WO2010070366A1

WO2010070366A1 - Cytometric method for the comparative analysis of the length of pcr products and uses of this method

Info

Publication number: WO2010070366A1
Application number: PCT/HU2009/000104
Authority: WO
Inventors: Gábor SZABÓ; László IMRE
Original assignee: Debreceni Egyetem
Priority date: 2008-12-15
Filing date: 2009-12-11
Publication date: 2010-06-24
Also published as: WO2010070366A4

Abstract

The present invention relates to a method for the comparative analysis of the length of PCR products by cytometer. The invention also relates to the various uses of said method, especially detecting genetic alterations by cytometric analysis of the length of PCR products. Different DNA size changes or sequence alterations, i.e. triplet-expansions, insertions, deletions, microsatellite polymorphisms, or SNPs (single nucleotide polymorphisms), mutations can be detected with the method of the invention. Therefore, this method is suitable for diagnosing or screening the diseases and unique characteristics associated with these genetic traits and for screening the genetic traits which are important from agricultural points of view. The present invention also relates to the kits for carrying out the method described above.

Description

Cytometric method for the comparative analysis of the length of PCR products and uses of this method

Field of the invention

The present invention relates to a method for the comparative analysis of the length of PCR products by cytometer. The invention also relates to the various uses of said method, especially detecting genetic alterations by cytometric analysis of the length of PCR products. Different DNA size changes or sequence alterations, i.e. triplet-expansions, insertions, deletions, microsatellite polymorphisms, or SNPs (single nucleotide polymorphisms), mutations can be detected with the method of the invention, detection of which by a cytometer has not always been a simply executable possibility. Therefore, this method is suitable for diagnosing or screening the diseases and unique characteristics associated with these genetic traits and for screening the genetic traits which are important from agricultural points of view.

The present invention also relates to the kits for carrying out the method described above. Background of the invention

It is known, that several human, animal, plant diseases are caused by the alterations in the genomic DNA. Many different alterations may occur in the nucleotide sequence of the DNA: SNP, which is the variation within the normal genotype population, mutation, deletion, insertion, triplet-expansion, rearrangement, etc. Among these detection of the triplet-expansion alteration and the SNPs/mutations belong to the methodically highest category. First, the background of the genetic analysis of the triplet-expansion diseases, then the diagnostic aspects of the SNP/point mutation are outlined.

It is known that expansion of one or more nucleotide triplets occurring in the genomic DNA are responsible for some diseases (see Table 1). For example the disease named Huntington-disease (Huntington chorea) is caused by the repetition of the CAG triplet localized in exon 1 of the Huntington gene (ITl 5). For diagnosing the disease, the CAG-repetitions are amplified by PCR (polymerase chain reaction) and the PCR products are analyzed in a known way by agarose or polyacrylamide gel electrophoresis (PAGE) [Russell et al.: CHn. Chem. 49(10):1726-1732 (2003); M. Muglia et al.: Clin. Chem. 42(10):1601-3 (1996); JM. Milunsky et al.: Clin. Genet. 64(l):70-3 (2003)], with Southern blot [Russell et al.: Clin. Chem. 49(10): 1726- 1732 (2003)], with capillary gel electrophoresis [Russell et al.: Clin. Chem. 49(10): 1726- 1732 (2003); M. FaIk et al.: Genet. Test. 10(2):85-97 (2006); T. Tόth et al.: Clin. Chem. 43(12):2422- 3 (1997)], or with sequencing. A disadvantage of these methods is that the small size (100-200 bp) PCR products can only be separated by the use of very concentrated gel and not absolutely reliably which increases the costs and the possibility of automation; and this way the possibility of the high-throughput investigation - except the more expensive capillary gel electrophoresis - cannot be realized. Case by case the investigations need longer time, for example the Southern blot requests many days.

Table 1

Type of Healthy Intermediary Pathogenic

Disease repetition length (n) length (n) length (n)

Fragile XA (FRAXA) (CGG)n 6-52 59-230 230-2000

Fragile XE (FRAXE) (CCG)n 4-39 31-61 200-900

Fragile XF(FRAXF) (CGG)n 7-40 unknown 306-1008

FRAl 6 A (CCG)n 16-49 unknown 1000-1900

Jacobsen Syndrome (FRAl IB) (CGC)n 11 80 100-1000

Kennedy Syndrome (SMBA) (CAG)n 14-32 unknown 40-55

80-1000

Myotonic Dstrophy (DM) (CTG)n 5-37 50-80 2000-3000

Huntington disease (HD) (CAG)n 10-34 36-39 40-121

Spinocerebellar ataxy 1 (SCAl) (CAG)n 6-39 unknown 40-81

Spinocerebellar ataxy 2 (SCA2) (CAG)n 14-31 unknown 34-59

Spinocerebellar ataxy 3 (SCA3)/Machado

Joseph disease (MJD) (CAG)n 13-44 unknown 60-84

Spinocerebellar ataxy 6 (SCA6) (CAG)n 4-18 unknown 21-28

Spinocerebellar ataxy 7 (SCA7) (CAG)n 7-17 28-35 38-130

Haw River syndrome (HRS; also DRPLA)) (CAG)n 7-25 unknown 49-75

Friedreich ataxy (FRDA) (GAA)n 6-29 34-40 200-900

A genetic abnormality or susceptibility to a disease may be caused by a point mutation (SNP) in the gene in question. It is known, for example, that the point mutations in the BRCAl are responsible in significant degree for the susceptibility for breast cancer [Antoniou et al: The American Journal of Human Genetics 72 1117-30 (2003); Narod S.A. - Foulkes W.D.: Nature Reviews Cancer 4 665-667 (2004)]. Generally used methods for the detection of these point mutations are gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), single-stranded conformation polymorphism (SSCP), heteroduplex analysis (HET), RNase A enzymatic cleavage, chemical cleavage method (CCM), enzymatic mismatch cleavage (EMC), cleavase fragment length polymorphism (CFLP), mutation detection by mismatch binding protein, protein translation test (PTT), allele specific oligonucleotide (ASO) hybridization on DNA-cbip, allele specific nucleotide insertion, allele specific primer extension, allele specific nucleotide ligation, allele specific PCR. In addition microarrays (chip) and qPCR methods are also known, by means of which the genetic characteristics, abnormalities mentioned above can be detected generally efficiently, but with significant costs. Moreover, with the exception of the more expensive qPCR, they are less suitable for the high-throughput measurements. Part of these methods is based on hybridization techniques.

It is known, that flow cytometry allows high speed sample analysis. The basis of the so- called ,,multiplex microbead assay" (MMA) methods developed for the flow cytometer is that reporter molecules are attached to the surface of microbeads of 2-10 μm diameter, labelled with fluorescent dye, which are able to recognize and bind proteins, nucleic acids or other molecules in biological samples [J. Pataki et al.: Cytometry A 68(l):45-52 (2005); L. Szekvδlgyi et al.: Cytometry A 69(10):1086-91 (2006); E. Hegedύs et al.: Cytometry A 73A: 238-245 (2008)]. The beads can be identified in flow cytometer, based on their size or fluorescence intensity. With the mixture of suitably chosen beads, large numbers of simultaneous measurements are possible, based on protein- or nucleic acid interactions. The material of the beads available on the market may include two or more fluorescent dyes. This way for example use of two different fluorescent dyes in 16-16 different concentrations results in 256 conveniently separable type of beads, to each of which different ligand binding reagent can be added, which allows 256 different measurements. Because of this, the MMA assay can be extremely useful for screening genetic abnormalities, and can be a cost effective, reliable alternative of the other detection methods. Furthermore, this method can be advantageous in all cases, when large number of samples must be analyzed in a very short period of time, in a cost effective way, or if we want to measure simultaneously multiple genetic characteristics mentioned above (multiplex measurement), even in a high-throughput way.

Methods and kits are known from the WO 2006/113590 international publication document for the detection of genetic abnormalities, primarily deletions, insertions and single- stranded lesions, in which heteroduplex analysis methods are used, and heteroduplexes attached to the avidin-coated microbeads are measured with flow-cytometry. However, the heteroduplex analysis method is unsuitable for the detection of triplet expansions. Detection of SNPs with flow-cytometry heteroduplex analysis is also impossible, and generally, it can be used very elaborately, and it is less successful, therefore it was not introduced into the clinical diagnostics.

It is also known, that the melting point, the so-called Tm temperature of the DNAstrands, DNA-fragments, PCR products of different length is different. The Tm point is the temperature, where the double-stranded DNA molecule becomes denatured, becomes single stranded in 50 %. This temperature can be reduced with chemical reagents. Objective of the invention

The purpose of the invention is to elaborate a method for the comparative analysis of the length of PCR products prepared from at least two DNA samples by means of which the size and sequence differences of the DNA from the respective DNA region can be detected cost- effectively optionally with a multiplex procedure by a cytometer, preferable fiow-cytometer, by detecting the size differences of the PCR products amplified by the suitable primers. Another purpose is to develop a conveniently executable method applicable in a screening procedure, and this way allowing further broadening the application possibilities of the fiow-cytometer. Summary of the invention

In the course of our investigations it has been found that, if the Tm analysis carried out by formamidee treatment is connected to flow-cytometry, a new method is obtained which allows for the simple, cost-effective, multiplex screening of the genetic alteration in a large population by the separation of the PCR products with different lenght. In the method of the invention the detachment of one strand of a double-stranded PCR product attached to a solid phase is measured in the course of denaturation with a cytometer. Contrary to the known methods based on hybridization, the method of the invention is based on the analysis of the denaturation of the DNA which is used in fewer methods than the widely used hybridization.

In the course of our investigations it was discovered, that the method of the invention for the separation of PCR products of different length is suitable for the detection of any kind of DNA sequence differences mentioned above, for example triplet-repetitions, deletions, insertions and microsatellite polymorphisms. This can be carried out by detecting the size-differences of the PCR products obtained by the amplification with the suitable primers. This way for example the method of the invention can be well used for the detection of the CAG-repetitions causing the Huntington-disease, and this way for the diagnosing the disease.

Moreover, it has been found that the method of the invention for the separation of PCR products of different length is suitable even for the detection of alterations not affecting the length of the DNA stretch, for example point mutations (SNPs) by using suitable primers of different length. Thus, for example, the method of the invention is extremely useful for the detection of one of the point mutations of the BRCAl gene, namely the 5382insC mutation. The great advantage of this method, that it can be adapted for screening purposes. The use of the primers of different length for this purpose is known, but its association with the fiow-cytometric Tm point analysis can be considered new.

Based on the difference in the Tm point point mutations can also be detected with realtime qPCR methods, by using primers hybridizing to the normal or altered genomic sequence. These procedures are based on the continuous measurement of the quantity of the PCR products produced in the reaction in qPCR equipments, therefore the discovery, that similar information can be obtained by the flow-cytometric measurement of the sample amplified by the use of the primer pair bordering the sequence to be investigated, is a new and surprising discovery. The applicability of the flow-cytometry for the detection of numerous genetic alterations is mentioned in the WO 2006/113590 international publication document mentioned above, but the method described there could not be used successfully for the detection of point mutations, SNPs, or for the detection of triplet expansions, despite all our efforts. Compared to the enzymatic and chemical methods described there the flow-cytometric approach based on the Tm point differences could only theoretically be considered suitable, its practicability and acceptable sensitivity could seem impossible even for someone skilled in the art. The invention is a new combination of the known methods, which is simply executable and gives unexpected results. In the method of the invention, detachment of one strand of the double-stranded PCR product attached to the solid phase is measured in the course of the denaturation. This approach is used in significantly fewer methods, than the opposite, hybridization based methods, for example the currently more and more widespread, but in the routine diagnostics still not used DNA chip technology, or other hybridization methods. The flow-cytometric method based on the Tm point difference of the DNA or on denaturation has not been described yet in the literature.

Based on the above, one aspect of the invention relates to a method for the comparative analysis of the length of the PCR products obtained from two or more DNA samples, on the basis of the difference of their Tm points comprising the following steps:

(i) PCR products are prepared by the amplification of the section of interest of the DNA samples in parallel reactions which are optionally labelled fluorescently; (ii) the obtained PCR products are attached to microbeads;

(iii) the samples containing double-stranded DNA of different length attached to the microbeads are divided in two parts and heat-treated at a given temperature in the solutions of predetermined concentration of a Tm point decreasing agent, when, during denaturation, one strand of the double-stranded DNA dissociates from the microbead in a degree depending on its size; then the microbeads are washed; (iv) the DNA attached to the microbeads is fluorescently labelled with a DNA dye, if it was not labelled in step (i);

(v) the fluorescence of the microbeads obtained this way is measured and the difference between the intensity changes of the two samples is evaluated. In a preferred embodiment the method relates to the comparative cytometric analysis of the length of the PCR product of a DNA sample compared to the PCR product amplified from a control DNA sample comprising the following steps:

(i) PCR product is prepared from the sample by the amplification of the DNA section of interest using a primer pair where one of the primer is labelled with a ligand and the other primer is optionally labelled at least with one fluorescent molecule;

(ii) the obtained PCR product is attached to microbeads coated with the molecules binding the ligand,

(iii) the samples containing double-stranded DNA of different length attached to the microbeads are divided in two parts and heat-treated at a given temperature in the solutions of predetermined concentration of a Tm point decreasing agent, where said concentrations are determined as the extreme values of a concentration series, where the unlabelled strand of the PCR product shorter than the control or identical with it gradually dissociates from the surface of the microbead by increasing the concentration of the agent, while the unlabelled strand of the PCR product longer than the control substantially does not dissociate; then the microbeads are washed;

(iv) the DNA attached to the microbeads is fluorescently labelled with a DNA dye, if it was not labelled in step (i);

(v) steps (i) - (iv) are also performed with the control DNA sample;

(vi) the fluorescence of the microbeads obtained this way is measured with a cytometer and the intensity of the obtained signals is evaluated in such a way that the fluorescence intensity of the PCR product treated with the more concentrated solution of the Tm point decreasing agent is compared to the fluorescence intensity of the PCR product treated with the less concentrated solution of said agent in case of the control and of the investigated sample and the difference between the intensity changes of the two samples is evaluated.

A second aspect of the invention relates to a method for the detection of the size differences of the DNAs by cytometer with the analysis of the length of PCR products comprising the following steps:

(i) DNA is purified from a biological sample;

(ii) the section of interest of said DNA carrying the difference is amplified by PCR by using a primer pair where one of the primer is labelled with a ligand and the other primer is optionally labelled at least with one fluorescent molecule; (iii) the obtained PCR products are attached to microbeads coated with the molecules binding the ligand,

(iv) the samples containing double-stranded DNA attached to the microbeads are divided in two parts and heat-treated at a given temperature in the solutions of predetermined concentration of a Tm point decreasing agent, where said concentrations are determined as the extreme values of a concentration series where the unlabelled strand of the PCR product of the negative or the positive control, whichever is shorter, gradually dissociates from the surface of the microbead by increasing the concentration, while the unlabelled strand of the PCR product of the negative or the positive control, whichever is longer, substantially does not dissociate; then the microbeads are washed; (v) the DNA attached to the microbeads is fluorescently labelled, if it was not labelled in step (ii);

(vi) the fluorescence of the microbeads obtained this way is measured with a cytometer and the intensity of the obtained signals is compared to the fluorescence intensities obtained with the normal negative control sample as well as with the positive control sample carrying the known difference.

A third aspect of the invention is a method for the detection of the sequence differences, especially point mutations of the DNA with the analysis of the length of the PCR products by cytometer comprising the following steps:

(i) DNA is purified from a biological sample;

(ii) the section of interest of said DNA carrying the point mutation is amplified by allele-specific PCR reaction by using three primers where the short forward primer specific of the wild type and the longer forward primer carrying GC-rich Tag are optionally labelled at least with one fluorescent molecule, while the common reverse primer is labelled with a ligand; (iii) the obtained PCR products are attached to microbeads coated with the molecules binding the ligand,

(iv) the samples containing double-stranded DNA attached to the microbeads are divided in two parts and heat-treated at a given temperature in the solutions of predetermined concentration of a Tm point decreasing agent, where said concentrations are determined as the extreme values of a concentration series where the shorter unlabelled strand of the PCR product carrying no mutation gradually dissociates from the surface of the microbead by increasing the concentration, while the longer unlabelled strand of the PCR product carrying mutation substantially does not dissociate; then the microbeads are washed; (v) the DNA attached to the microbeads is fluorescently labelled, if it was not labelled in step (ii);

(vi) the fluorescence of the microbeads obtained this way is measured with a cytometer and the intensity of the obtained signals is compared to the fluorescence intensities obtained with the negative control sample not carrying the mutation of interest as well as with the positive control sample carrying said mutation.

The method of the invention can be a simple diagnostic method for the detection of genetic abnormalities as an alternative of the methods mentioned in the introduction or for the confirmation of the results obtained with these methods or for fast and cost-efficient prescreening, since it does not require expensive agents and equipment, further, it can widely be used and allows for the possibility of performing multiplex investigations and screenings. Detailed description of the invention

With the method of the invention PCR products of different lengths can be distinguished, in such a way that the fluorescence intensity distribution of the microbeads carrying the PCR products is measured with a Tm point decreasing agent (i.e. formamide) with preset concentration, after heat treatment, with a cytometer. In one variation of the methods of the invention, the fluorescent marker can be introduced in the course of the amplification. In this case PCR products of different length are prepared, labelled with a fluorescent molecule and ligand providing the attachment (i.e. biotin), which in separate reaction are attached to the microbeads coated with a molecule (i.e. streptavidin) recognizing and binding the ligand, and are treated in a predetermined concentration solution of a Tm point decreasing agent for a few minutes, at a given temperature. Following heat treatment the fluorescent molecule-carrying strand of the shorter PCR product dissociates from the microbead, therefore the fluorescence of the microbead significantly decreases, close to the background fluorescence value, while the fluorescent molecule-carrying strand of the longer PCR product does not dissociate and the microbead continues to emit fluorescent light. For this purpose, the temperature used for the heat treatment should be between the Tm points of the two PCR products of different length. For example the Tm point of the DNA is reduced by formamide, therefore lower temperature, in the method of the invention even 40 °C is sufficient for the heat treatment, which does not damage the bond between the ligand and the ligand binding molecule (i.e. biotin-streptavidin), or the connection between the ligand binding molecule (i.e. streptavidin) and the microbead, or even the material of the microbead. The change of the fluorescence because of heat treatment can be detected by the measurement of the microbeads carrying the PCR products of two different lengths, even in a high-throughput and multiplex way. Detection is carried out preferably with a flow-cytometer, but scanning laser microscopy can also be used.

In an alternative method the double-stranded DNA attached to the microbeads is labelled with a DNA dye after heat treatment, preferably with an intercalating dye, which does not stain the single-stranded DNA. The DNA can be labelled with a dye, whose fluorescence changes in the course of the DNA becoming single-stranded.

The "predetermined concentrations of the agent reducing the Tm point" means the extreme values of such a concentration series of the agent reducing the Tm point, which is separately determined for each measurement in advance at the given temperature. At one extreme value the fluorescent molecule-carrying strand of the short PCR product does not dissociate from the microbeads, its average fluorescent intensity is considered to be 100%, while at the other extreme value the fluorescent molecule-carrying strand of the short PCR product significantly dissociates from the microbeads.

In the description the expression "the given temperature" means, that the temperature used for the heat treatment is between the reduced Tm point of the two different length PCR products.

When genetic abnormalities are investigated, the formamide concentration is adjusted to the DNA sample originating from the normal, healthy sample, arbitrarily at 40 °C, where for example in case of triplet-expansion the two strands of the normal DNA separate, but the defective DNA does not separate yet, but in case of a deletion the two strands of the normal DNA do not separate, but the defective DNA already separates at this concentration.

Preferably the method can be executed in a multiplex way too, when two different microbeads are used, or the two different PCR products are labelled with different fluorescent dyes, therefore these can be measured simultaneously, and/or in a high-throughput way, if an automated equipment is used (FACSarray), with which 96 or 384 wells' plates can also be measured. In case of a multiplex measurement, depending on the number of the different microbeads, the number of the examinable genetic characters increases, since the flow-cytometer can separate these beads, can separately measure the intensity of their fluorescence. There is a possibility of using microbeads of different size or different color, and the dyes used for labeling the PCR products can also be different, further increasing the number of measurable genetic characters. The procedure can be executed even on a microscopic slide, for example on polystyrene or glass slides. In this case, the fluorescence of the microbeads is measured with scanning laser microscopy.

In the method of the invention amplification of the DNA is carried out by polymerase chain reaction (PCR) (US Patent No. 4,683,202). It is obvious for someone skilled in the art, that the reaction conditions must always be optimized for the actual primers.

In the method of the invention the DNA section of interest is amplified with the available, or designed primers. Extended mutation-specific primer is also used for the detection of point- mutation. The necessary primers can be designed and prepared without any difficulties by someone skilled in the art.

In order to execute the method of the invention preliminary determination of the concentration of the Tm point decreasing agent is necessary at the actual temperature (this was chosen for 40 °C, but can be a different temperature too) in each case, in order to adjust the melting point of the control DNA, the Tm point. Someone skilled in the art without any problem can carry this out.

In the method of the invention the sample means primarily biological sample, i.e. a sample containing animal, plant or human genomic DNA, for example peripheral blood, isolated lymphocytes, or the cells of any other animal, plant or human tissue types.

In the method of the invention the DNA can be of any origin, i.e. prokaryotic, eukaryotic, especially animal, plant or human genomic or mitochondrial or chloroplast DNA, but the viral, i.e. the phage, or plasmid DNAs are also included here.

The agents decreasing the Tm point can be chemicals, which reduce the melting point of the DNA by destabilizing the hydrogen bridges between the complementary bases. These are for example the formamide, DMSO, carbamide and alcohol. In the method of the invention, preferably formamide is used.

The microbeads used in the method of the invention can be made for example from polystyrene, but beads made from any other chemical substances, with the size and material suitable for cytometric analysis, even so-called magnetic beads, made of ferromagnetic material, can also be used. The advantage of the polystyrene beads is that the multiplexity of the measurement can be increased not just by their sizes, but the beads may also contain different fluorescent dyes, or they can contain the same dye in different concentration. It is an advantageous characteristic of the magnetic beads, that in the washing steps the centrifugation time, and this way the washing time can also be shortened, since the beads can be conveniently and quickly sedimentated, and although the multiplexity in this case is not so broad as in case of the polystyrene beads, the possibility of using different size beads remains. In the methods of the invention, preferably polystyrene beads are used.

For the PCR reaction the primers are partly conjugated with ligands, partly labelled with fluorescent dyes. The microbeads used for binding the PCR products are coated by molecules recognizing and binding the ligands used for labeling the primers. Generally used for this purpose is the biotin-avidin system, where the molecule attached to the surface of the molecule can be any kind of avidin-derivative, i.e. streptavidin, extravidin or anti-biotin antibody (monoclonal or polyclonal). In addition to the biotin-avidin system any ligand-ligand binding system is suitable for executing the procedure, which can be built enzymatically or chemically into the primers, for example digoxigenin, and the molecule recognizing and binding it can be built into the microbeads, for example the anti-digoxigenin antibody. In the method of the invention, preferably the biotin-streptavidin system is used.

Any fluorescent dye can be used for the fluorescent staining of the primers, with which the nucleotides can be modified for their use in the PCR reaction. These are for example 6-FAM, Alexa Fluor, Cy3, Cy5, Cy5.5, TET, HEX, Fluorescein dT, Rhodamine Green-X, Rhodamine Red-X, their esters (manufacturer: IDT, Coralville, USA). In addition to these the so-called intercalating dyes suitable for staining double-stranded DNA (i.e. ethidium-bromide, propidium- iodide, Sybr Gold, etc.) can also be used for fluorescent labeling of the PCR products, which do not stain the single stranded DNA. Such dyes can also be applied, which, although they are able to stain the single-stranded DNA too, but their fluorescence is different, when they are attached to double-stranded or single-stranded DNA, or it changes, when the DNA becomes single- stranded (i.e. acridine orange, or the DAPI-stains binding into the minor groove (Hoechst)). In the method of the procedure, preferably the Cy3 and Cy5 stains are used.

Determination of the obtained fluorescent signal is carried out by cytometry, preferably by flow-cytometry, with the flow-cytometers generally used for this purpose like for example FACSarray, FACS Scan, FACS Calibur (manufacturer: Beckton Dickinson, Sweden). In another advantageous measurement method, when the method is executed on a microscopic slide, for example on polystyrene or glass slide, fluorescence of the samples is detected by scanning laser microscopy, for example with LSC (iCys laser scanning cytometer, manufacturer: CompuCyte Corp., Cambridge, MA, USA).

According to the invention evaluation of the fluorescent signals obtained is carried out by giving in % value that how many percent is the average fluorescence intensity of the sample treated with the more concentrated formamide solution of the average fluorescence intensity of the sample treated with the more diluted formamide solution, this is plotted practically in a bar diagram, and compared to the signal obtained from a predetermined positive and negative control. The control fluorescence value can be the average fluorescence intensity obtained in the course of the investigation of the PCR product obtained by the amplification of shorter DNA, or in case of genetic alteration the average fluorescence intensity obtained by the investigation of the PCR product obtained by the amplification of the predetermined DNA region obtained from the non-sick (negative control) or sick (positive control) subject.

One embodiment of the method of the invention is the detection of size-differences of a DNA sequence. The size-difference of the DNA can be for example triplet-expansion, deletion, insertion, recombination, repair mechanism or microsatellite polymorphism. The DNAsize difference is responsible in many cases for a genetic abnormality. For example, the cause of the Huntington-disease is the expansion of a base-triplet. A preferred embodiment of the method of the invention is the detection of the genetic abnormalities caused by the triplet-expansions; it is especially advantageous for the detection and screening of the Huntington disease.

In another preferred embodiment the size-difference of the DNA is not causing genetic abnormality. In this case the method of the invention may serve for example the characterization of the degree of immunological identity (HLA typing), or identification of a person based on microsatellite markers.

Another preferred embodiment of the invention is a method for the detection of triplet- expansions causing genetic abnormalities by the analysis of the length of PCR products with a cytometer comprising the following steps:

(i) DNA is purified from a biological sample;

(ii) the section of said DNA carrying the triplet-expansion of interest is amplified by a PCR reaction using a primer pair where one of the primers is labelled with biotin and the other primer is labelled at least with one fluorescent molecule; (iii) the obtained PCR products are attached to microbeads coated with streptavidin, (iv) the samples containing double-stranded DNA attached to the microbeads are divided in two parts and heat-treated at a given temperature in formamide solutions of predetermined concentration, where the formamide concentrations are determined as the extreme values of a concentration series where the fluorescently labelled strand of the PCR product identical with the DNA carrying no triplet-expansion or a strand shorter than that gradually dissociates from the surface of the microbead by increasing the concentration, while the fluorescently labelled strand of the PCR product longer than the DNA carrying no triplet- expansion substantially does not dissociate; then the microbeads are washed; (v) the fluorescence of the microbeads obtained this way is measured with a flow- cytometer and the intensity of the obtained signals is compared to the fluorescence intensities of the normal negative control sample as well as to those of the positive control sample carrying the known differences.

Another preferred embodiment of the method of the invention is the detection of the DNA sequence differences. This means primarily the detection of SNPs, preferably SNP markers associated with a disease. A preferred embodiment of the invention can be used for the detection and screening of the SNP in the BRCAl gene, responsible for the susceptibility for breast cancer, more preferably for the detection and screening of the 5382insC point-mutation of the BRCAl gene.

The method of the invention can also be used in the agriculture for the detection of already known SNPs, for the selection of a plant or animal characteristic associated to a point mutation, advantageous for the agriculture in the course of cultivation or breeding, this way the individuals carrying the variation of the given characteristic most advantageous for us can be selected from a large population.

The fourth aspect of the invention relates to the kit for executing the method, which, together with the necessary instructions includes two or more labelled primers suitable for the detection of the DNA-alterations listed above, or a dye for staining the DNA attached to the microbeads, the microbeads with the suitable coating, a Tm point decreasing agent, the adequate controls, the solutions necessary for the method in one or more containers.

The method of the invention can be summarized as follows. Until know, with the agarose- or polyacrylamide gel electrophoresis, capillary electrophoresis or Southern blot method used for the investigation of the PCR products of different size only few samples could be investigated simultaneously, and these required a longer time, but with the method of the invention simultaneous investigation of many samples can be realized in a short time, with low expenses. Furthermore, deriving from the measuring instrument or from the microbead technique used for the measurement, this method has the possibility of the multiplex investigation, allowing simultaneous screening of many diseases in larger populations. The method can be widely used, among others it is suitable for the detection of SNPs, for example as a flow- cytometric alternative of the method currently used in the clinical diagnostics for the SNP of the BRCAl gene correlating with the breast cancer, based on the SDS-PAGE analysis of the PCR products; as a flow-cytometric alternative of the of the agarose or polyacrylamide gel electrophoresis, capillary electrophoresis, or Southern blot methods used for diagnosing the triplet-expansion diseases, for example the Huntington-chorea, and it can be used for detecting in/del polymorphisms or microsatellite polymorphisms.

Another advantage of the method of the invention that it is cost-effective. Since the flow- cytometric equipment is already in use in most of the clinical laboratories, introduction of the method does not require specific investment, only the kits must be purchased, which include the adequate primers and standards. For example in case of a BRCA investigation the cost of the method of the invention is about 500 HUF/test, together with the cost of DNA purification, this is 50.000 HUF for 100 tests. At least 100 tests can be executed in a day, therefore calculated for 3 years, with partial use, at least 50.000 test can be carried out, the material cost of which is 25 million HUF; the full cost, calculating with the amortization of the flow-cytometer or the LSC, with the labor costs and with the profit is about 45 million HUF. This means that the full cost of a test is 54 million/50.000 = 900 HUF, i.e. about 6 USD. By calculating with lower use, the full cost of a test is calculated to be 9000 HUF, i.e. 60 USD. In case of direct sequencing, which is the most exact method for detecting point-mutation, the cost of an investigation for example at the University of Minnesota is 950-1200 USD, and compared to the method of the invention, it can be seen that the difference is very significant, about 15x. The cost of the methods based on direct sequencing in other ^■ clinical laboratories or private laboratories is similarly high; depending on the number of the mutations to be detected it is 300-3.000 USD. In Hungary, this sum is 25.000 HUF for a BRCA mutation, for the five most frequent mutations it is 90.000 HUF. The conventional screening procedures using methods not based on sequencing, focusing to some mutations, can be carried out 6-8 times cheaper than sequencing, but still significantly more expensively than the method of the invention. It is a European tendency that the number of genetic tests executed in the EU countries is increasing year by year, or the number of the clinical and private laboratories, which carry out genetic tests for diagnostic purposes, is also increasing [Ibaretta D. et al.: Nat. Biotechnol. 22(10): 1230-5(2004)]. Additionally the demand for these kinds of tests, for genetic screenings is constantly growing in the population, which requires the development of cost-effective, high-throughput multiplex detection methods, just like the method of the invention.

Moreover, the use is not limited exclusively to clinical diagnosing, or to human investigations. The method of the invention can also be used in the agriculture. The possibility of the high-throughput measurement and the multiplexity makes the method of the invention especially suitable for using in the agriculture. It is obvious for one skilled in the art, that the method of the invention requests individual adjustment in any of the concrete application fields, which includes selection and testing of the suitable primers. Description of the drawings

Figure 1: depicts the formamide concentration dependence of the dissociation of the PCR products amplified from the plasmids containing 27 CAG-repetitions (Cy3 labelled), and the PCR products amplified from the plasmids containing 51 CAG-repetitions (Cy5 labelled), at 40 ⁰C.

Figure 2: depicts the formamide concentration dependence of the dissociation of the PCR products amplified from the plasmids containing 27 CAG-repetitions (Cy5 labelled), and the PCR products amplified from the plasmids containing 51 CAG-repetitions (Cy3 labelled), at 40 °C.

Figure 3: depicts the formamide concentration dependence of the dissociation of the PCR products amplified from the plasmids containing 51 CAG-repetitions (Cy3 and Cy5 labelled), at 4O ⁰C.

Figure 4: depicts the formamide concentration dependence of the dissociation of the PCR products amplified from the plasmids containing 27 CAG-repetitions (Cy3 and Cy5 labelled), at 4O ⁰C.

Figure 5: depicts the average fluorescence intensity measured on the microbeads treated with 75 v% formamide solution, in percentage, compared to the sample treated with 65 v% formamide solution, in case of the PCR products amplified from the plasmids containing 27, 32, 39 and 51 CAG-repetitions (Cy5 labelled), by modeling the homozygote case.

Figure 6: depicts the average fluorescence intensity measured on the microbeads treated with 75 v% formamide solution, in percentage, compared to the sample treated with 65 v% formamide solution, in case of the PCR products amplified from the plasmids containing 27, 32, 39 and 51 CAG-repetitions (Cy3 labelled), by modeling the homozygote case.

Figure 7: depicts the average fluorescence intensity measured on the microbeads treated with 75 v% formamide solution, in percentage, compared to the sample treated with 65 v% formamide solution, in case of the PCR products amplified from the plasmids containing 27, 32, 39 and 51 CAG-repetitions (Cy5 labelled), by modeling the heterozygote case. For modeling the heterozygote case, each sample contains also PCR products amplified from plasmids containing 27 repetitions (Cy5 labelled) in 1:1 ratio.

Figure 8: depicts the average fluorescence intensity measured on the microbeads treated with 75 v% formamide solution, in percentage, compared to the sample treated with 65 v% formamide solution, in case of the PCR products amplified from the plasmids containing 27, 32, 39 and 51 CAG-repetitions (Cy3 labelled), by modeling the heterozygote case. For modeling the heterozygote case, each sample contains also PCR products amplified from plasmids containing 27 repetitions (Cy3 labelled) in 1:1 ratio.

Figure 9: depicts in case of the predetermined 10 heterozygote patient sample, or the two negative controls (27 CAG and Jurkat) the average fluorescence intensity measured on the microbeads treated with 75 v% formamide solution, in percentage, compared to the sample treated with 65 v% formamide solution. The number of the CAG-repetitions of the two alleles of the heterozygote patient samples are plotted on the X axis. Here the 27 CAG indicates the PCR products amplified from the plasmid containing 27 CAG-repetitions. Jurkat indicates the PCR products amplified from the genomic DNA isolated from Jurkat cells.

Figure 10: depicts in case of 5 healthy samples, two negative controls (27 CAG and Jurkat) and three positive control patient samples the average fluorescence intensity measured on the microbeads treated with 75 v% formamide solution, in percentage, compared to the sample treated with 65 v% formamide solution. The number of the CAG-repetitions of the two alleles of the heterozygote patient samples is plotted on the X axis. Here the 27 CAG indicates the PCR products amplified from the plasmid containing 27 CAG-repetitions. Jurkat indicates the PCR products amplified from the genomic DNA isolated from Jurkat cells. Numbers indicate the PCR products amplified from the genomic DNA isolated from the healthy volunteers.

Figure 11 : depicts the formamide concentration dependence of the dissociation of the PCR products amplified by allele-specific PCR reaction from genomic DNA isolated from a patient carrying a predetermined mutation, or from wild type Jurkat cells, not carrying mutation, at 40 ⁰C.

Figure 12: depicts in case of a patient sample carrying a predetermined mutation, or wild type Jurkat sample, not carrying mutation, the average fluorescence intensity measured on the microbeads treated with 75 v% formamide solution, in percentage, compared to the sample treated with 65 v% formamide solution.

As an example the method of the invention is demonstrated through the detection of a triplet-expansion disease (Huntington-chorea) and an SNP (mutation of the BRCAl gene), but these are only for the illustration of the invention, and they are not limiting the scope of the invention in any way, which includes similar detection of arbitrary base-sequence changes, through the detection of the length difference of the PCR product prepared from the investigated and a control DNA sample. Example 1

Detection of the Huntington-chorea

The Huntington-chorea is a neurodegenerative disease, caused by the extension of the CAG-repetition localized in exon 1 of the Huntington gene (ITl 5) found in the short arm of chromosome No. 4. The disease is autosomal dominant, therefore the existence of a single sick allele results in the appearance of the symptoms. About 5 persons from 100.000 are affected by the disease (in Europe and in the US), where the symptoms appear between 35-50 years of age, and 15-20 years after the appearance lead to death (Russell et al.). There are four categories based on the number of CAG-repetitions: absolutely healthy (<27 CAG), intermediary (27-35 CAG), with reduced penetrance (35-39 CAG), and the one expressing the sick phenotype for sure (40 < CAG) (Russel et al., Richard H. Myers, Semaka A. et al.) Based on the detection of the Huntington-chorea diagnosis of all such triplet-expansion diseases becomes possible with flow-cytometry, in which the disease is triggered by a triplet-expansion, affecting a short stretch (see Table 1).

The method of the invention was elaborated on the plasmid model system developed for the Huntington-chorea disease. In the first step the formamide concentration was determined with which the PCR product containing the maximum length CAG-repetition characteristic of the healthy subject (27 CAG), and a PCR product containing 51 CAG-repetition can be distinguished. The experiment was carried out with two different fluorescent markers, in all possible concentrations, to prove, that the method works reliably. In the next step the measurements were carried out in a construction, in which it turns out, whether the CAG- repetitions of intermediary length can be separated from the maximum length (characteristic for a healthy subject), in case of a homozygote or heterozygote. Finally, measurements were conducted with the genomic DNA samples of 5 healthy subjects, and 10 patients carrying a predetermined CAG-repetition, where each sample gave the expected result, both in case of the sample containing the healthy and the disease carrying DNA. Steps of the method: 1. PCR reaction: template:

- 200 ng genomic DNA isolated from human lymphocytes primers:

- sense primer: biotin-5'-3'CAT GGC GAC CCT GGA AAA GCT G-3'

- antisense primer: Cy5-5'-3'GGC GGT GGC GGC TGT TGC TGC TGC TGC TG-3' reaction mixture: - H₂O 28,5 μl

- Taq buffer (Fermentas) 5 μl

- MgCl₂ (Fermentas) (25 mM) 5 μl

- dNTP (Fermentas) (2,5 mM) 5 μl

- β-mercaptoethanol (100 mM) 0,5 μl

- cone, formamide 1,5 μl - BSA (Promega) (10 mg/ml) 1 μl

- sense primer (IDT) (1 pmol/μl) 1 μl

- antisense primer (IDT) (1 pmol/μl) 1 μl

- template (200 ng/μl) 1 μl

- Taq polimerase (Fermentas) (5 U/μl) 0,5 μl

Total: 50 μl

- temperature profile of the PCR reaction: Step l:

- denaturation: 96 ⁰C, 2 min Step 2: 12 cycles

- denaturation: 94 ⁰C, 30 sec

- anellation: 67 °C, 30 sec

- extension: 72 °C, 2 min Step 3 : 23 cycles

- denaturation: 92 ⁰C, 30 sec

- anellation: 67 °C, 30 sec

- extension: 72 ⁰C, 2 min Step 4:

- extension: 72 ⁰C, 10 min.

2. Attachment to microbeads:

- 40 μl PCR product + 16 μl 40xmicrobead (Polysciences, Inc.) (~10-20000pcs) + 100 μl

IxPBS

- 40 min, in room temperature, in darkness

- washing 3 times in 600 μl IxPBS (centrifugation 10 min, 15000/min)

- after the last wash suspending in 150 μl 1 xPBS (Vortex) 3. Heat treatment in formamide solution:

- FA cc. FA H₂O microbead+DNA 65 v% 130μl 30μl 40μl

75 v% 150μl lOμl 40μl

- heat treatment 3 min, 40 ⁰C

- washing 3 times in 600 μl I xPBS (centrifugation 10 min, 15000/min)

- after the last wash suspending in 150 μl 1 xPBS

4. Measurement with FACSarray flow-cytometer:

- settings: FSC: 795

SSC: 320 Far Red: 625 threshold: 20000 Setting the formamide concentration:

In the first series of experiments, the stretch containing the repetitions was amplified by PCR reaction, using plasmids containing 27 and 51 CAG-repetitions as template. Primer pairs labelled with biotin and Cy5 were used for the PCR reaction carried out from the plasmid containing 51 CAG-repetitions, primer pairs labelled with biotin and Cy3 were used for the PCR reaction carried out from the plasmid containing 27 CAG-repetitions. The products obtained this way were attached to the surface of the microbeads coated with streptavidin in 1 : 1 ratio, and the microbeads carrying the DNA fragments were treated at 40 °C in formamide solution, between 65 and 75 v% concentration, and the change of the fluorescence intensity was measured with FACSarray equipment (Beclcton Dickinson) (Figure 1). The results show, that depending on the formamide concentration, the strand carrying the fluorescent molecule of the PCR products containing the long, 51 CAG- and the short, containing 21 CAG-repetitions dissociate in different degree from the microbeads, therefore the PCR products of different length can be well distinguished.

This series of experiments was also carried out with opposite labeling, where the long PCR product (51 CAG) was labelled with Cy3, and the short PCR product (27 CAG) with Cy5. The results were similar to the ones above (Figure 2).

In the next two control experiments PCR products of identical length, but labelled with two different fluorescent molecules were used for the attachment to microbeads. In the first case, two different PCR reactions were carried out from a plasmid containing 51 CAG-repetitions. Biotin and Cy5 labelled primer pairs were used for the first reaction, for the second reaction biotin and Cy3 labelled primer pairs were used. The PCR products obtained were attached to streptavidin coated microbeads in 1:1 ratio, and were heat-treated in formamide solutions between 65-75 v% at 40 ⁰C as above, and the change in the fluorescence intensity was measured by a FACSarray equipment (Figure 3). In another experiment, this same measurement was carried out with a PCR product containing short, 27 CAG-repetitions (Figure 4). The result of the measurement demonstrated, that the average fluorescence of the microbeads in case of Cy5 and Cy3 labeling also changed similarly, therefore the measurement is independent of the identity of the fluorescent molecule.

Measurement of a PCR product containing CAG-repetition of intermediary length in case of a homozygote

In the next series of experiment plasmids containing 27, 32, 39 and 51 CAG-repetitions were used in the PCR reaction as template. The plasmid carrying the 32 CAG-repetitions represents the intermediary repetition length, while the plasmid containing 39 CAG-repetitions represents the lower limit of the repetition length characteristic of a patient. Following attachment to microbeads the products obtained were divided in two parts, and treated in 65 v% and 75v% formamide solution at 40 °C, and the change of the fluorescence intensity in the sample treated with 75 v% formamide was measured, compared to the control, treated with 65 v% formamide. The series of experiments was carried out with both Cy5 (Figure 5) and Cy3 (Figure 6) labeling. It was observed, that the PCR products amplified from the plasmids containing intermediary length, 32 CAG-repetitions, can be well separated from the PCR products amplified from plasmids containing 27 CAG-repetitions.

Measurement of a PCR product containing CAG-repetition of intermediary length in case of a heterozygote

Since the patients suffering from Huntington-disease are mostly heterozygotes for the triplet-expansion, i.e. they carry an allele of normal length and an extended allele, the first experiment was repeated, in such a way that healthy, 27 CAG-repetitions containing PCR products are mixed in 1 : 1 ratio to each sample, modeling this way the heterozygote case, when in the course of the PCR reaction two different products are obtained, one from the allele of normal length (short PCR product) or from the extended allele (extended PCR product). This experiment was also carried out in two different ways, with PCR product labelled with Cy5 (Figure 7), or with PCR product labelled with Cy3 (Figure 8). Well measurable signals were obtained, which indicates, that he abnormality can be detected even in heterozygotes. Measurement of healthy and sick, heterozygotic human genomic DNA samples

Following the development in a model system, the experiment was also carried out with clinical samples. Genomic DNA isolated from lymphocytes of healthy humans and humans suffering from Huntington-disease was used for the PCR reaction. Samples were provided by Professor BeIa Melegh (Pecsi Tudomanyegyetem Klinikai Kδzpont Orvosi Genetikai es Gyermekfejlόdestani Intezet, 7624 Pecs, Szigeti ύt 12. (Molecular Genetic Laboratory)), with irreversible anonymity coding. The PCR products labelled with biotin and Cy5 were attached to the surface of streptavidin-coated microbeads, as before. After attachment to microbeads the products obtained were divided in two parts, and treated in 65 v% and 75v% formamide solution at 40 ⁰C, and the change of the fluorescence intensity in the sample treated with 75 v% formamide was measured with FACSarray equipment, compared to the control, treated with 65 v% formamide. In the first measurement (Figure 9) 10 samples with CAG-repetitions of predetermined length, isolated from sick subjects were tested, and a plasmid containing 27 CAG- repetitions, and genomic DNA from Jurkat tissue culture cells (ATCC number: CRL- 1990) were used as positive control. In the second measurement (Figure 10) DNA sample taken from 5 healthy humans, and as positive control three samples from sick subjects, tested already in the previous measurement were measured, and again a plasmid containing 27 CAG-repetitions, and Jurkat cells were used as negative control. It can be seen from Figure 10 that the 5 healthy samples gave low average fluorescence value, similar to the negative control, that is they really do not carry extended allele, longer than the 27 CAG-repetitions, while in case of the positive control - similarly to the previous measurement - significant fluorescence values were measured.

Example 2

Detection of the 5382insC mutation of the BRCAl gene

In Hungary — as a consequence of the inherited mutations of the BRCA gene — 7% of the breast cancers, 11% of the ovarian cancers, 33% of the male breast cancers is hereditary [Van der Looij et al.: International Journal of Cancer 86:737-740 (2000); Csόkay B. et al: Cancer Research 59:995-998 (1999)]. The BRCA genes show autosomal dominant inheritance, therefore even the heterozygotes inherit the susceptibility for tumor.

Half of the hereditary breast cancers (in Hungary almost two third of them) can be ascribed to mutation of the BRCAl gene. Disposition of the subjects carrying such BRCAl mutations to breast cancer or to ovarian cancer is very high, therefore screening of the mutations is of high priority. According to the risk assessments related to the BRCA-mutations 80% of women carrying the BRCAl gene get sick in breast cancer in her lifetime [Narod S.A. - Foulkes W.D.: Nature Reviews Cancer 4:665-667 (2004)]. Based on the results of another risk assessment carried out on 12.000 patients carrying BRCAl mutation, the cumulative risk of breast cancer for those carrying the BRCAl mutation is 65% until seventy years of age [Antoniou A. et al.: The American Journal of Human Genetics 72: 1117-1130 (2003)].

Probably most of the hereditary ovarian cancers is also caused by the mutation of the BRCAl gene. In case of the defect of the BRCAl gene the possibility of development of the ovarian cancer is 40%. In a family stricken with a BRCAl gene defect where both breast and ovarian cancer occur, the possibility is over 80% for a woman carrying the BRCAl mutation that she gets sick in one of the cancers until her 70 years of age. In case of the BRCAl carriers in addition to the breast and ovarian cancer significant risk increase was detected for pancreatic cancer and for the malignant tumors of the cervix and the uterus. Increased risk may be supposed for prostate cancer less than 65 years of age. In addition to the ones mentioned above the risk of the gynecological (tube) tumors and the tumors of the peritoneum is also increased [Antoniou A. et al.: The American Journal of Human Genetics 72: 1117-1130 (2003)].

In order to prove the suitability of the method of the invention for detecting the SNPs, experiments were carried out for detecting the 5382insC mutation of the BRCAl gene, most frequently occurring in Hungary.

In the first step of the method of the invention the DNA stretch to be studied is purified, and amplified with multiplex allele specific PCR reaction. Three primers are used for the amplification: two forward and a common reverse primer. One of the two forward primers is specific for the mutation, the other for the wild type. This means that the forward primers were designed in such a way, that their 3' end should fall exactly at the location of the mutation, in this case the product amplifies from the mutation-specific primer only if the mutation is present in the sample studied, at least in one copy. The same is valid for the forward primer specific for the wild type. Additionally, another difference between the two forward primers, that a Tag- sequence (including 6 CAG-repetitions, altogether 18 base pairs) was made synthesized to the 5' end of the mutation-specific primer, in order to be able to separate the mutation-carrying and the wild type PCR products from each other. Instead of the CAG-repetition, this plus sequence may contain a GC-rich sequence, with any nucleotide sequence. The high GC-content is necessary to increase the difference between the Tm points of the PCR products, to the extent that the formamide heat-treatment could be used.

The reverse primer used in the PCR reaction is labelled with biotin, while the two forward primers are labelled with a fluorescent Cy5 molecule. The produced PCR products are attached to the surface of streptavidin-coated microbeads, through biotin. With heat-treatment of the microbeads carrying the PCR product in a suitable formamide solution (the concentration is defined below) the strand carrying the fluorescent molecule dissociates from the surface of the microbead, depending on the length of the PCR product.

First, the formamide concentration is determined for the BRCAl mutation test, with which the difference between the short and long PCR product can be measured. Next it was investigated, whether the mutation can be detected in case of heterozygote sample or not. Steps of the method: 1. PCR reaction: template:

- 200 ng genomic DNA isolated from human lymphocytes primers:

- P4 (common reverse): biotin-5'-AGT CTT ACA AAA TGA AGC GGC CC-3¹

- P5 (wild type forward): Cy5-5'-AAA GCG AGC AAG AGA ATC GCA-3'

- P6 (mutant forward): Cy5-5'-CAG CAG CAG CAG CAG CAG CAC CTT AGC GAG CAA GAG AAT CAC C-3' reaction mixture:

- H₂O 31,5 μl

- Taq buffer (Fermentas) 5 μl

- MgCl₂ (Fermentas) (25 mM) 3 μl

- dNTP (Fermentas) (2,5 mM) 5 μl

- reverse primer (IDT) (1 pmol/μl) 2 μl

- forward primer 1 (IDT) (1 pmol/μl) 1 μl

- forward primer 2 (IDT) (1 pmol/μl) 1 μl

- template (200 ng/μl) 1 μl

- Taq polymerase (Fermentas) (5 U/μl) 0 ,5 μl

Total: 50 μl

- temperature profile of the PCR reaction: Step l

- denaturation: 95⁰C 12 min Step 2: 37 cycles

- denaturation: 94° C 15 sec

- anellation: 62°C 15 sec

- extension: 72°C 30 sec Step 3

- extension: 72⁰C 5 min

2. Attachment to microbeads:

- 40 μl PCR product + 16 μl 40^χmicrobead (Polysciences, Inc.) (~10-20000ρcs) + 100 μl

IxPBS

- 40 min, in room temperature, in darkness

- washing 3 times in 600 μl I xPBS (centrifugation 10 min, 15000/min)

- after the last wash suspending in 150 μl 1 xPBS (Vortex)

3. Heat treatment in formamide solution:

- FA cc. FA H₂O microbead+DNA 57 v% 114μl 46μl 40μl

62 v% 124μl 36μl 40μl

- heat treatment 3 min, 40 °C

- washing 3 times in 600 μl I xPBS (centrifugation 10 min, 15000/min)

- after the last wash suspending in 150 μl 1 xPBS

4. Measurement with FACSarray flow-cytometer:

- settings: FSC: 795

SSC: 320 Far Red: 625 threshold: 20000

Setting the formamide concentration:

Two PCR products are used for setting the formamide concentration, one contains the short product, characteristic only for the wild type, wile the other contains the long, mutation- specific product. Amplification was carried out from human genomic DNA, in both cases a primer pair is used: in case of the wild type a biotin-labelled common reverse, or a Cy5 labelled, wild type specific short forward primer; while in case of the mutation-carrying sample a biotin- labelled common reverse, or a Cy5 labelled, mutation-specific long (carrying CAG Tag) forward primer. The PCR products obtained this way are attached to the surface of streptavidin-coated microbeads in two different reactions, and the microbeads carrying the DNA fragments are heat- treated in 57 v% and 62 v% formamide solutions at 40 °C, and the change of the fluorescence intensity is measured with a FACSarray equipment (Figure 11). The results show, that depending on the formamide concentration, the fluorescence-carrying strand of the long (mutation-carrying) and the short (wild type) PCR products dissociate in a different degree from the microbeads, therefore the mutation-carrying or the wild type PCR products are well distinguishable from each other. The wild type genomic DNA used in the PCR reactions is isolated from Jurkat cells (ATCC number: CRL-1990), while the genomic DNA originating from a patient carrying BRCAl mutation was provided by Professor Janos Kappelmayer (DE-OEC Klinikai Biokemiai es Molekularis Patolόgiai Intezet (Debrecen)).

Detecting the 5382insC mutation in case of a heterozygotic sample

This experiment was carried out similarly to the previous one with the difference that all the three primers are used in the PCR reaction in multiplex mode. The obtained products are divided in two parts (after binding them to the microbeads) and heat-treated in 57 v% and 62 v% formamide solution, and the change of the fluorescence intensity in the sample treated with 62 v% formamide solution is determined in comparison with the control treated with 57 v% formamide solution (Figure 12). On the basis of the results obtained this way it can be said that the method of the invention is also suitable for the detection of the 5382insC mutation of the BRCAl gene.

Claims

1. A method for the comparative analysis of the length of PCR products obtained from two or more DNA samples, on the basis of the difference of their Tm points comprising the following steps:

(i) PCR products are prepared by the amplification of the section of interest of the DNA samples in parallel reactions which are optionally labelled fluorescently;

(ii) the obtained PCR products are attached to microbeads;

(iii) the samples containing the double-stranded DNA of different length attached to microbeads are divided in two parts and at a given temperature are heat-treated in the solutions of predetermined concentration of a Tm point reducing agent, when, during denaturation one strand of the double-stranded DNA dissociates from the microbeads in a degree depending on its size; then the microbeads are washed;

(v) the fluorescence of the microbeads obtained this way is measured and the difference between the intensity changes of the two samples is evaluated.

2. The method according to Claim 1 for the comparative cytometric analysis of the length of the PCR product of a DNA sample compared to the PCR product amplified from a control DNA sample comprising the following steps:

(i) PCR product is prepared from the sample by the amplification of the DNA stretch, using a primer pair, where one of the primer is labelled with a ligand, and the other primer is optionally labelled at least with one fluorescent molecule;

(ii) the obtained PCR products are attached to microbeads coated with the molecule binding the ligand,

(iii) the samples containing double-stranded DNA of different length attached to the microbeads are divided in two parts and heat-treated at a given temperature in the solutions of predetermined concentration of a Tm point decreasing agent, where said concentrations are determined as the extreme values of a concentration series, where the unlabelled strand of the PCR product shorter than the control or identical with it gradually dissociates from the surface of the microbead by increasing the concentration, while the unlabelled strand of the PCR product longer than the control substantially does not dissociate; then the microbeads are washed; (iv) the DNA attached to the microbeads is fluorescently labelled, if it was not labelled in step (i);

(v) steps (i) - (iv) are also executed with the control DNA sample;

3. The method according to Claim 1 or 2 wherein the PCR product is labelled in step

4. The method according to Claim 3 wherein the labelling is carried out with a primer labelled at least with one fluorescent molecule.

5. The method according to Claim 1 or 2 wherein the DNA attached to the microbeads is labelled fluorescently in step (iv).

6. The method according to Claim 5 wherein the labelling is carried out with an intercalating or another DNA dye.

7. The method according to one of Claims 2-4 wherein biotin is used as ligand and an avidin derivative, for example streptavidin is used as ligand binding molecule.

8. The method according to one of Claims 2-4 wherein digoxigenin is used as ligand and an anti-digoxigenin antibody is used as ligand binding molecule.

9. The method according to one of Claims 1-8 wherein the Tm point reducing agent is formamide.

10. The method according to one of Claims 1-9 wherein the measurement of the fluorescence is carried out with a cytometer or a scanning laser microscopy.

11. Use of the method according to Claim 2 for detecting genetic abnormalities.

12. A method for the detection of the size differences of the DNAs by the analysis of the length of PCR products with a cytometer comprising the following steps:

(i) DNA is purified from a biological sample;

(iv) the samples containing double-stranded DNA attached to the microbeads are divided in two parts, and heat-treated at a given temperature in the solutions of predetermined concentration of a Tm point decreasing agent, where said concentrations are predetermined as the extreme values of a concentration series where the unlabelled strand of the PCR product of the negative or the positive control, whichever is shorter, gradually dissociates from the surface of the microbead by increasing the concentration, while the unlabelled strand of the PCR product of the negative or the positive control, whichever is longer, substantially does not dissociate; then the microbeads are washed;

(v) the DNA attached to the microbeads is fluorescently labelled, if it was not labelled in step (ii);

13. The method according to Claim 12 wherein the cause of DNA size difference is triplet-expansion, deletion, insertion, recombination, repair process or microsatellite polymorphism.

14. The method according to Claim 12 or 13 wherein the DNA size difference causes a genetic abnormality.

15. The method according to Claim 14 wherein the genetic abnormality is caused by triplet-expansion.

16. The method according to Claim 15 wherein the genetic abnormality is Huntington-disease.

17. The method according to Claim 12 wherein the determination of the DNA size difference serves the characterization of the degree of the immunological identity or on the basis of the microsatellite markers it serves personal identification.

18. A method for the detection of sequence differences, especially point mutations of the DNA by the analysis of the length of PCR products with a cytometer comprising the following steps:

(i) DNA is purified from a biological sample; (ii) the section of interest of said DNA carrying the point mutation is amplified by allele- specific PCR reaction by using three primers where the short forward primer specific of the wild type and the longer forward primer carrying GC-rich Tag are optionally labelled at least with one fluorescent molecule, while the common reverse primer is labelled with a ligand;

(iii) the obtained PCR products are attached to microbeads coated with the molecules binding the ligand;

(iv) the samples containing double-stranded DNA attached to the microbeads are divided in two parts and heat-treated at a given temperature in the solutions of predetermined concentration of a Tm point decreasing agent, where said concentrations are determined as the extreme values of a concentration series where the shorter unlabelled strand of the PCR product carrying no mutation gradually dissociates from the surface of the microbead by increasing the concentration, while the longer unlabelled strand of the PCR product carrying mutation substantially does not dissociate; then the microbeads are washed;

19. The method according to Claim 18 wherein the DNA sequence difference causes a genetic abnormality.

20. The method according to Claim 19 wherein the genetic abnormality is caused by the 5382insC point mutation of the BRCAl gene.

21. The method according to Claim 12 or 18 wherein the PCR product is labelled in step (ii) by carrying out the amplification with a primer labelled with a fluorescent molecule.

22. The method according to Claim 12 or 18 wherein the DNA attached to microbeads is labelled in step (v) by staining with an intercalating or an other DNA dye.

23. The method according to Claim 12 or 18 wherein biotin is used as ligand and an avidin derivative, for example streptavidin is used as ligand binding molecule.

24. The method according to Claim 12 or 18 wherein digoxigenin is used as ligand and an anti-digoxigenin antibody is used as ligand binding molecule.

25. The method according to Claim 12 or 18 wherein the Tm point reducing agent is formamide.

26. The method according to Claim 12 or 18 wherein the measurement of the fluorescence is carried out with a cytometer or with a scanning laser microscopy.

27. A method according to Claim 12 for the detection of triplet-expansions causing genetic abnormalities by the analysis of the length of PCR products with a cytometer comprising the following steps:

(i) DNA is purified from a biological sample;

(ii) the section of said DNA carrying the triplet-expansion of interest is amplified by a PCR reaction using a primer pair where one of the primers is labelled with biotin and the other primer is labelled at least with one fluorescent molecule;

(iii) the obtained PCR products are attached to microbeads coated with streptavidin,

(iv) the samples containing double-stranded DNA attached to the microbeads are divided in two parts and heat-treated at a given temperature in the solutions of predetermined concentration of formamide, where the formamide concentrations are determined as the extreme values of a concentration series where the fluorescently labelled strand of the PCR product identical with the DNA carrying no triplet-expansion or a strand shorter than that gradually dissociates from the surface of the microbead by increasing the concentration, while the fluorescently labelled strand of the PCR product longer than the DNA carrying no triplet-expansion substantially does not dissociate; then the microbeads are washed;

(v) the DNA attached to the microbeads is labelled fluorescently, if it was not labelled in step (ii);

(vi) the fluorescence of the microbeads obtained this way is measured with a flow- cytometer and the intensity of the obtained signals is compared to the fluorescence intensities of the normal negative control sample as well as to those of the positive control sample carrying the known differences.

28. The method according to Claims 1, 12 or 18 is carried out in a multiplex way.

29. Kit for applying the method according to Claim 12 or 18 which includes two or more primers suitable for the detection of the DNA alterations listed in Claim 12 or 18, or a dye for staining the DNA attached to the microbeads, the microbeads with the suitable coating, a Tm point decreasing agent, the adequate controls, the solutions necessary for the method in one or more containers altogether with the necessary instructions.