligonucleotide probes for digital recognition by computer
PCT/KR2000/001166 WO2002033123A1 (fr) 2000-10-18 2000-10-18 Jeux ordonnes d'echantillons d'oligonucleotides pour reconnaissance numerique par ordinateur

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
PCT/KR2000/001166 WO2002033123A1 (fr) 2000-10-18 2000-10-18 Jeux ordonnes d'echantillons d'oligonucleotides pour reconnaissance numerique par ordinateur

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WO2002033123A1 true WO2002033123A1 (fr) 2002-04-25

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Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997022720A1 (fr) * 1995-12-21 1997-06-26 Kenneth Loren Beattie Cartographie peptidique d'oligonucleotides en sequences arbitraires
EP1026259A1 (fr) * 1999-02-08 2000-08-09 Fuji Photo Film Co., Ltd. Chip d 'ADN et sa préparation
WO2000053811A1 (fr) * 1999-03-11 2000-09-14 Orion Genomics, Llc Puces genomiques et cartographie optique de transcrits

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997022720A1 (fr) * 1995-12-21 1997-06-26 Kenneth Loren Beattie Cartographie peptidique d'oligonucleotides en sequences arbitraires
EP1026259A1 (fr) * 1999-02-08 2000-08-09 Fuji Photo Film Co., Ltd. Chip d 'ADN et sa préparation
WO2000053811A1 (fr) * 1999-03-11 2000-09-14 Orion Genomics, Llc Puces genomiques et cartographie optique de transcrits

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