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    • 专利摘要:
    Mutation identification method. The present invention relates to a method for the identification of the position of a genetic mutation and to the use of said method to simplify the screening of said genetic mutation. (Machine-translation by Google Translate, not legally binding)
    公开号:ES2641690A1
    申请号:ES201630599
    申请日:2016-05-09
    公开日:2017-11-13
    发明作者:Carmen María GAYOSO BABÍO；Óskar MARTÍNEZ DE ILÁRDUYA RUIZ DE LARRAMENDI；Iván Aarón LESENDE RODRÍGUEZ
    申请人:Health In Code S L；Health In Code SL；
    IPC主号:
    专利说明:

    image 1 DESCRIPTION
    Mutation Identification Method 5 Field of the invention
    The present invention belongs to the field of molecular biology techniques. Specifically, it refers to a method for identifying the position of a genetic mutation and the use of said method to simplify the screening of said genetic mutation. The
    The present invention finds application in those fields that require the precise knowledge of a genetic sequence or the exact point of a genetic mutation (clinical, agronomy, biotechnology, etc.). Background of the invention
    15 The determination of sequences adjacent to a known region of the chromosome is a technically complicated task, and different methodologies have been developed to achieve it. Among the techniques described are “ligation mediated PCR” (LM-PCR or “genome walking”), reverse PCR (i-PCR), “thermal asymmetric interlaced PCR” (TAIL-PCR),
    20 "anchored PCR" (a-PCR) or "randomly primed PCR" (rm-PCR). All these methods suffer from low detection sensitivity or low specificity and are also only effective when the point at which the mutation occurs in the genome is a maximum of a few hundred base pairs of the known sequence. More recently, other methodologies such as “Linear Amplification Mediated Polymerase Chain Reaction” (LAM PCR) have been developed,
    25 which requires the generation of a double strand DNA fragment and the digestion of this fragment. Subsequent modifications of this technique obviate the need for this digestion, which replaces the initial digestion of genomic DNA and the ligation of a double-stranded adapter. All these methods are based on exponential DNA amplification.
    30 There are different well-established techniques for the identification of regions of the genome that exhibit loss or gain of genetic material. These include techniques based on PCR (multiplex ligation-dependent probe amplification, MLPA) or hybridization (comparative genomic hybridization array (CGH array), single nucleotide polymorphism,
    35 English single nucleotide polymorphism, array (SNP arrays ”), etc.). Depending on the design of oligonucleotides or probes, these techniques allow to identify regions of the genome where there is loss or gain of genetic material, although in no case do they identify the exact starting or ending points of these regions nor, in the case of Insertions, offer no information about the region of the genome in which the insertion occurs. In the case of MLPA, this technique offers very little processivity, since only
    image2
    5 It is possible to analyze a limited number of genetic regions (usually exons). In addition, it is a technique that offers problems of false negatives.
    In the case of SNP arrays and CGH array, it is possible to analyze the complete genome of samples without prior knowledge of the sequence. However, it suffers from a capacity
    10 of relatively low resolution since it is rarely able to detect deletions or insertions of a size smaller than 50 Kb.
    The use of techniques such as MLPA (Stuppia et al., Use of the MLPA assay in the molecular diagnosis of gene copy number alterations in human genetic diseases. Int J Mol Sci. 2012; 15 13: 3245–76), CGH array (Lai et al., Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 2005; 21: 3763-70), SNP arrays (Zhang et al., Evaluation of copy number variation detection for a SNP array platform. BMC Bioinformatics 2014; 15: 50) or “NGS targeted sequencing” (Zhao et al., Computational tools for copy number variation (CNV) detection using next-generation sequencing data: 20 features and perspectives. BMC Bioinformatics 2013; 14 (Suppl 11): S1) allows to detect the presence of mutations due to loss (deletions) or gain (insertions) of genetic material. The result obtained by any of these techniques delimits the minimum chromosomal region that with a certainty of 100% comprises the structural variant, but none of them identifies the exact limits of the structural variant in question. That
    The nucleic acid region which, with a certainty of 100%, comprises a mutation in question, is hereinafter referred to as an "accurate nucleic acid region" or "ANC region".
    There are also other genetic modifications that do not imply a change in the amount of
    30 genetic material, such as translocations, and therefore not detected with the mentioned methods. Specific techniques are used to detect the ANC region of these structural variants, such as Southern blot, karyotype analysis or fluorescent in situ hybridization (FISH) in translocations of large chromosome segments, or real-time PCR (RT-PCR) or ∆-PCR to identify other translocations that may result
    35 to gene fusions.
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    As for gene fusions, gene fusions, produced by chromosomal translocations, inversions, deletions, etc., are currently considered to be of great relevance in frequent epithelial cancers, such as prostate or lung carcinomas. For example, most prostate cancers have an androgen-regulated fusion of some of the transcription factors of the ETS gene family. Clinically, some neoplasms are classified or managed according to the presence of a particular gene fusion: for example, promyelocytic leukemias that carry a PML-RARα fusion of the retinoic acid α receptor are treated with retinoic acid, while chronic myeloid leukemias with the presence of the BCR – ABL fusion they are treated with the drug
    10 imatinib However, the tests carried out by RT-PCR require that both merged elements be known and in turn give rise to a previously characterized variant, when sometimes only one of the genes that may be involved in the gene fusion Said single known gene would therefore correspond to the ANC region.
    15 The recent emergence of mass ultrasequencing technologies (“next generation sequencing”, NGS) has allowed enormous advances in the knowledge of nucleic acid sequences of many organisms. In turn, it has served to reveal sources of genetic variability that previously went unnoticed;
    These include genomic structural variants and variation in the number of copies of a gene (CNV).
    There are different methods of sample preparation for NGS sequencing. In one of its forms, the methodology includes a “target enrichment” step that consists of
    25 in the selection, by different methods (for example by capture with a solution of specific probes), of that region of the genome that you are interested in studying (for example to sequence a panel of specific genes, to sequence only exomes, etc.), regardless from the rest of the genome. These methods get very reliable readings of a region of interest but virtually no information from the rest of the genome.
    30 Another option to characterize this type of mutations is the sequencing of the complete genome (“Whole Genome Sequence”, WGS) of those samples in which there is suspicion of modifications of this type. Although this methodology offers results that cover the entire genome, there are recalcitrant areas where few or
    35 no reading. In addition, the WGS methodology is expensive and presents problems when the region of interest is located in repetitive regions of the genome, which does not guarantee the correct characterization of genetic variants of this type.
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    The authors of the present invention have developed a method that overcomes the problems of the prior art and allows a simplification of the method of identifying 5 mutations and screening them. Object of the invention
    The present invention relates in a first aspect to a method for identifying the
    10 position of a genetic mutation characterized by comprising the following stages: a) determine the ANC region comprising the genetic mutation under study; b) carry out a PCR, where the PCR template is DNA extracted from a biological sample taken from the subject under study and the primers are:
    b1) a degenerate primer, and 15 b2) a specific primer that specifically hybridizes:
    - within the ANC region, at a distance of 0.2-100 Kb from any of the ends of the ANC region, if the mutation comprises a gain of genetic material, a translocation or a gene fusion, and is extended by PCR out of the ANC region, or
    20-outside the ANC region, at a distance of 0.2-100 Kb from any of the ends of the ANC region, if the mutation comprises a loss of genetic material, and is extended by PCR to the ANC region, and where in the PCR reaction the hybridization step comprises two consecutive hybridizations, a first hybridization at a hybridization temperature equal to the Tm of the
    25 specific primer ± 10 ° C, and a second hybridization at a hybridization temperature equal to the Tm of the degenerated primer ± 5 ° C; c) sequencing the amplification product obtained in step b); and d) align the sequence obtained in step c) with a reference genome to identify the position of the mutation.
    A second aspect of the present invention relates to a method for screening a genetic mutation characterized in that it comprises the following steps: i) identifying the position of the genetic mutation following the method according to the first aspect of the invention;
    Ii) carry out a PCR where the model DNA is DNA extracted from a biological sample taken from the subject under study and the primers are a direct primer and a reverse primer that specifically hybridize upstream and downstream, respectively, of the position of the mutation identified in step i) so that a PCR product comprising said position is amplified; iii) analyze the size of the amplified PCR product in ii), where a PCR product of the
    image5
    The expected size according to the direct and reverse primers used in stage ii) is indicative of the presence of the genetic mutation under study, and the absence of said PCR product is indicative of the absence of the genetic mutation.
    A third aspect of the present invention relates to a method of diagnosing a
    10 pathology associated with a genetic mutation comprising carrying out the method according to the second aspect of the invention, the subject being diagnosed as being affected by the pathology when the PCR product of stage iii) is the expected size according to the primers direct and inverse used in stage ii).
    A fourth aspect of the present invention relates to a kit for carrying out any one of the methods according to the first, second or third aspect of the invention, which comprises a degenerate primer b1), and a specific primer b2), such and as defined in the first aspect of the invention. 20 Brief description of the figures
    Figure 1: Scheme of the deletion of exons 59-66 of the FBN1 gene. DUT refers to the deoxyuridine triphosphatase gene, adjacent to the FBN1 gene towards the centromere. Numbers in italics represent the number of nucleotides. Bold numbers represent the
    25 position on the chromosome. The term "Enº" means "exon no." For example "E58" means "exon 58". The arrow FBN1-Ex58-FW denotes the specific primer, the arrow head representing the extension direction of said primer. Figure 2: Diagram showing the prediction of the secondary structure at 30 ° C (panel B) of the specific primer of SEQ ID No. 5. Panel A shows the structure at 60 ° C, where the
    30 arrow marks the region of homology to intron 45 of the DMD gene. Figure 3: Scheme of duplication of exons 46 and 47 of the DMD gene. Numbers in italics represent the number of nucleotides. Bold numbers represent the position on the chromosome. The term "En °" means "exon No.", for example E46 means Exon 46. The arrow DMDdup-Ex47-RV denotes the specific primer, representing the
    35 arrow head the extension direction of said primer.
    image6 Detailed description of the invention
    As used in the present application, the singular forms "one / one", "one" and "the" include their corresponding plurals unless the context clearly indicates otherwise. Unless otherwise defined, All the technical and scientific terms used herein have the same meaning that a person skilled in the art to which this invention belongs usually understands in order to facilitate understanding and clarify the meaning of certain terms in the context of the This invention provides the following definitions and particular and preferred embodiments of the
    10, applicable to all embodiments of the various aspects of the present invention:
    "PCR" means polymerase chain reaction. In general, it consists of the repetition of successive incubations at a denaturation temperature, a temperature of
    15 hybridization and a polymerization temperature, although there are countless modifications to the general method. PCR-based methods are included, such as PCR touchdown (TD-PCR), “nested PCR”, “first extension”, etc.
    "Amplification product" or "PCR product" is the mixture of DNAs in solution 20 obtained as a result of a PCR reaction.
    "Primer" or "first" (its English name) is an oligonucleotide capable of hybridizing with the sequence to be amplified, and which serves as a starting point for the polymerase to begin the amplification reaction. This molecule may include
    25 modifications, such as biotinylation, phosphorylation, addition of blocked nucleic acids (LNA).
    "Specific primer" refers to a primer that is capable of specifically binding or hybridizing specifically with the sequence to be amplified. In a particular embodiment, the primer is a deoxyoligonucleotide with a size of 15-35 nucleotides, preferably 18-25 nucleotides.
    "Specifically hybridize" refers to the recognition between nucleic acid molecules that have exact complementarity (100% complementarity) among their nucleotide sequences.
    image7
    "Degenerate primer" refers to mixtures of oligonucleotides that are composed of N nucleotides (N is A, T, C or G). In particular, the length of the oligonucleotides is 5-16 nucleotides, preferably 5-11 and more preferably 7 nucleotides. In the oligonucleotides, all N can be the same nucleotide or they can be different, thus comprising the oligonucleotide variations in the sequence in some of its positions. In particular, it may comprise variations in at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15 positions, depending on the size of the oligonucleotide. In a preferred embodiment the degenerate primer comprises
    10 a mixture of all possible oligonucleotides. In a preferred embodiment the oligonucleotides are phosphorylated (degenerate phosphorylated primer), preferably they are monophosphorylated. Preferably the oligonucleotides are phosphorylated at their 5 'end (degenerate primer phosphorylated at their 5' end).
    "Direct primer" is the primer that extends in the PCR from the initiation codon to the termination codon (Stop codon) of the template DNA.
    "Reverse primer" is the primer that extends from the termination codon to the initiation codon of the template DNA.
    "Reference genome" refers to a digital nucleic acid sequence, previously assembled as a representative example of the gene set of a species.
    "Hybridization stage" refers to the hybridization phase of the PCR. This phase is called
    25 also annealing, pairing or alignment phase. The melting temperature (Tm, melting temperature) depends on several factors and is relatively specific for each first. The length of the primers and the sequence are critical in the designation of the parameters of an amplification, a simple formula for calculating the Tm is as follows: Tm = 4 (G + C) + 2 (A + T), although there are many others that
    30 can also be used. In the case of a degenerate primer, Tm refers to the average Tm of the mixture of oligonucleotides composed of N nucleotides.
    "Structural variants" involve changes in some parts of the chromosomes instead of changes in the number of chromosomes or sets of chromosomes in the genome. 35 There are four common types of mutations that result in structural variants: deletions and insertions, for example duplications (which involve a change in the amount of
    image8
    DNA in a chromosome, loss and gain of genetic material respectively), inversions (which imply a change in the disposition of a chromosomal segment) and translocations (which imply a change in the location of a chromosomal segment and can lead to gene fusions) . In the present invention the term "variant
    Structural "comprises a structural variant selected from the group consisting of a structural variant characterized by (comprising) a loss of genetic material, a structural variant characterized by a gain of genetic material, a translocation, a gene fusion and combinations thereof.
    10 "Loss of genetic material" refers to the existence of regions of the genome in which at least one of the alleles shows the disappearance of a segment of DNA that does appear in that allele in the reference genome. This loss can lead to changes in the phenotype.
    "Gain of genetic material" refers to the existence of regions of the genome in which at least one of the alleles shows the insertion of a segment of DNA absent in said allele into the reference genome. The inserted DNA segment can be of endogenous origin (duplications, pseudogenes, retrotransposons, etc.) or exogenous (transgenes, virus integration, etc.). This gain of genetic material can lead to changes in
    20 the phenotype depending on the place of insertion or the sequence of the inserted element. In the context of the present invention, the term "insertion" refers to any of the structural variants that entails a gain of genetic material, in particular to those mentioned in this paragraph: duplication, pseudogen, retrotransposon, transgene and virus integration.
    "Translocation" refers to the reorganization of regions of the genome that results in the presence of a segment of DNA in a region of the genome other than its location in the reference genome. A translocation can lead to changes in the phenotype depending on the place of insertion or excision and the sequence of the element
    30 inserted.
    "Gene fusion" refers to the result of the rupture and fusion of a segment of DNA that occurs in sequences contained within genes. It usually occurs as a result of a translocation and may result in a fused transcript that produces a protein.
    35 chimeric. Gene fusion can lead to changes in the phenotype, depending on the genes affected by the rearrangement.
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    "Region of certain nucleic acids" (ANC Region) refers to the region of nucleic acids (sequence of contiguous nucleotides in a nucleic acid molecule) that with a certainty of 100% comprises a genetic mutation under study. The ANC region can be determined from genetic material extracted from a biological sample taken from the subject under study. In particular, from DNA or RNA extracted from a biological sample taken from the subject under study, preferably DNA. As indicated above, the ANC region is determinable through a multitude of techniques known to the person skilled in the art. Among others, MLPA, CGH array, SNP array, NGS, Southern blot, karyotype analysis, FISH, RT-PCR and ∆-PCR stand out. The person skilled in the art also knows how to determine the region that with 100% certainty comprises the mutation under study (ANC region).
    "Gen" includes not only regions encoding gene products but also regulatory regions, including, for example, promoters, termination regions, translation regulatory sequences (such as ribosome binding sites and internal ribosome entry sites), enhancers , silencers, insulators, border elements, origins of replication, matrix binding sites and locus control regions. The term "gene" also includes all introns and other splicing DNA sequences of the mRNA transcript, together with variants resulting from alternative splicing sites. The term "gene" further includes any portion of a gene, for example, any portion of the regions mentioned above.
    "Subject" refers to any member of the Monera, Protista, Fungi, Plantae or Animalia kingdoms. In a preferred embodiment, the subject is a member of the Magnoliophyta subdivision including, without limitation, model organisms, such as Arabidopsis thaliana or rice, and species of monocotyledonous and dicotyledonous plants with agronomic interest, such as, wheat and other cereals, sunflower, cotton, soy and other legumes, ornamental plants, fruit trees, conifers and other crops. In another preferred embodiment, the subject is any member of the Mammalia class, including, without limitation, humans and nonhuman primates such as chimpanzees and other apes and species of monkeys; farm animals, such as cattle, sheep, pigs, goats and horses; domestic mammals such as dogs and cats; laboratory animals including rodents, such as mice, rats and guinea pigs, and the like. The term does not indicate a specific age or sex. Therefore, adult and newborn subjects, as well as fetuses, whether male or female, are intended for inclusion within the scope of this term. The subject is preferably a human being. Before carrying out any of the methods of the present invention, the presence of the mutation in the subject under study may be known, or there may be suspicion that the subject has the mutation, for example based on clinical data, or may
    image9
    5 completely ignore whether or not the subject has the mutation.
    The "biological sample" taken from a subject under study contains any biological material that allows nucleic acid extraction and is a material that comprises genetic material from a subject or a mixture of subjects. In the present invention, the sample comprises genetic material of the subject under study. In a particular embodiment the genetic material is DNA or RNA. DNA refers to any type of DNA, such as: genomic DNA (gDNA), mitochondrial DNA (mDNA), complementary DNA (cDNA), circulating DNA (cDNA). In a particular embodiment, the genetic material is cDNA, cDNA, cDNA or cDNA. In a preferred embodiment, the DNA is genomic DNA or cDNA, preferably genomic DNA. Nucleic acid isolation from the sample can be performed by standard procedures known to the person skilled in the art, such as those described in Sambrook et al., (Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Press, 1989) . In a particular embodiment, the biological sample is fresh or fixed tissue obtained from biopsy or autopsy or a biological fluid. In a preferred embodiment of any of the methods of the present invention, the biological sample is a biological fluid thus being the method of the invention non-invasive, minimally invasive or less invasive than those requiring a tissue sample taken by biopsy. . The biological fluid is selected from the group consisting of saliva, blood, serum, plasma, urine, feces, ejaculate, bone marrow, buccal or buccal exudate
    Pharyngeal, pleural fluid, peritoneal fluid, pericardial fluid, cerebrospinal fluid, intraarticular fluid, amniotic fluid, and mixtures thereof. Preferably, the biological fluid is selected from blood, plasma, serum or saliva, more preferably the biological sample is blood or saliva. In a further embodiment, the biological sample is a maternal sample that includes fetal DNA, thus allowing a prenatal analysis.
    The present invention relates in a first aspect to a method for identifying the position of a genetic mutation, characterized in that it comprises the following steps: a) determining the ANC region comprising the mutation under study; b) carry out a PCR, where the PCR template is DNA extracted from a sample
    The biological taken from the subject under study and the primers are: b1) a degenerate primer, and
    image10
    b2) a specific primer, which specifically hybridizes:
    - within the ANC region, at a distance of 0.2-100 Kb from any of the ends of the ANC region, if the mutation comprises a gain of genetic material, a translocation or a gene fusion, and is extended by PCR (in direction 5´ to 3´)
    5 out of the ANC region, or
    -out of the ANC region, at a distance of 0.2-100 Kb from any of the ends of said region, if the mutation comprises a loss of genetic material, and is extended by PCR (in the direction 5´ to 3´ ) towards the ANC region, and where in the PCR reaction the hybridization stage comprises two hybridizations
    10 consecutive, a first hybridization at a hybridization temperature equal to the Tm of the specific primer ± 10 ° C, and a second hybridization at a hybridization temperature equal to the Tm of the degenerate primer ± 5 ° C; c) sequencing the amplification product obtained in step b); and d) align the sequence obtained in step c) with a reference sequence for
    15 identify the position of the mutation.
    The present invention relates to methods for characterizing genetic mutations, in particular to identify the exact position of said genetic mutations, thus delimiting the exact limits of said mutations, and for screening said mutations (detecting the presence of said mutations). The methods described herein may be useful in characterizing a variety of genetic mutations. Mutations that can be characterized using the methods described in the present invention include, for example, an insertion, a deletion, a duplication, and a rearrangement (eg, a translocation or a gene fusion), as well as any combination thereof. . The
    25 insertion may be of a transgene. The genetic mutation can be a germline mutation or a somatic mutation.
    Thus, in a particular embodiment, the genetic mutation is a structural variant, more particularly the structural variant is selected from the group consisting of a structural variant 30 characterized by a loss of genetic material, a structural variant characterized by a gain of genetic material, a translocation, a gene fusion and combinations thereof. In a preferred embodiment the structural variant is selected from the group formed by insertion, deletion, duplication, transgeneration, translocation and gene fusion. More preferably the structural variation is an insertion, duplication or
    35 deletion
    image11
    The mutation under study may be a recurrent mutation that has been associated with one or more types of diseases, such as with family heart disease. In this case, step a) can be carried out in a particular region of the DNA, for example that which comprises the genes associated with pathologies or the coding region of the genome (the
    5 exome), which is only 1% of the genome but in which 85% of hereditary diseases are present (Bick and Dimmock. Whole exome and whole genome sequencing, Curr Opin Pediatr 2011; 23: 594-600; Biesecker et al Exome sequencing: the expert view, Genome Biol 2011: 12: 128), thus avoiding the analysis of the entire genome.
    In a particular embodiment step a) of the method of the invention is carried out from genetic material extracted from a biological sample taken from the subject under study, more particularly said genetic material is DNA or RNA. Step a) can be carried out by any method known to the person skilled in the art that allows the determination of the ANC region, such as: MLPA, CGH, SNP-arrays, NGS, etc. So, in one
    Particular embodiment step a) is carried out by a technique selected from the group consisting of MLPA, CGH array, SNP-arrays, NGS, Southern blot, karyotype analysis, FISH, RT-PCR and ∆-PCR. In a preferred embodiment according to any one of the above embodiments, step a) is carried out by MLPA, CGH array, SNParrays, NGS and more preferably by NGS. In a preferred embodiment according to a
    20 any of the embodiments of this paragraph the genetic material is DNA.
    In a particular embodiment according to any one of the above embodiments, in step b) the PCR template is cDNA, cDNA or cDNA, preferably cDNA or cDNA and more preferably cDNA. In the case of gene fusions, the PCR template is
    Preferably cDNA.
    In a preferred embodiment according to any one of the above embodiments, the degenerate primer has between 5 and 11 nucleotides, and more preferably 7 nucleotides. Preferably, the degenerate primer has the sequence SEQ ID NO: 1 (NNNNNNN). The degenerate primer may comprise modified nucleotides, for example locked nucleic acids (LNAs). Likewise, the degenerate primer may be mono-, di- or tri-phosphorylated. In a preferred embodiment according to any one of the previous embodiments of the first aspect of the invention, the degenerate primer is phosphorylated, preferably monophosphorylated, at its 5 'end. In a preferred embodiment the degenerate primer
    35 has the sequence SEQ ID No. 1 and is phosphorylated at its 5 'end (5’-pNNNNNNN-3 ’).
    image12
    In a particular embodiment according to any one of the above embodiments, in step b) the hybridization temperature of the second hybridization is between 20-40 ° C, preferably 27-33 ° C and more preferably 30 ° C.
    In another particular embodiment according to any one of the above embodiments, in step b) the second hybridization is carried out for a time of between 1 and 10 seconds, preferably 1-3 seconds and more preferably 1 second. Advantageously, brief hybridization limits the incorporation of degenerated oligonucleotides in the newly synthesized chains and prevents the appearance of nonspecific reaction products.
    In a preferred embodiment according to any one of the above embodiments, in step b) the second hybridization is carried out at 30 ° C for 1 second, thus achieving amplification with the least amount of nonspecific reaction products.
    15 Thus, the PCR reaction includes a low temperature hybridization step for a very short time to allow the incorporation of degenerate primers into the newly synthesized chains. Therefore, and to reduce or prevent the specific primer from binding at that low temperature to other regions of the genome, the specific primer may include at its 5 'end a sequence complementary to that of its 3' end. In this way, it
    20 favors the formation of hairpin structures by hybridization between both ends of the primer at low annealing temperatures. This reduces the possibility of nonspecific homology of the specific primer with the study DNA during the low temperature annealing step (second hybridization). Figure 2 shows the secondary structure predicted at 30 ° C (panel B) for a specific first in which the extension has been designed
    25 of 7 nucleotides at their 5 ’end that favor the formation of intramolecular structures by complementing 9 nucleotides. The size of this region with complementation may vary depending on the GC content of the primer, but always so that it forms structures secondary to the hybridization temperature of the second hybridization that are not stable at the hybridization temperature of the first hybridization.
    In a preferred embodiment, according to any one of the above embodiments, the specific primer comprises at the 5'-end a sequence complementary to that of its 3'-end, preferably 5-12 nucleotides and more preferably 7-9 nucleotides. Thus, the formation of secondary fork structures at low temperatures is favored
    35 hybridization, such as those required for hybridization of the degenerate primer, reducing the possibility of nonspecific homology with the DNA under study.
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    In a particular embodiment according to any one of the above embodiments, the specific primer has the sequence SEQ ID No. 2 or SEQ ID No. 5.
    As indicated above, the specific primer is designed to hybridize specifically inside or outside the ANC region according to the type of mutation being characterized. Said primer is extended by PCR in the 5'a to 3 'direction by PCR towards the position of the mutation under study. Thus, in the case where the mutation comprises a gain of genetic material, translocation or gene fusion, where the mutation is outside the ANC, the specific primer hybridizes within the ANC region and extends outward from the ANC region, In the case where the mutation comprises a loss of genetic material, the specific primer hybridizes outside the ANC region and extends to the ANC region. Specifically, the specific primer hybridizes specifically in a region that is 0.2-100 Kb from any of the ends (3 'or 5') of the ANC region, inside or outside the ANC region depending on the mutation (within of the ANC region in mutations that comprise gain of genetic matter, translocations or gene fusions and outside the ANC region in mutations that comprise loss of genetic matter). More particularly, the specific primer specifically hybridizes to 0.5-80 Kb of the ends of the ANC region. Preferably at 0.5-40 Kb and more preferably at 0.5-20 Kb at the ends of the ANC region.
    In a preferred embodiment, when the mutation is a structural variant characterized by a gain of genetic material, the specific primer hybridizes to 0.2-10 Kb of the 5 'or 3' end, within the ANC region of genetic material gain.
    In the present invention, in step b) the PCR is carried out with only primers b1) and b2). As a result of the use of a single specific primer, linear amplification is obtained. Furthermore, in the preferred embodiment in which the degenerate primer is phosphorylated, the incorporation of said degenerate phosphorylated primer into the reaction allows the linear chains to prevail and generate local double-stranded regions on which the polymerase regenerates a double-stranded nucleic acid. This is an important advantage since the established methods for preparing samples for NGS sequencing use double stranded DNA as the starting material. Thus, in a preferred embodiment, according to any one of the above embodiments, the sequencing of step c) is carried out by NGS. And in another preferred embodiment according to any one of the above embodiments, in step b) the degenerate primer is phosphorylated at its 5 'end, preferably monophosphorylated, and the sequencing of step c) is carried out by NGS.
    image13
    In a particular embodiment, the method of the first aspect of the invention comprises, after
    5 stage d) in which the position of the mutation is identified, a stage e) in which the design of primers that flank the position of the genetic mutation is carried out, a PCR reaction with said primers and DNA extracted of a biological sample of the subject under study and a Sanger sequencing of the amplified product. Thus stage e) includes the reconfirmation of the position identified in stage d) by
    10 Sanger sequencing. Sequencing by the method described by Sanger et al in 1977 (Sanger et al., DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977; 74: 5463-7) is of clinical standard, so this stage is recommended when the method of the invention is used to detect or diagnose diseases characterized by the genetic mutation under study.
    15 Genetic abnormalities, such as duplication, deletion, chromosomal translocation, gene fusion and point mutation often lead to pathological conditions. Some diseases, such as cancer, are due to genetic abnormalities acquired in a few cells during life, while in other diseases the genetic abnormality is
    20 present in all body cells and present from conception, as occurs in some family heart disease. Thus, in a particular embodiment the genetic mutation under study is a mutation that is associated with the development of a pathology, such as heart disease, cancer, neurodevelopmental disorders, Crohn's disease, rheumatoid arthritis, type 1 and type 2 diabetes. , etc. In a preferred embodiment, the pathology
    25 is a family heart disease, more preferably it is a cardiomyopathy or canalopathy.
    In a particular embodiment according to any one of the above embodiments, the mutation is a deletion. More particularly, the deletion is from a gene whose deletion is associated with a pathology, preferably a family heart disease.
    In a particular embodiment according to any one of the above embodiments, the mutation is an insert. More particularly, the insertion is a duplication of at least one gene or at least a part of a gene and said duplication is associated with a pathology, preferably a family heart disease.
    35
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    In a particular embodiment, the mutation is a deletion in the FBN1 gene and the specific primer has the sequence SEQ ID No. 2. In another particular embodiment, the mutation is a duplication of the DMD gene and the specific primer has the sequence SEQ ID No. 5. The deletion of the FBN1 gene is associated with Marfan syndrome and the duplication of the DMD gene.
    5 is associated with muscular dystrophy and dilated cardiomyopathy.
    The methodology of the present invention according to the first aspect of the invention, allows to know the sequence of regions that reach several tens of kilobases from a known sequence, with greater extension and specificity than the methods
    10 described above in the state of the art. To carry out the method of the invention, it is sufficient to have a known sequence on which to design a single specific oligonucleotide and no prior knowledge of the sequence to be characterized is required.
    15 As indicated above, prior art methods are based on exponential amplification of DNA. Surprisingly, the method of the present invention eliminates the need for this step and integrates into the PCR reaction an additional reagent that regenerates the double strand without the need to add adapters. The need to synthesize oligonucleotides with modifications that favor the capture of the
    20 PCR products (for example, biotinylation), since the sequencing of step c), in particular by means of NGS, provides the sensitivity needed to identify DNA fragments that cover the exact limits of genetic modification. Thus, in a preferred embodiment, according to any one of the above embodiments according to the first aspect of the invention, the specific primer does not comprise modifications.
    Thus, the method of the present invention finds special interest for its application on samples of subjects in which, after the application of some or several of the techniques mentioned in the background section or others, loss or gain of genetic material. The application of this invention allows the exact characterization of the limits
    30 exact deletion, insertion, translocation or gene fusion as well as, in case of insertion, translocation and gene fusion, the determination of the exact location of the genome in which it occurs.
    The invention also finds application in the characterization of insertion sites of
    35 transgenes in organisms in which, through genetic manipulation, a known exogenous sequence is introduced into its genome.
    image15
    The invention is also applicable in the characterization of gene fusions. Surprisingly, and unlike the techniques in use, the present invention serves for the identification and characterization of fusions from the sequence of only one of the 5 genes involved in the fusion. For example, the tests carried out by RT-PCR to detect gene fusions, require that both fused elements be known and in turn give rise to a previously characterized variant. In the present invention, gene fusion can be characterized from the only gene known and involved in said gene fusion. In this case, the ANC region corresponds to said single known gene.
    The present invention thus supposes an important advantage, since, as previously indicated, it is considered that gene fusions, produced by chromosomal translocations, inversions, deletions, etc., have great relevance in frequent epithelial cancers, such as prostate or lung carcinomas. .
    Once the position of the mutation has been identified following the method of the first aspect of the present invention, it is possible to design primers that allow specifically amplifying the exact point of the mutation. And once these primers are available, the study of the presence or absence of the mutation in related individuals is limited to PCR and Sanger sequencing, a method established for years and much more
    20 economically and less technically demanding than NGS. Thus, in a second aspect the present invention relates to a method for screening a genetic mutation characterized in that it comprises the following steps: i) identifying the position of the genetic mutation following the method of the invention according to any one of the embodiments of the first aspect of the invention;
    Ii) carry out a PCR where the model DNA is DNA extracted from a sample taken from a subject under study and the primers are a direct primer and a reverse primer that specifically hybridize upstream and downstream, respectively, of the exact position of the mutation so that a PCR product comprising said position is amplified;
    30 iii) analyze the size of the amplified PCR product in ii), where a PCR product of the expected size according to the direct and inverse primers of step ii) (ie, expected size according to the position in which said primers hybridize) it is indicative of the presence of the genetic mutation, and the absence of said PCR product with the expected size is indicative of the absence of the genetic mutation.
    35
    image16
    In a particular embodiment of the second aspect of the invention according to any one of the previous embodiments, when the analysis of stage iii) indicates the presence of the genetic mutation, the method further comprises a stage iv), in which the product is sequenced PCR obtained in stage ii).
    In another particular embodiment of the second aspect of the invention according to any one of the previous embodiments, alternatively to step iii) a stage iv) is carried out, in which the PCR product obtained in step ii) is sequenced. In this case, the result of the sequencing will show the presence or not of the genetic mutation under study.
    In a preferred embodiment according to any one of the particular embodiments of the two preceding paragraphs, the product obtained in stage ii) is purified and concentrated before being sequenced in stage iv). In a preferred embodiment, the sequencing of step iv) is a Sanger sequencing, which as indicated above is a
    15 clinical standard sequencing.
    As indicated above, many of the genetic mutations characterized by the methods of the present invention are associated with pathologies. Thus, in a particular embodiment according to any one of the embodiments of the second aspect of the
    In the invention, the genetic mutation is associated with a pathology, such as heart disease, cancer, neurological development disorders, Crohn's disease, rheumatoid arthritis, type 1 and type 2 diabetes, etc. In a preferred embodiment, the pathology is a family heart disease, more preferably it is a cardiomyopathy or canalopathy.
    25 Since the method according to the second aspect of the present invention makes it possible to determine the presence or not of a mutation and said mutation can be associated with a pathology, said method can be used in the diagnosis of said pathology. Thus, in a third aspect, the present invention relates to a method of diagnosing a pathology associated with a given genetic mutation comprising the steps of the method according to a
    Any of the embodiments of the second aspect of the invention in which stage iii) is carried out, the subject being diagnosed as being affected by the pathology when the PCR product of stage iii) is the expected size according to direct and reverse primers used in stage ii).
    The third aspect of the invention also relates to a method of diagnosing a pathology associated with a given genetic mutation comprising the steps of the method.
    5
    10
    fifteen
    twenty
    25
    30
    35
    according to any one of the embodiments of the second aspect of the invention in which stage iv) is carried out instead of stage iii), the subject being diagnosed as being affected by the pathology when sequencing stage IV) reveals the presence of the genetic mutation.
    The third aspect of the invention also relates to the use of a method according to any one of the embodiments of the first or second aspect of the present invention, for the diagnosis of a pathology associated with a genetic mutation.
    In a preferred embodiment according to any of the embodiments of the third aspect of the invention, the pathology is selected from the group consisting of heart disease, cancer, neurological development disorders, Crohn's disease, rheumatoid arthritis, type 1 diabetes and type 2 diabetes. In a preferred embodiment, the pathology is a family heart disease, more preferably it is a cardiomyopathy or canalopathy. In another preferred embodiment the pathology is selected from the group formed by Marfan syndrome, muscular dystrophy and dilated cardiomyopathy.
    Other applications or uses of the methods of the present invention include the identification of the sequence of a haplotype along a segment of the chromosome (as, for example, to determine the origin of various mutations in the case of compound heterozygotes), or the determination of DNA insertion points in biological materials used in gene therapy, production of transgenic organisms, etc.
    Finally, in a fourth aspect, the present invention relates to a kit for carrying out the method according to the first, second or third aspects, comprising: a degenerate primer b1), as defined in any of particular embodiments of the first aspect of the invention, preferably of sequence SEQ ID No. 1, - a specific primer b2) as defined in the first aspect of the invention, preferably of sequence SEQ ID No. 2 or SEQ ID No. 5 .
    In a preferred embodiment according to any one of the embodiments of the preceding paragraph the degenerate primer is a degenerate primer phosphorylated at its 5 'end. Examples
    The following are concrete examples of embodiments of the invention that serve to illustrate the invention without limiting the scope thereof.
    image17 EXAMPLE 1: Characterization of the deletion of exons 59-66 of the FBN1 gene.
    1.1.-Identification of the ANC region - loss of genetic material (deletion) The DNA was extracted from 1 mL of blood in an automatic nucleic acid extractor 5 QIAsymphony SP (QIAGEN) using the QIAsymphony DSP DNA Midi Kit.
    Samples were obtained from different subjects, specifically, the subject under study and other subjects without the heart disease under study. Mutations in the FBN1 gene are associated with the development of Marfan syndrome, a pathology consistent with the clinical data of the subject under study.
    10 Samples were prepared using the “SureSelectXT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library” (Agilent, SureSelectXT Target Enrichment System for Illumina Paired-End Multiplexed Sequencing Library Protocol Version B4, August 2015 SureSelect platform manufactured with Agilent SurePrint Technology ), by
    15 hybridization with a solution of probes homologous to the exonic region of 214 genes, and sequenced in a HiSeq 1500 (Illumina). Comparison of coverage depth between samples sequenced in parallel (Yoon et al., Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 2009; 19: 1586–92) allowed to identify, in one of the DNA samples, the deletion of the last 8
    20 exons (exons 59-66) of the FBN1 gene. The deletion began at an indeterminate point of intron 58 and extended into the intergenic space downstream of the FBN1 gene (ANC region = chr15: 48703095-48718147; reference genome hg19). Thus, the ANC region comprises exons 59-66 of the FBN1 gene.
    25 Mutations in this gene are associated with the development of Marfan syndrome, a pathology consistent with the clinical data of the subject under study of DNA. The deletion extends into the intergenic space, in an area not covered by the enrichment method used in the sample preparation. Therefore, the deletion could range from 14 Kb to 6 Mb (distance to which the nearest gene present in the enriched region is located). Be
    30 uses the method of the invention to characterize the exact extent of the mutation.
    1.2.-Amplification 1.2.1.-Composition of the PCR reaction: 10X Long PCR buffer with 15 mM MgCl2 5 µL 35 dNTP Mix, 2 mM each 5 µl (0.2 mM each). Specific primer FBN1-Ex58-FW 1 µM
    image18
    DNA template 50 ng N7 * 0.2 µM Long PCR Enzyme (Thermo Scientific, K0181) 2.5 U H2O nuclease free up to 50 µL
    5 (*): N7 = mixture of 5 ’phosphorylated degenerate primers (SEQ ID No. 1 phosphorylated at its 5 ′ end: 5’-pNNNNNNN-3’). Primer FBN1-Ex58-FW: GCTTTCCCCTCTTGCTTCTTCT (SEQ ID No. 2), hybridizes out of the ANC region and extends to the ANC region.
    10
    1.2.2.-PCR reaction conditions: 3 min, 94 ° C; 10 cycles [94 ° C, 20s; 60 ° C 30 s; 30 ° C, 1 s; 68 ° C, 20 min]; 25 cycles [94 ° C, 20s; 60 ° C; 30 s 30 ° C, 1 s; 68 ° C, 20 min, with an extension of 15 s
    15 per cycle] Final extension of 10 min at 68 ° C.
    Reaction mixture and PCR conditions optimized to amplify 30 Kb.
    20 1.3.-Preparation of amplification products for sequencing: 1.3.1.-Elimination of primers and fragments of low molecular weight using Agencourt AMPure XP (Beckman Coulter, A63881) following the manufacturer's instructions. 1.3.2.-Preparation of libraries with NEXTflex ™ Rapid DNA Sequencing Kit (Bioo Scientific, 5144-02) and NEXTflex ™ DNA Barcodes-96 (Bioo Scientific, 514105) kits following the
    25 manufacturer's instructions. 1.3.3.-Sample quantification and preparation of a pool for the sequencing of libraries.
    1.4.-NGS sequencing of libraries:
    30 NGS sequencing was performed on an Illumina Hi-Seq 1500 ultrasequencer. Sequencing was carried out in Rapid mode and “Paired-end” format at 2x100 (HISEQ Rapid SBS Kit v2).
    1.5.-Bioinformatic analysis 35 The demultiplexing of libraries was done with CASAVA 1.8.2 software (Illumina). The files corresponding to each sample (in Fastq format) were aligned in front of the
    image19
    human reference sequence GRCh37 / hg19 using the BWA-MEM software.
    This analysis allowed to detect several non-duplicated and localized chimeric sequences
    5 upstream of the deletion (Figure 1). Comparison of these chimeric sequences with the reference genome using the BLAT tool (UCSC Genome Browser) showed that these sequences included, covering both ends, an apparent deletion of ~ 73.8 Kb (Figure 1).
    10 1.6.-Confirmation and screening To confirm that said deletion was real, oligonucleotides were designed and synthesized at both 3 'and 5' ends of the deletion. A PCR reaction on the DNA of the sample that presented the deletion and with the direct (FBN1_del8-FW) and reverse (FBN1_del8-RV) primers of sequence SEQ ID No. 3 (TGGAAAAGCACAAGCTCCTT) and SEQ ID No. 4
    15 (CCAGGCAAGTGTCAGCATTA), respectively, produced an amplicon of ~ 500 bp that did not appear in control samples. This amplicon was sequenced by means of Sanger sequencing and confirmed the presence of a deletion with coordinates NC_000015.9: g.48645275_48719058del (marked with * in Figure 1). Thus, the study of the possible presence of the mutation in samples of relatives
    20 of the subject under study is simplified to the analysis of the amplicon obtained from the primers flanking the deletion, such as the oligonucleotides of SEQ ID No. 3 and SEQ ID No. 4.
    EXAMPLE 2: Characterization of the duplication of exons 46 and 47 of the DMD gene.
    25 2.1.-Identification of the ANC region - gain of genetic material (insertion) It was carried out as in section 1.1, but the duplication of exons 46 and 47 and part of the adjacent introns of the DMD gene was analyzed. Mutations in this gene are associated with the development of muscular dystrophy and dilated cardiomyopathy, a pathology consistent with the clinical data of the DNA donor. Duplication includes full exons 46 and 47 and
    30 part of introns 45 and 47, but not exons 45 or 48 (ANC region = chrX: 3194670531951957; reference genome, hg19), so it could range from 5.2 Kb to 100 Kb. No information is obtained on the point of insertion in the genome. The method of the invention is used to characterize the exact extent and location of the mutation.
    35 2.2.-Amplification In this case, an oligonucleotide is designed that includes in its region 5 ’a sequence complementary to that of the 3’ end to minimize the possibility of nonspecific hybridization at low temperatures of “annealing” (second hybridization).
    image20
    The specific primer is used:
    5 Primer DMDdup-Ex47-RV 5’-CACATAGTTGTTTTGTTGTCTTTTGGGAACTATGTG (SEQ ID NO: 5). The underlined sequence (positions 8-36 of the primer) is complementary to the coordinates NC_000023.10: g. 31951631-31951659, contained within the duplicated zone. Positions 1-9 of the oligonucleotide are complementary to positions 28
    10 36 (both in bold). It is predicted according to different models (RNAstructure: Reuter & Mathews, RNAstructure: Software for RNA secondary structure prediction and analysis. BMC Bioinformatics 2010; 11: 129; RNAfold: Hofacker et al., Fast folding and comparison of RNA secondary structures. Monatsh Chemie 1994 ; 125: 167-8) that this primer has a secondary structure at 30 ° C (temperature of the second hybridization) (see Figure 2). The
    15 same programs predict absence of secondary structure at 60 ° C (temperature of the first hybridization).
    The PCR reaction was the same (except for the specific primer) as in Example 1 and was carried out under the same conditions as in Example 1.
    20 2.3-2.5 The preparation of the amplification products, NGS sequencing and bioinformatic analysis were carried out as explained in Example 1.
    The analysis allowed detecting paired sequences (identified by sequencing “pairedend”) not duplicated and that are compatible with the presence of a tandem duplication (Figure 3). Comparison of these sequences with the reference genome using the BLAT tool (Kent, BLAT - the BLAST-like alignment tool. Genome Res 2002; 12: 656-64. UCSC Genome Browser) suggested that these sequences encompassed the
    30 extremes of a possible tandem duplication of ~ 32.4 Kb which includes exons 46 and 47 of DMD (Figure 3).
    2.6.-Confirmation and screening To confirm that said duplication was real, primers were designed and synthesized at both ends of the possible duplicated region. A PCR reaction on the DNA of the sample that presented duplication with the DMD_46-47dup-FW oligonucleotides of SEC
    image21
    ID No. 6 (CAGTTGGCAGAGAAAACACG) and DMD_46-47dup-RV of SEQ ID No. 7 (TATCGCTTTGCCTACGCTCT) produced an ~ 500 bp amplicon that did not appear in control samples. This amplicon was sequenced by means of Sanger sequencing and the presence of a tandem duplication of the chromosomal region corresponding to the coordinates NC_000023.10: g.31920489_31953173dup was confirmed. Thus, the study of the possible presence of the mutation in samples of relatives of the subject under study is simplified to the analysis of the amplicon obtained from primers SEQ ID NO. 6 and 7 that flank the insertion point of the duplication.
    权利要求:
    Claims (15)
    [1]
    image 1
    1.-Method to identify the position of a genetic mutation characterized by comprising the following stages:
    5 a) determine the ANC region comprising the genetic mutation under study; b) carry out a PCR, where the PCR template is DNA extracted from a biological sample taken from the subject under study and the primers are:
    b1) a degenerate primer, and b2) a specific primer that specifically hybridizes:
    10 - within the ANC region, at a distance of 0.2-100 Kb from any of the ends of the ANC region, if the mutation comprises a gain of genetic material, a translocation or a gene fusion, and is extended by the PCR out of the ANC region, or
    -out of the ANC region, at a distance of 0.2-100 Kb from any of the
    15 ends of the ANC region, if the mutation comprises a loss of genetic material, and is extended by PCR to the ANC region, and where in the PCR reaction the hybridization stage comprises two consecutive hybridizations, a first hybridization at a temperature of hybridization equal to the Tm of the specific primer ± 10 ° C, and a second hybridization at a hybridization temperature
    20 equal to the Tm of the degenerated primer ± 5 ° C; c) sequencing the amplification product obtained in step b); and d) align the sequence obtained in step c) with a reference genome to identify the position of the mutation.
    2. Method according to the preceding claim, wherein step a) is carried out from DNA or RNA extracted from a biological sample taken from the subject under study.
    [3]
    3. Method according to the preceding claim, wherein step a) is carried out from DNA and by a technique selected from the group consisting of MLPA, CGH array, SNP array, 30 NGS, Southern blot, karyotype analysis, FISH, RT-PCR and ∆-PCR, preferably MLPA, CGH array, SNP array and NGS and more preferably NGS.
    [4]
    4. Method according to any one of the preceding claims, wherein in step b) the PCR template is cDNA, cDNA or cDNA, preferably cDNA or cDNA and more preferably cDNA.
    image2
    [5]
    5. Method according to any one of the preceding claims, wherein in step b) the degenerate primer is a degenerate primer phosphorylated at its 5 'end, preferably mono-phosphorylated.
    6. Method according to any one of the preceding claims, wherein the specific primer comprises at the 5'-end a sequence complementary to that of its 3'-end, preferably 5-12 nucleotides and more preferably 7-9 nucleotides.
    [7]
    7. Method according to any one of the preceding claims, wherein the degenerated primer 10 has between 5 and 16 nucleotides, preferably between 5 and 11, and more preferably 7 nucleotides.
    [8]
    8. Method according to any one of the preceding claims, wherein the hybridization temperature of the second hybridization is between 20-40 ° C, preferably 27-33 ° C and more preferably 30 ° C.
    [9]
    9. Method according to any one of the preceding claims, wherein the second hybridization is carried out for a time between 1 and 10 seconds, preferably 13 seconds and more preferably 1 second.
    Method according to any one of the preceding claims, wherein the specific primer hybridizes at 0.5-80 Kb, preferably 0.5-40 Kb and more preferably 0.5-20 Kb of the 3'o 5 'end of the ANC region.
    11. Method according to any one of the preceding claims, wherein the degenerated primer has the sequence SEQ ID No. 1.
    [12]
    12. Method according to any one of the preceding claims, wherein the specific primer has the sequence SEQ ID No. 2 or SEQ ID No. 5.
    13. Method according to any one of the preceding claims, wherein the sequencing of step c) is carried out by NGS.
    [14]
    14. Method according to any one of the preceding claims, wherein after step d) in which the position of the mutation is identified, a step e) is carried out in which said position is reconfirmed by Sanger sequencing.
    image3
    [15]
    15. Method according to any one of the preceding claims, wherein the genetic mutation is a structural variant.
    16. Method according to the preceding claim, wherein the structural variant is selected from the group consisting of a structural variant characterized by a loss of genetic material, a structural variant characterized by a gain of genetic material, a translocation, a gene fusion and combinations from the same.
    17. Method according to any one of the preceding claims, wherein the genetic mutation is selected from the group consisting of insertion, deletion, duplication, transgeneration, translocation and gene fusion, preferably insertion, duplication or deletion.
    [18]
    18.-Method for screening a genetic mutation characterized by comprising the
    The following steps: i) identify the position of a genetic mutation following the method according to any one of claims 1-17; ii) carry out a PCR where the model DNA is DNA extracted from a sample taken from a subject under study and the primers are a direct primer and a primer
    20 that specifically hybridize upstream and downstream, respectively, of the exact position of the mutation under study; iii) analyze the size of the amplified PCR product in ii), where a PCR product of the expected size according to the direct and reverse primers of step ii) is indicative of the presence of the genetic mutation, and the absence of said product of PCR is indicative of
    25 absence of the genetic mutation.
    [19]
    19. Method according to claim 18, further comprising a stage iv), subsequent to stage iii), wherein the PCR product obtained in stage ii) is sequenced.
    20. Method according to claim 19, wherein the sequencing is a Sanger sequencing.
    [21]
    21. Method according to claim 18, which comprises instead of step iii) a stage iv) in which the PCR product obtained in stage ii) is sequenced, wherein the result of the sequencing will show the presence or absence of the genetic mutation under study.
    image4
    [22]
    22. Method according to claim 21, wherein the sequencing is a Sanger sequencing.
    [23]
    23.-Diagnostic method of a pathology associated with a genetic mutation
    5 characterized in that it comprises the steps of the method according to any one of claims 18-20, the subject being diagnosed as being affected by the pathology when the PCR product of stage iii) is the expected size according to the direct and reverse primers used in stage ii).
    10 24-Method of diagnosis of a pathology associated with a genetic mutation characterized in that it comprises the steps of the method according to any one of claims 21-22, the subject being diagnosed as being affected by the pathology when sequencing stage IV ) reveals the presence of the genetic mutation.
    25. Method according to any one of the preceding claims, wherein the biological sample is selected from the group consisting of fresh or fixed tissue obtained from biopsy or autopsy, blood, plasma, serum, urine, feces, saliva, ejaculate, bone marrow, cerebrospinal fluid, ascites fluid, synovial fluid, amniotic fluid, buccal or buccal exudate
    20 pharyngeal, pleural fluid, peritoneal fluid, pericardial fluid, cerebrospinal fluid, intraarticular fluid, and mixtures thereof.
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    同族专利:
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    ES2641690B1|2018-09-06|
    引用文献:
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    GB2364054A|2000-03-24|2002-01-16|Smithkline Beecham Corp|Amplification of quinolone resistance determining regions using degenerate primers|
    US20070148637A1|2005-12-27|2007-06-28|Bureau Of Animal And Plant Health Inspection And Quarantine, Council Of Agriculture, Executive Yuan|Species-specific probes for identification of target virus and identification method using said probes|
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