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• • 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
  • C12Q1/6869—Methods for sequencing

Definitions

• This invention pertains to high-throughput methodology that directly identifies previously- unidentified sequence alterations in DNA, including specific disease-causing DNA sequences in mammals.
• the methods of the present invention can be used to identify genetic polymorphisms, to determine the molecular basis for genetic diseases, and to provide carrier and prenatal diagnosis for genetic counseling.
• DNA sequences e.g. mutations and polymorphisms
• RFLPs restriction fragment length polymorphisms
• Southern blotting technique Southern blotting technique
• 5:488-93, 1995 disclose a method for multiple allele-specific disease analysis in which multiple ASOs are first hybridized to a target DNA, followed by elution and sequencing of ASOs that hybridize. This method allows the identification of a mutation without the need for many individual hybridizations involving single ASOs and requires prior knowledge of relevant mutations.
• SSCP single- strand conformational polymorphisms
• DGGE denaturing gradient gel electrophoresis
• HET heteroduplex analysis
• the present invention encompasses high-throughput methods for identifying one or more genetic alterations in a target sequence present in a first DNA sample.
• the method is carried out by the steps of: a) hybridizing the first sample with a second DNA sample not containing genetic alterations to form heteroduplex DNA containing a mismatch region at the site of a genetic alteration(s) ; b) cleaving one DNA strand of the heteroduplex in the target sequence to form a single-stranded gap across the site of the alteration; c) treating the cleaved heteroduplex with a DNA polymerase in the presence of dideoxynucleotides to determine the sequence across the gap; and d) comparing the nucleotide sequence across the gap with a predetermined cognate wild-type sequence to identify the genetic alteration(s) .
• the first DNA sample containing the target sequence is hybridized under stringent conditions with a second DNA sample not containing the alteration.
• the hybrids that form contain mismatch regions, which are recognized and endonucleolytically cleaved on one or both sides of the mismatch region by mismatch recognition protein-based systems.
• one or more exonucleases are used to form the single-stranded gap.
• endonucleolytic cleavage occurs on both sides of the mismatch region, the single-stranded fragment is released by the action of a helicase to form the single-stranded gap. Determination of the sequence across the gap is achieved in a single step by an enzymatic DNA sequencing reaction using dideoxynucleotides and DNA polymerase I, DNA polymerase III, T4 DNA polymerase, or T7 DNA polymerase.
• the present invention encompasses high-throughput methods for identifying one or more genetic alterations in a target sequence present in a first DNA sample.
• This method is carried out by the steps of: a) hybridizing the first sample with a second DNA sample not containing genetic alterations to form heteroduplex DNA having free ends and containing a mismatch region at the site of a genetic alteration(s) ; b) cleaving the DNA at or in the vicinity of the alteration, forming new ends; c) ligating an oligonucleotide of predetermined sequence to the new ends; d) determining the nucleotide sequence adjacent to the ligated oligonucleotide; and e)comparing the nucleotide sequence determined in d) with a predetermined cognate wild-type sequence to identify the genetic alteration(s) .
• Specific cleavage at or near the alteration is achieved by hybridizing the first DNA sample containing the target sequence with a second DNA sample not containing the alteration, so that heteroduplexes are formed that contain mismatch regions, which can be recognized and cleaved by mismatch recognition systems.
• the first DNA sample comprises genomic DNA from a patient suffering from a genetic disease whose genome does not contain any of the known mutations that cause that disease, and the target sequence comprises a known disease-causing gene.
• the genetic alterations identified by these methods include additions, deletions, or substitutions of one or more nucleotides.
• Mismatch recognition, cleavage, and excision systems useful in practicing the invention include without limitation bacteriophage resolvases, mismatch repair proteins, nucleotide excision repair proteins, chemical modification of mismatched bases followed by excision repair proteins, chemical modification and cleavage, and combinations thereof, with or without supplementation with exonucleases as required.
• the present invention finds application in high- throughput methods for multiplex identification of new mutations or previously unidentified polymorphisms, in which DNAs obtained from a multiplicity of patients are immobilized on a single solid support, followed by one or more of the following steps: hybridization, mismatch recognition, excision, cleavage, ligation, sequencing, and sequence comparison steps as set forth above. Furthermore, multiple specific target sequences can be analyzed simultaneously by amplifying the target sequences prior to immobilization, followed by the steps as set forth above.
• the present invention provides methods for positional cloning of a disease- causing gene.
• Invention methods are carried out using the following steps: a) hybridizing a first DNA sample derived from an individual suffering from the disease with a second DNA sample derived from a multiplicity of individuals not suffering from the disease, to form hybrids containing mismatch regions at sites at which the sequence of the first DNA sample diverges from the sequence of the second DNA sample; b) cleaving one DNA strand in the hybrids to form a single-stranded gap across the site of the alteration; c) determining the nucleotide sequence across the gap; d) preparing a synthetic oligonucleotide comprising all or part of the nucleotide sequence determined in c) ; and e) identifying a DNA clone derived from a cosmid or a Pi library containing the sequence of the synthetic oligonucleotide prepared in d) .
• mismatch regions are recognized and endonucleolytically cleaved on one or both sides of the mismatch region by mismatch recognition protein-based systems.
• one or more exonucleases are used to form the single-stranded gap.
• endonucleolytic cleavage occurs on both sides of the mismatch region, the single- stranded fragment is released by the action of a helicase to form the single-stranded gap. Determination of the sequence across the gap is achieved in a single step by an enzymatic DNA sequencing reaction using dideoxynucleotides and DNA polymerase I, DNA polymerase III, T4 DNA polymerase, or T7 DNA polymerase.
• the present invention further provides alternative methods for positional cloning of a gene of interest. These methods are carried out by: a) hybridizing a first DNA sample derived from an individual displaying a given phenotype with a second DNA sample derived from one or more individuals not displaying the phenotype, to form heteroduplex DNA having free ends and containing a mismatch region at sites at which the sequence of the first DNA sample diverges from the sequence of the second DNA sample; b) blocking the free ends on the hybrids formed in a) ; c) cleaving one or both DNA strands within or adjacent to the mismatch regions to form new ends; d) ligating a single-stranded oligonucleotide of predetermined sequence to the new ends formed in c) ; e) determining the nucleotide sequence adjacent to the ligatedpredetermined sequence; f) preparing a synthetic oligonucleotide comprising all or part of the nucleotide sequence determined in e) ; and
• positional cloning refers to a process by which a previously unknown disease-causing gene is localized and identified.
• the genetic alterations identified by invention methods include additions, deletions, or substitutions of one or more nucleotides.
• Mismatch recognition, cleavage, and excision systems useful in practicing the invention include without limitation mismatch repair proteins, nucleotide excision repair proteins, bacteriophage resolvases, chemical modification of mismatched bases followed by excision repair proteins, and combinations thereof, with or without supplementation with exonucleases as required.
• the present invention encompasses high-throughput methods for identifying specific target sequences in DNA isolated from a patient.
• the term high- throughput refers to a system for rapidly assaying large numbers of DNA samples at the same time. The methods are applicable when one or more genes or genetic loci are targets of interest.
• the specific sequences typically contain one or more sequence alterations relative to wild- type DNA, including additions, deletions, or substitutions of one or more nucleotides.
• the first DNA sample containing the target sequence is hybridized with a second sample of DNA (or a pool of DNA samples) containing one or more wild-type versions of the targeted gene.
• the methods of the present invention take advantage of the physico-chemical properties of DNA hybrids between almost-identical (but not completely identical) DNA strands (i.e., heteroduplexes) .
• the heteroduplexes contain a mismatch region that is embedded in an otherwise perfectly matched hybrid.
• mismatch regions are formed under controlled conditions and are chemically and/or enzymatically modified; the sequences adjacent to, and including, the mismatch are then determined.
• the mismatch region may comprise any number of bases, preferably from 1 to about 1000 bases.
• the methods of the invention can be employed to identify specific disease-causing mutations in individual patients (when the gene or genes responsible for the disease are known) or previously unidentified polymorphisms and for positional cloning to identify new genes.
• the specific DNA sequence comprises a portion of a particular gene or genetic locus in the patient's genomic DNA known to be involved in a pathological condition or syndrome.
• genetic syndromes include cystic fibrosis, sickle-cell anemia, thalassemias, Gaucher's disease, adenosine deaminase deficiency, alphal-antitrypsin deficiency, Duchenne muscular dystrophy, familial hypercholesterolemia, fragile X syndrome, glucose-6- phosphate dehydrogenase deficiency, hemophilia A, Huntington disease, myotonic dystrophy, neurofibromatosis type 1, osteogenesis imperfecta, phenylketonuria, retinoblastoma, Tay-Sachs disease, and Wilms tumor (Thompson and Thompson, Genetics in Medicine, 5th Ed. ) .
• the specific DNA sequence comprises part of a particular gene or genetic locus that may not be known to be linked to a particular disease, but in which polymorphism is known or suspected.
• obesity may be linked with variations in the apolipoprotein B gene
• hypertension may be due to genetic variations in sodium or other transport systems
• aortic aneurysms may be linked to variations in ⁇ -haptoglobin and cholesterol ester transfer protein
• alcoholism may be related to variant forms of alcohol dehydrogenase and mitochondrial aldehyde dehydrogenase.
• an individual's response to medicaments may be affected by variations in drug modification systems such as cytochrome P450s, and susceptibility to particular infectious diseases may also be influenced by genetic status.
• the methods of the present invention can be applied to HLA analysis for identity testing.
• the specific DNA sequence comprises part of a foreign genetic sequence e.g. the genome of an invading microorganism.
• a foreign genetic sequence e.g. the genome of an invading microorganism.
• Non-limiting examples include bacteria and their phages, viruses, fungi, protozoa, and the like.
• the present methods are particularly applicable when it is desired to distinguish between different variants or strains of a microorganism in order to choose appropriate therapeutic interventions.
• the target sequence is contained within a sample of DNA isolated from an animal or human patient.
• This DNA may be obtained from any cell source or body fluid.
• Non-limiting examples of cell sources available in clinical practice include blood cells, buccal cells, cervicovaginal cells, epithelial cells from urine, fetal cells, or any cells present in tissue obtained by biopsy.
• Body fluids include blood, urine, cerebrospinal fluid, and tissue exudates at the site of infection or inflammation.
• DNA is extracted from the cell source or body fluid using any of the numerous methods that are standard in the art. It will be understood that the particular method used to extract DNA will depend on the nature of the source.
• the preferred amount of DNA to be extracted for analysis of human genomic DNA is at least 5 pg (corresponding to about 1 cell equivalent of a genome size of 4 x 10 9 base pairs) .
• variable amounts of DNA may be extracted.
• the sample DNA containing the target sequence may be employed in the present invention without further manipulation.
• one or more specific regions present in the sample DNA may be amplified.
• the amplified regions are specified by the choice of particular flanking sequences for use as primers.
• Amplification at this step provides the advantage of increasing the concentration of specific sequences within the sample DNA population.
• the length of DNA sequence that can be amplified ranges from 80 bp to up to 30 kbp (Saiki et al. , 1988, Science, 239:487).
• the use of amplification primers that are modified by, e.g., biotinylation allows the selective incorporation of the modification into the amplified DNA.
• the first DNA containing the target sequence, with or without prior amplification of particular sequences is bound to a solid-phase matrix.
• matrices suitable for use in the present invention include nitrocellulose or nylon filters, glass beads, magnetic beads coated with agents for affinity capture, treated or untreated microtiter plates, and the like. It will be understood by a skilled practitioner that the method by which the DNA is bound to the matrix will depend on the particular matrix used. For example, binding to nitrocellulose can be achieved by simple adsorption of DNA to the filter, followed by baking the filter at 75-80°C under vacuum for 15 min. to 2h.
• charged nylon membranes can be used that do not require any further treatment of the bound DNA.
• Beads and microtiter plates that are coated with avidin can be used to bind DNA that has had biotin attached (via e.g. the use of biotin-conjugated primers) .
• antibodies can be used to attach DNA to any of the above solid supports by coating the surfaces with the antibodies and incorporating an antibody-specific hapten into the DNA.
• DNA that has been amplified using biotinylated primers is bound to streptavidin-coated beads (Dynal, Inc., Milwaukee, Wl) .
• the untreated or amplified first DNA preferably bound to a solid-phase matrix
• the second DNA sample preferably comprises one or more "wild-type” version(s) of the target sequence.
• a "wild-type” version of a gene is one prevalent in the general population that is not associated with disease (or with any discernable phenotype) and is thus carried by "normal" individuals.
• wild-type genes may include multiple prevalent versions, which contain alterations in sequence relative to each other that cause no discernable pathological effect; these variations are designated “polymorphisms" or "allelic variants”.
• a mixture of DNAs from "normal" individuals is used for the second DNA sample, thus providing a mixture of the most common polymorphisms. This insures that, statistically, hybrids formed between the first and second DNA sample will be perfectly matched except in the region of the mutation, where discrete mismatch regions will form. In some applications, it is desired to detect polymorphisms; in these cases, appropriate sources for the second DNA sample will be selected accordingly.
• the wild-type DNA may also be chemically or enzymatically modified, e.g., to remove or add methyl groups.
• Hybridization reactions according to the present invention are performed in solutions ranging from about 10 mM NaCl to about 600 mM NaCl, at temperatures ranging from about 37°C to about 65°C. It will be understood that the stringency of a hybridization reaction is determined by both the salt concentration and the temperature; thus, a hybridization performed in 10 mM salt at 37°C may be of similar stringency to one performed in 500 mM salt at 65°C.
• any hybridization conditions may be used that form perfect hybrids between precisely complementary sequences and mismatch loops between non-complementary sequences in the same molecules. Preferably, hybridizations are performed in 600 mM NaCl at 65°C. Following the hybridization step, DNA molecules that have not hybridized to the first DNA sample are removed by washing under stringent conditions, e.g. , 0.1X SSC at 65°C.
• the hybrids formed by the hybridization reaction may then be treated to block any free ends so that they cannot serve as substrates for further enzymatic modification such as, e.g., by RNA ligase.
• Suitable blocking methods include without limitation removal of 5' phosphate groups, homopolymeric tailing of 3' ends with dideoxynucleotides, and ligation of modified double- stranded oligonucleotides to the ends of the duplex.
• the hybrids are treated so that one or both DNA strands are cleaved within, or in the vicinity of, the mismatch region.
• cleavage may occur at some predetermined distance from either boundary of the mismatch region, and may occur on the wild-type or mutant strand.
• the "vicinity" of the mismatch as used herein thus encompasses from 1 to 2000 bases from the borders of the mismatch.
• Non-limiting examples of mismatch recognition and cleavage systems suitable for use in the present invention include mismatch repair proteins, nucleotide excision repair proteins, bacteriophage resolvases, chemical modification, and combinations thereof. These embodiments are described below.
• the mismatch recognition and/or modification proteins necessary for each embodiment described below are isolated using methods that are well known to those skilled in the art.
• the protein-coding region of the relevant gene is isolated from the source organism by subjecting genomic DNA of the organism to amplification using appropriate primers.
• the isolated protein-coding DNA sequence is cloned into commercially available expression vectors that, e.g., insert an amino acid "purification tag" at either the amino- or carboxyterminus of the recombinant protein.
• the recombinant expression vector is then introduced into an appropriate host cell (e.g., E. coli) , and the protein is recovered from the cell lysate by affinity chromatography that recognizes the "tag".
• the bacterial expression vector pQiexl2 is used to express proteins with a polyhistidine tag, allowing purification of the recombinant product by a single step of chromatography on Ni-Sepharose (QiaGen, Chatsworth, CA) .
• Other methods involve the expression of recombinant proteins carrying glutathione-S-transferase sequences as tags, allowing purification of the recombinant products on glutathione affinity columns (Pharmacia Biotech, Uppsala, Sweden) . If necessary, proteins containing purification tags are then treated so as to remove the tag sequences.
• the protein may be isolated from its cell of origin using standard protein purification techniques well- known in the art, including, e.g., molecular sieve, ion- exchange, and hydrophobic chromatography; and isoelectric focusing.
• Isolation denotes purification of the protein to the extent that it can carry out its function in the context of the present invention without interference from extraneous proteins or other contaminants derived from the source cells.
• mismatch recognition and modification proteins used in practicing the present invention may be derived from any species, from E. coli to humans, or mixtures thereof.
• functional homologues for a given protein exist across phylogeny.
• a "functional homologue" of a given protein as used herein is another protein that can functionally substitute for the first protein, either in vivo or in a cell-free reaction.
• E. coli A number of different enzyme systems exist across phylogeny to repair mismatches that form during DNA replication.
• one system involves the MutY gene product, which recognizes A/G mismatches and cleaves the A- containing strand (Tsai-Wu et al., J. Bacteriol . 178:1902,1991).
• Another system in E. coli utilizes the coordinated action of the MutS, MutL, and MutH proteins to recognize errors in newly-synthesized DNA strands specifically by virtue of their transient state of undermethylation (prior to their being acted upon by dam methylase in the normal course of replication) .
• Cleavage typically occurs at a hemimethylated GATC site within 1-2 kb of the mismatch, followed by exonucleolytic cleavage of the strand in either a 3 '-5' or 5'-3 ' direction from the nick to the mismatch. In vivo, this is followed by re- synthesis involving DNA polymerase III holoenzyme and other factors (Cleaver, Cell , 76:1-4, 1994).
• Mismatch repair proteins for use in the present invention may be derived from E. coli (as described above) or from any organism containing mismatch repair proteins with appropriate functional properties.
• useful proteins include those derived from Salmonella typhimurium (MutS, MutL) ; Streptococcus pneumoniae (HexA, HexB) ; Saccharomyces cerevisiae ("all- type", MSH2, MLH1, MSH3); Schizosaccharomyces po be (SWI4) ; mouse (repl, rep3); and human ("all-type", hMSH2, hMLHl, hPMSl, hPMS2, duel).
• the "all-type" mismatch repair system from human or yeast cells is used (Chang et al., Nuc. Acids Res . 19:4761, 1991; Yang et al., J. Biol . Chem. 266:6480,1991).
• heteroduplexes formed between patients' DNA and wild-type DNA as described above are incubated with human "all-type" mismatch repair activity that is purified essentially as described in International Patent Application WO/93/20233.
• Incubations are performed in, e.g., lOmM Tris-HCl pH 7.6, lOmM ZnCl 2 , ImM dithiothreitol, lmM EDTA and 2.9% glycerol at 37°C for 1-3 hours.
• purified MutS, MutL, and MutH are used to cleave mismatch regions (Su et al., Proc . Natl . Acad. Sci . USA 83:5057,1986; Grulley et al. , J. Biol . Chem. 264:1000,1989).
• UvrA an ATPase
• UvrB binds to the site of the lesion, unwinds and kinks the DNA, and causes a conformational change in UvrB that allows it to bind tightly to the lesion site.
• UvrA then dissociates from the complex, allowing UvrC to bind.
• UvrB catalyzes an endonucleolytic cleavage at the fifth phosphodiester bond 3' from the lesion;
• UvrC then catalyzes a similar cleavage at the eighth phosphodiester bond 5' from the lesion.
• UvrD (helicase II) releases the excised oligomer. Jn vivo, DNA polymerase I displaces UvrB and fills in the excision gap, and the patch is ligated.
• heteroduplexes formed between patients' DNA and wild-type DNA are treated with a mixture of UvrA, UvrB, UvrC, with or without UvrD.
• the proteins may be purified from wild-type E. coli , or from E. coli or other appropriate host cells containing recombinant genes encoding the proteins, and are formulated in compatible buffers and concentrations.
• the final product is a heteroduplex containing a single-stranded gap covering the site of the mismatch.
• Excision repair proteins for use in the present invention may be derived from E. coli (as described above) or from any organism containing appropriate functional homologues.
• useful homologues include those derived from S. cerevisiae (RADl, 2, 3, 4, 10, 14, and 25) and humans (XPF, XPG, XPD, XPC, XPA, ERCC1, and XPB) (Sancar, Science 266:1954, 1994).
• the excised patch comprises an oligonucleotide extending 5 nucleotides from the 3 ' end of the lesion and 24 nucleotides from the 5' end of the lesion.
• Aboussekhra et al. disclose a reconstituted in vi tro system for nucleotide excision repair using purified components derived from human cells.
• Heteroduplexes formed between patients' DNA and wild-type DNA according to the present invention may be chemically modified by treatment with osmium tetroxide (for mispaired thymidines) and hydroxylamine (for mispaired cytosines) , using procedures that are well known in the art (see, e.g., Grompe, Nature Genetics 5:111, 1993; and Saleeba et al., Meth. Enzymol . 217:288, 1993).
• the chemically modified DNA is contacted with excision repair proteins (as described above) .
• the hydroxylamine- or osmium-modified bases are recognized as damaged bases in need of repair, one of the DNA strands is selectively cleaved, and the product is a gapped heteroduplex as above.
• Resolvases are enzymes that catalyze the resolution of branched DNA intermediates that form during recombination events (including Holliday structures, cruciforms, and loops) via recognition of bends, kinks, or DNA deviations (Youil et al., Proc. Natl . Acad. Sci . USA 92:87, 1995) .
• Endonuclease VII derived from bacteriophage T4 (T4E7) recognizes mismatch regions of from one to about 50 bases and produces double-stranded breaks within six nucleotides from the 3 ' border of the mismatch region.
• T4E7 may be isolated from, e.g., a recombinant E.
• T7E1 Endonuclease I of bacteriophage T7 (T7E1) , which can be isolated using a polyhistidine purification tag sequence (Mashal et al., Nature Genetics 9:177, 1995) .
• heteroduplexes formed between patients' DNA and wild-type DNA as described above are incubated in a 50 ⁇ l reaction with 100-3000 units of T4E7 for 1 hour at 37°C.
• immobilized DNA from a patient is hybridized to wild-type DNA to form mismatch regions and then treated with mismatch repair proteins, excision repair proteins, resolvases, chemical 15 modification and cleavage reagents, or combinations of such agents, to introduce single- or double-stranded breaks at some predetermined location relative to the site of the mismatch regions.
• the introduction of single- stranded breaks at predetermined locations on one or both sides of a mismatch region causes the selective excision of a single-stranded fragment covering the mismatch region.
• the resulting structure is a gapped heteroduplex in which
• the gap may be from about 5 to about 2000 bases in length, depending on the mismatch recognition system used.
• the heteroduplexes 30 are incubated with an appropriate DNA polymerase enzyme in the presence of dideoxynucleotides.
• Suitable enzymes for use in this step include without limitation DNA polymerase
• - 35 be capable of accurate DNA synthesis using the gapped heteroduplex as a substrate.
• the sequence obtained using this method will correspond to the wild-type strand and not to the patient's DNA in which the mutation is sought. This result is easily accomodated by a second round of sequencing, with or without prior amplification of the relevant DNA region.
• the sequence of the mutation is determined using as a template the patient's unmodified DNA in conjunction with sequencing primers derived from the sequence determined in the first round.
• the hybrids formed between the wild-type DNA and the patient's DNA are then dissociated by denaturation, and the wild-type DNA and any cleavage products of the target DNA are removed by washing.
• the immobilized remaining target DNA is then ligated to a synthetic single- stranded oligonucleotide of predetermined sequence, designated a "ligation oligonucleotide", that serves as a primer for enzymatic DNA sequencing.
• the oligonucleotide may be from about 15 to about 25 nucleotides in length.
• a preferred ligation oligonucleotide has the sequence 5'- CAGTAGTACAACTGACCCTTTTGGGACCGC-3 ' . Ligation is achieved using, e.g., RNA ligase (Pharmacia Biotech, Uppsala, Sweden) .
• a typical ligation reaction is performed at 37°C for 15 min in a 20 ⁇ l reaction containing 50mM Tris-HCl, pH 7.5, lOmM MgCl 2 , 20mM dithiothreitol, ImM ATP, 100 ⁇ g/ l bovine serum albumin, at least 1 ⁇ g immobilized target DNA, a 10-fold molar excess of the ligation oligonucleotide, and 0.1-5.0 units/ml T4 RNA ligase. Following the ligation, unligated oligonucleotides are removed by washing. The sequence of DNA immediately adjacent to the ligated oligonucleotide is then determined by any method known in the art.
• enzymatic sequencing is performed according to the dideoxy Sanger technique, using as a sequencing primer a second oligonucleotide of predetermined sequence that is complementary to the ligation oligonucleotide (Sanger et al., Proc . Natl . Acad. Sci . USA 74:5463, 1977).
• Each microsequencing reaction is then resolved by techniques well-known in the art, including without limitation gel electrophoresis, and the sequence is determined.
• an oligonucleotide complementary to the ligated oligonucleotide is used to prime DNA synthesis using DNA polymerase I in the presence of all four nucleoside triphosphates.
• the newly synthesized strand is then analyzed using hybridization to oligonucleotide arrays as described in Pease et al., Proc. Natl . Acad. Sci . USA 91:5022, 1994.
• Identification of a sequence alteration according to the present invention is preferably achieved in a single round of mismatch recognition and cleavage, oligonucleotide ligation, and D ⁇ A sequencing. This occurs when the ligated oligonucleotide becomes covalently attached to a) the immobilized truncated target D ⁇ A that contains the alteration b) within 10-500 bp of either boundary of the mismatch region. If either of these conditions is not fulfilled, further rounds of sequencing may be required to localize and identify the sequence alteration. It will be understood by those of ordinary skill in the art that sequencing primers for one or more further rounds of sequencing will be dictated by the sequence obtained in the first round (either the same or complementary strands) .
• one or two sequencing rounds will reveal the divergence between a known wild-type sequence and that contained within the DNA of a particular patient (see below) .
• the methods of the present invention are particularly suitable for high-throughput analysis of DNA, i.e., the rapid and simultaneous processing of DNA samples derived from a large number of patients. Furthermore, in contrast to other methods for e novo mutation detection, the methods of the present invention are suitable for the simultaneous analysis of a large number of genetic loci in a single reaction; this is designated "multiplex" analysis. Therefore, for any one sample or for a multiplicity of samples, the present invention allows the analysis of both intragenic loci (several regions within a single gene) and intergenic loci (several regions within different genes) in a single reaction mixture.
• the manipulations involved in practicing the methods of the present invention lend themselves to automation, e.g., using multiwell microtiter dishes as a solid support or as a receptacle for, e.g., beads; robotics to perform sequential incubations and washes; and, finally, automated sequencing using commercially available automated DNA sequencers. It is contemplated that, in a clinical context, 500 patient DNA samples can be analyzed within 1-2 days in a cost-effective manner.
• the methods of the present invention are also suitable for positional cloning of unknown genes that cause pathological conditions or other detectable phenotypes in any organism.
• "Positional cloning" as used herein denotes a process by which a previously unknown disease-causing gene is localized and identified. For example, identification of multiplex families in which several members exhibit signs of a genetically-based syndrome often occurs even when the particular gene responsible for the syndrome has not been identified.
• the search for the unknown gene involves one or more of the following time- and labor-intensive steps: 1) cytogenetic localization of the gene to a relatively large segment of a particular chromosome; 2) assembly of overlapping cosmid or PI clones that collectively cover several hundred thousand nucleotides corresponding to the identified chromosomal region; 3) sequencing the clones; and 4) transcript mapping to identify expressed protein-encoding regions of the gene.
• the present invention offers an alternative, cost-effective method for localizing a disease-causing gene.
• DNA from affected individuals is hybridized with normal DNA as described above to form mismatch regions at the site of the mutation.
• large regions of DNA corresponding to the chromosomal location are amplified from the patient's genomic DNA prior to inclusion in the hybridization reaction.
• the hybrids are then treated by any of the methods described above so that mismatch regions are recognized and cleaved, forming gapped heteroduplexes across the mismatch region. Finally, the sequence in the vicinity of the mismatch region is determined.
• determination of even a short sequence in the vicinity of the mismatch facilitates definitive identification of the disease-causing gene.
• the short sequence that is determined in the first round of sequencing can be used to design oligonucleotide probes for use in screening genomic or cDNA libraries.
• Buccal cells were collected on a sterile cytology brush (Scientific Products) or female dacron swab (Medical Packaging Corp.) by twirling the brush or swab on the inner cheek for 30 seconds.
• DNA was prepared as follows, immediately or after storage at room temperature or at 4°C.
• the brush or swab was immersed in 600 ⁇ l of 50mM NaOH contained in a polypropylene microcentrifuge tube and vortexed. The tube, still containing the brush or swab, was heated at 95°C for 5 min, after which the brush or swab was carefully removed.
• the solution containing DNA was then neutralized with 60 ⁇ l of 1M Tris, pH 8.0, and vortexed again (Mayall et al., J.Med. Genet . 27:658, 1990) .
• the DNA was stored at 4°C.
• DNA from patients with CF was amplified by PCR in a Perkin-Elmer Cetus 9600 Thermocycler. Five primer sets were used to simultaneously amplify relevant regions of exons 4, 10, 20, and 21 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene (Richards et al., Hum. Mol . Gen . 2:159, 1993) .
• CFTR cystic fibrosis transmembrane conductance regulator
• the 50 ⁇ l PCR reaction mix contained the following components: 0.2-1 ⁇ g CF patient DNA, lOmM Tris pH 8.3, 50mM KCl, 1.5mM MgCl 2 , 0.01% (w/v) gelatin, 200 ⁇ M of each deoxynucleotide triphosphate, 0.4 ⁇ M of each amplification primer, and 2.5 units of Taq polymerase.
• An initial denaturation was performed by incubation at 94°C for 20 seconds, followed by 28 cycles of amplification, each consisting of 10 seconds at 94°C, 10 seconds at 55°C, 10 seconds at 74°C, and a final soak at 74°C for 5 min.
• 8 ⁇ l of the PCR products were electrophoresed in a 2% agarose gel to verify the presence of all five products.
• the amplification reactions described above are performed in the present of biotinylated primers.
• the biotinylated products are then incubated with Dynabeads®M-280
• DNA is prepared from blood or buccal cells of healthy individuals as described in Example 1.
• a representative "wild-type" DNA sample is prepared by combining and thoroughly mixing DNA samples derived from 10-200 individuals.
• Hybridizations are carried out in microtiter dishes containing bead-immobilized DNA prepared as in Example ID above.
• the hybridization solution contains approximately 500 ⁇ g/ml wild-type DNA (prepared as in Example 2A above) and approximately 50 ⁇ g/ml amplified immobilized target DNA (prepared as in Example 1) in lOmM Tris HC1 pH 7.5 - 650mM NaCl.
• the reaction mixtures are heated at 90°C for 3 minutes, after which hybridizations are allowed to proceed for 1 hour at 65°C.
• the hybridization solution is then removed and the beads are washed three times in O.lx SSC at 65°C.
• the beads containing DNA:DNA hybrids prepared as described above are treated so that free ends become blocked and no longer accessible to modification by, e.g., RNA ligase.
• the wells are incubated in 100 ⁇ l of a solution containing 0.4M potassium cacodylate, 50 mM Tris HC1, pH 6.9, 4 mM dithiothreitol, 1 mM CoCl 2 , 2mM ddGTP, 500 ⁇ g/ml bovine serum albumin, and 2 units of terminal transferase for 15 minutes at 37°C.
• Example 3 Mismatch recognition, cleavage, and sequencing
• Termination mix contains 8 ⁇ M of a single ddNTP (i.e., ddGTP, ddATP, ddTTP, or ddCTP) and 80 ⁇ M of all four dNTPs, one of which is labelled with a radioactive or fluorescent label.
• ddNTP i.e., ddGTP, ddATP, ddTTP, or ddCTP
• 10X T4 polymerase buffer is added, and the reaction is allowed to proceed for 5 minutes at 37°C.
• the reaction mix is removed and the beads are washed three times with 100 ⁇ l TE (10 mM Tris-HCl, pH 7.5, 1 mM EDTA) . Finally, the beads are resuspended in 6 ⁇ l gel loading buffer (95% formamide, 20 mM EDTA, 0.05% bromphenol blue, 0.05% Xylene Cyanol FF) . The buffer is removed from the beads and loaded on a 6% denaturing polyacrylamide DNA sequencing gel.
• T4 endonuclease 7 is obtained as described in Kosak et al., Eur. J. Biochem . 194:779,1990. After the incubation, the beads are heated to 90°C for three minutes, after which the solution is quickly removed and replaced with prewarmed TE, and the beads are washed three times with TE at room temperature. This procedure effectively denatures DNA:DNA hybrids and removes wild-type DNA strands.
• microtiter wells prepared as described in Examples 1 and 2 above are treated sequentially with hydroxylamine and osmium tetroxide.
• Hydroxylamine obtained from Aldrich, Milwaukee, Wl
• distilled water distilled water
• the pH is adjusted to 6.0 with diethylamine (Aldrich) so that the final concentration is about 2.5 M.
• 200 ⁇ l of the solution are incubated within the wells at 37°C for 2 hours.
• the reaction is stopped by replacing the hydroxylamine solution with an ice-cold solution containing 0.3 M sodium acetate, O.lmM EDTA, pH5.2-, and 25 ⁇ g/ml yeast tRNA (Sigma, St. Louis, MO) .
• the wells are then washed in an ice-cold solution of lOmM Tris-HCl, pH 7.7, ImM EDTA prior to osmium tetroxide treatment.
• Osmium tetroxide (Aldrich) is dissolved in lOmM Tris-HCl, pH 7.7, ImM EDTA, and 1.5% (v/v) pyridine to a concentration of 4% (w/v) .
• the wells are incubated with this solution for 2 hours at 37°C.
• the reaction is stopped by replacing the osmium tetroxide solution with an ice-cold solution containing 0.3 M sodium acetate, 0.ImM EDTA, pH5.2, and 25 ⁇ g/ml yeast tRNA.
• Immobilized DNAs prepared as described in Examples 1 and 2 above and subjected to mismatch recognition and cleavage are incubated with a single- stranded oligonucleotide having the sequence 5 ' - CAGTAGTACAACTGACCCTTTTGGGACCGC-3 ' under conditions in which efficient ligation of the oligonucleotide to free 5 ' ends is achieved.
• oligonucleotide and immobilized DNA are combined in a solution containing 50 mM Tris HCl, pH 7.5, 10 mM MgCl 2 , 20 mM dithiothreitol, 1 mM ATP, and 100 ⁇ g/ml bovine serum albumin, after which RNA ligase (Pharmacia Biotech, Uppsala, Sweden) is added to the solution to achieve a final enzyme concentration of 0.1-5.0 U/ml. The reaction is allowed to proceed at 37°C for 15 min. Following the ligation reaction, the solution is removed, and the wells are washed with distilled water.
• RNA ligase Pharmacia Biotech, Uppsala, Sweden
• a multiplex family in which a genetic disease is expressed is identified using standard clinical indicators. DNA samples are obtained from affected and unaffected individuals as described in Example 1 above; if by patterns of transmission the disease appears to be an autosomal recessive syndrome, DNA samples are obtained from those individuals presumptively heterozygous for the disease gene.
• all DNA samples are subjected to mismatch analysis by hybridization to wild- type DNA as described in Example 2 above.
• the hybrids are then treated with T4 endonuclease 7 as described in Example 3B above.
• an oligonucleotide having the sequence 5'-CAGTAGTACAACTGACCCTTTTGGGACCGC-3 ' is ligated to the cleaved hybrids using RNA ligase, and the products are subjected to enzymatic DNA sequencing as described in Example 5 above.
• sequences obtained from unaffected, affected, and presumptively heterozygous family members are compared with each other and with available sequence databases, using, for example, Sequencher (Gene Codes, Ann Arbor, MI) and Assembly Lign (Kodak, New Haven, CT)
• Sequencher Gene Codes, Ann Arbor, MI
• Assembly Lign Kodak, New Haven, CT
• the sequences are also serve as the basis for design of oligonucleotide probes, which are chemically synthesized and used to probe human genomic DNA libraries.

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