EP1242632A2 - Matrices d'adn et leur utilisation pour examiner des individus d'une population - Google Patents

Matrices d'adn et leur utilisation pour examiner des individus d'une population

Info

Publication number
EP1242632A2
EP1242632A2 EP01901142A EP01901142A EP1242632A2 EP 1242632 A2 EP1242632 A2 EP 1242632A2 EP 01901142 A EP01901142 A EP 01901142A EP 01901142 A EP01901142 A EP 01901142A EP 1242632 A2 EP1242632 A2 EP 1242632A2
Authority
EP
European Patent Office
Prior art keywords
dna
population
matrix
individuals
specific
Prior art date
Legal status (The legal status 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 status listed.)
Withdrawn
Application number
EP01901142A
Other languages
German (de)
English (en)
Inventor
Gottfried Brem
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Agrobiogen GmbH Biotechnologie
Original Assignee
Agrobiogen GmbH Biotechnologie
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 Agrobiogen GmbH Biotechnologie filed Critical Agrobiogen GmbH Biotechnologie
Publication of EP1242632A2 publication Critical patent/EP1242632A2/fr
Withdrawn legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips

Definitions

  • DNA matrices and their use to study individuals in a population
  • the present invention relates to the production of genotype arrays of a population on DNA matrices.
  • the invention relates in particular to the use of such DNA matrices for the determination of features, specific genes, alleles, mutations, expression patterns etc. in the individuals of the population examined in each case.
  • a chip which can be divided into hundreds of thousands of raster segments, is equipped with a certain number of cDNA fragments, synthetic oligonucleotides or other probes that represent certain known mutations, and a DNA sample obtained from the individual to be examined is then prepared examined the chip.
  • Chips that are suitable for the detection of the same known mutations In order to be able to carry out this process at all from the point of view of costs, a large number of identical chips must be produced at the same time, i.e. Chips that are suitable for the detection of the same known mutations.
  • analysis for known mutations requires a series of individual analyzes to be carried out or the use of a specific chip with which these specific changes can be determined for each individual. This means that millions of analyzes or chips are required to examine a population for a certain property or mutation.
  • Another problem with current chip technology is that the genomic DNA samples from millions of untyped individuals must be kept in order to be able to carry out the analyzes at a later point in time or to be able to carry out additional or more extensive analyzes. This is costly and requires a large amount of storage space. Logistical problems also arise if, for example, individual individuals have to be selected from the entire sample quantity for re-typing. An object of the present invention is therefore to solve the above problems.
  • This object is achieved according to the invention by a method in which the genomic DNA of an individual of a population is transferred to at least one DNA matrix in a first step and this matrix is then used to demonstrate whether an individual from the population has a specific property or mutation , is examined with a probe that detects the property / mutation.
  • Fig. 1 shows schematically a matrix and the implementation of the method.
  • a prerequisite for the use of the invention is that DNA-containing samples of a certain population of individuals in a population, such as certain parts or all members of a population group, a social class or country, of animals, such as farm animals, for example cattle, pigs, etc. obtained and applied to the matrix or fixed there.
  • the term population therefore encompasses not only a population of individuals but also only mating communities.
  • the DNA-containing samples can be obtained in a conventional manner, for example by collecting blood, saliva, mucous membrane or skin samples, etc., and the samples can be preserved as soon as they are obtained.
  • Containers suitable for obtaining and preserving DNA-containing samples are described, for example, in DE 199 57 861.3.
  • the samples can be obtained in the same way or also using the sample collection system described in WO 99/61882.
  • the DNA is isolated and prepared from the samples obtained in accordance with conventional techniques (see, for example, Maniatis, 1992, Cold Spring Harbor, A Laboratory Manual) or using commercially available kits (such as, for example, Nucleo Spin Multi # 740629,24,123813 from Mackery-Nagel).
  • the DNA samples obtained are then processed in such a way that they can be fixed using pipetting robots (for example Packard's BioChipArrayer) to predetermined coordinates of the one or more matrices (see FIG. 1), ensuring that a specific coordinate is assigned to a specific individual on the DNA matrix.
  • pipetting robots for example Packard's BioChipArrayer
  • the materials known in the prior art such as glass, silicon, nylon, cellulose, etc., are suitable as the matrix, and there are no restrictions with regard to the size of the matrix.
  • the matrix can be larger than the known DNA chips, but can also be larger.
  • the size of the matrix to be used will essentially depend on the number of the population to be examined and the possibilities of the automated devices available.
  • the genomic DNA of the individual (corresponds in its entirety to the genotype of the individual) on the matrix can also be carried out in a duplicate or quadruplet in order to improve the evaluability or increase the accuracy, since a later statement based on an examination only then will be considered correct if both or all four order points of the same genotype lead to the same result.
  • these control analyzes can also be achieved by real repetitions, by examining two or more identical chips with one probe and comparing the results.
  • the matrix is divided into raster segments such that each individual DNA sample that is fixed on the matrix is assigned to a section and can thus be identified.
  • populations comprising millions of individuals can also be assembled on a few matrix units.
  • the population recorded in this way can then be examined for certain features, such as the presence of certain alleles, mutations, the predisposition to develop certain diseases or the resistance to diseases, etc.
  • the at least one chip i.e. examines the complete set of matrices bearing all of the genotypes of this particular population with a specific probe that allows a specific statement regarding the property.
  • a segment of a (mutated) gene can be used as a probe, which is known to cause a certain predisposition to a certain disease, such as MHS in pigs, BLAD in cattle, etc.
  • These sensors can be linked to conventional materials, such as radioactive isotopes, dyes or fluorescent substances, for visual detection if necessary.
  • the genotype template set can also be used to directly carry out a PCR, a TMA (Transcription Mediated Amplification), a bDNA reaction (branched DNA) or another method for specific DNA Carrying out and evaluating evidence.
  • a PCR Transcription Mediated Amplification
  • a bDNA reaction branched DNA
  • solid phase PCR for example, all individuals of a population can be examined for a property of interest in a single approach, which represents an enormous cost advantage, since millions of individuals are analyzed for a variant in a single PCR reaction, because of the effort for the PCR approach on the individuals of the whole population is then not significantly larger than for a PCR reaction for an individual.
  • the evaluation of the genotype matrices after hybridization or PCR reaction is generally carried out using an automated device, since this would be too high due to the error rate that would occur if the miniaturized, complex result patterns on the matrices were assigned manually to the individuals , The hybridization or PCR pattern is therefore recorded with a scanner and evaluated with an image analysis system.
  • the position on the matrix generally determines which individual is located there and the result of the hybridization or PCR reaction at this position is linked to the identity of the individual and is shown in an evaluation protocol or an evaluation file.
  • individual individuals who are also on the matrices can be determined in an extra, individual conventional singular PCR reaction or another detection method with separately stored DNA and then as positive and negative controls for the matrix approach can be used.
  • the results of the matrix analyzes which may be stored in files, can then be made available for authorized persons or facilities to query.
  • the DNA chips according to the invention can also be used to determine the tolerability or responsiveness of drugs.
  • Effective drugs sometimes behave like poisons in the body.
  • the recommended dose may be effective for some individuals, may have no positive effect on others, and may be toxic or even fatal to others.
  • Side effects from medications are known to be among the ten most common types of death in humans.
  • the goal of modern pharmacogenetics is therefore to adapt drug administration to the individual genotype. Genetic differences, such as certain SNPs that can influence these effects, must be identified and analyzed.
  • each approved or new drug can now be examined before it is launched on the market - as far as the corresponding genetic components are known and the genotype arrays are available - with what certainty it will work, which or how many Individuals cannot be cured and to what extent there are intolerances.
  • the population matrices can be stored easily and unproblematically for a long time, with little space requirement, that is to say almost unlimitedly inexpensively. This is a major advantage over conventional methods, in which the storage of millions of samples causes enormous logistical problems and relatively high costs. 2) These matrices can then be examined or analyzed in total with a single probe, for example by hybridization or with other techniques such as PCR, LCR, bDNA, TMA or the like for a specific feature, variant or mutation etc.
  • the melting temperature differences in hybridization with sequences that do not clearly correspond can be used excellently for the detection of base exchanges. Since only one probe is used per matrix, the hybridization conditions, such as the temperature, can be optimally selected for the respective probe. The person skilled in the art will choose the appropriate hybridization temperature based on his general knowledge, taking into account the length of the probe and its G / C content.
  • Post-typing with newly discovered markers, mutations, etc. can be carried out at any time and very cost-effectively in a single approach for the entire population recorded up to that point, without having to resort to the individual samples again.
  • An analysis of the chips / matrices created in stock makes this procedure completely unproblematic. For example, within a week after the discovery / publication and the decision to use a new marker, the entire population can be typed using the invention and the results made available to millions of individuals for interested / authorized users.
  • Example 1 illustrate the invention and are not intended to limit it in any way.
  • Example 1 illustrate the invention and are not intended to limit it in any way.
  • the EU labeling regulation stipulates that they must be labeled in the EU using double-ear tags. These ear tags must be retracted within the first week of life. If one uses this identification with ear tags to take a tissue sample from the animals, which is easily possible by means of the system described in WO 99/61882, a genotype collection of all cattle in the EU can be constructed simply and inexpensively. This means that after a certain time all 80 million EU cattle are collected on these genotype matrices, with the new calves being added to new matrices and assigned to the pool.
  • the template set of the farm animal species can now be examined with 50 different SNP markers (one set for each marker). This means that a genetic fingerprint can be recorded for all 80 million animals, which allows an individual animal to be uniquely identified from billions of genotypes or to ensure its identity and, if applicable, its parentage.
  • Analyzes with specific markers can be used to determine for all cattle in the EU which genetic constellation they have, for example, with various milk protein genes, or to find out which animals are carriers of positive QTLs, whether they have certain mutations (e.g. BLAD) make them appear suitable as models for human diseases, for example certain hemoglobin variants, whether they have specific genetic intolerances, how they will respond to treatment with medication, which medication is optimal for a particular disease for this genotype, which dosage is helpful, which animal dispositions or have resistance to or against certain pathogens or influences, etc.
  • certain mutations e.g. BLAD
  • ancestry, origin and identity assurance can be carried out for all animals easily, reliably and quickly and can be carried out.
  • meat samples could be taken from all imported carcasses, from which DNA is isolated and used to produce genotype matrices. This is also possible with frozen products.
  • the DNA of the suspect sample is compared with the genotypes preserved on the matrices, which makes it easy and inexpensive to determine whether the suspect sample is identical to a reserve sample from imported meat or not.
  • transgenic grain that is exported to Europe from overseas, it often happens that non-transgenic grain is mixed with a small amount of transgenic grain.
  • DNA samples could be collected from all residents and applied to genotype matrices. Such an agreement has already been reached in Iceland, so that samples can be collected, stored and anonymized analyzed by all residents. With the corresponding legal situation under the Data Protection Act, the basis can also be created in other countries for DNA samples from a human sub-population or population group to be collected on a voluntary basis and then for medical applications (for example to identify the right medication, the appropriate dosage, evidence of genetic incompatibilities or problems etc.) may be used. The present invention thus shows how these samples, if they are collected, can be stored and analyzed optimally and inexpensively.

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

La présente invention concerne la production d'ensembles de génotypes d'une population sur des matrices d'ADN. L'invention concerne en particulier l'utilisation de matrices d'ADN de ce type pour déterminer des caractéristiques, des gènes, allèles, mutations, modèles d'expression déterminés, etc., chez les individus de la population qui fait l'objet de l'examen.
EP01901142A 2000-01-01 2001-01-01 Matrices d'adn et leur utilisation pour examiner des individus d'une population Withdrawn EP1242632A2 (fr)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
DE10000001 2000-01-01
DE10000001A DE10000001A1 (de) 2000-01-01 2000-01-01 DNA-Matrizes und deren Verwendung zur Untersuchung von Individuen einer Population
PCT/EP2001/000001 WO2001049881A2 (fr) 2000-01-01 2001-01-01 Matrices d'adn et leur utilisation pour examiner des individus d'une population

Publications (1)

Publication Number Publication Date
EP1242632A2 true EP1242632A2 (fr) 2002-09-25

Family

ID=7626669

Family Applications (1)

Application Number Title Priority Date Filing Date
EP01901142A Withdrawn EP1242632A2 (fr) 2000-01-01 2001-01-01 Matrices d'adn et leur utilisation pour examiner des individus d'une population

Country Status (6)

Country Link
US (1) US20030104425A1 (fr)
EP (1) EP1242632A2 (fr)
AU (1) AU2677101A (fr)
CA (1) CA2395916A1 (fr)
DE (1) DE10000001A1 (fr)
WO (1) WO2001049881A2 (fr)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DE60136335D1 (de) * 2000-02-16 2008-12-11 Illumina Inc Parallele genotypisierung mehrerer patientenproben
AU2003283575A1 (en) * 2002-11-14 2004-06-03 John Nicholas Housby Polymorphism assay
DE10261529A1 (de) * 2002-12-23 2004-07-08 Indivumed Gmbh Verfahren zur Erstellung einer Sammlung von biologischem Probenmaterial und Probensammlung
EP4077728A4 (fr) * 2019-12-22 2024-05-22 Ramot at Tel-Aviv University Ltd. Procédés et réseaux pour identifier la cellule ou l'origine tissulaire d'un adn

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0228075B1 (en) * 1986-01-03 1991-04-03 Molecular Diagnostics, Inc. Eucaryotic genomic dna dot-blot hybridization method
US5418133A (en) * 1986-08-12 1995-05-23 The Australian National University Sex determination in cattle, sheep and goats using y-chromosome polynucleotides
US5633134A (en) * 1992-10-06 1997-05-27 Ig Laboratories, Inc. Method for simultaneously detecting multiple mutations in a DNA sample
US5834181A (en) * 1994-07-28 1998-11-10 Genzyme Corporation High throughput screening method for sequences or genetic alterations in nucleic acids
US6013486A (en) * 1997-09-17 2000-01-11 Yale University Method for selection of insertion mutants
US6355419B1 (en) * 1998-04-27 2002-03-12 Hyseq, Inc. Preparation of pools of nucleic acids based on representation in a sample
US6913879B1 (en) * 2000-07-10 2005-07-05 Telechem International Inc. Microarray method of genotyping multiple samples at multiple LOCI

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See references of WO0149881A2 *

Also Published As

Publication number Publication date
AU2677101A (en) 2001-07-16
US20030104425A1 (en) 2003-06-05
CA2395916A1 (fr) 2001-07-12
DE10000001A1 (de) 2001-07-19
WO2001049881A2 (fr) 2001-07-12
WO2001049881A3 (fr) 2002-06-13

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