• 专利附录
  • 专利说明
  • 权利要求
  • 类似技术
  • 同族专利
  • 引用文献
  • 法律状态
  • 优先权
    • 专利摘要:
    Method for the study of mutations in embryos in in vitro reproduction processes with the particularity that it combines the techniques of detection of Aneuploidy (DPG-A) and the study of monogenic diseases in embryos (DGP-M) and that is understood, a SNP selection process where the values of some n candidate SNPs (t1 ... tk) of each individual x, in a chromosomal region of interest and specifically extracted for a population under study; a selection process for SNPs, all combinations of SNPs are evaluated to obtain a minimum set t of tagSNPs from the matrix M obtained in the first selection process for SNPs; and an in-silical validation process of the tagSNPs panel obtained in the second process. (Machine-translation by Google Translate, not legally binding)
    公开号:ES2738176A1
    申请号:ES201830731
    申请日:2018-07-20
    公开日:2020-01-20
    发明作者:Mas Luis A Alcaraz；Fernandez Natalia Castejon
    申请人:Bioarray S L；
    IPC主号:
    专利说明:

    [0001]
    [0002] METHOD FOR THE STUDY OF EMBRYO MUTATIONS IN PROCESSES OF
    [0003]
    [0004] The object of the present invention is a method for the study of mutations in embryos in in vitro reproduction processes with the particularity that it combines the techniques of detection of Aneuploidy (DPG-A) and the study of monogenic diseases in embryos (DGP- M) according to claim 1.
    [0005]
    [0006] FIELD OF THE TECHNIQUE
    [0007]
    [0008] The present invention relates to a method for the study of mutations in embryos of couples subjected to in vitro reproduction cycles by SNP (single nucleotide polymorphisms) analysis by massive sequencing combining the detection of Aneuploidies (DGP-A Preimplantation Genetic Diagnosis of Aneuploidies) and the study of monogenic diseases in embryos (DGP-M, Preimplantation Genetic Diagnosis for Monogenic diseases) with a single biopsy.
    [0009]
    [0010] STATE OF THE PREVIOUS TECHNIQUE
    [0011]
    [0012] A single nucleotide polymorphism or SNP is a variation in the DNA sequence that affects a single base (adenine (A), thymine (T), cytosine (C) or guanine (G)) of a genome sequence.
    [0013]
    [0014] Preimplantation genetic diagnosis (PGD) was developed in the 80s of the twentieth century as an option for those couples who were at risk of having a child affected by a monogenic disease or a certain chromosomal alteration and who wanted to avoid the possibility of requiring a voluntary termination of pregnancy.
    [0015]
    [0016] The DGP consists in performing a biopsy of one or more cells of the embryos generated during an in vitro fertilization cycle when the embryos have between 3 and 5 days, to use said material in the elaboration of a genetic diagnosis. Thus, only those embryos diagnosed as unaffected by a certain genetic alteration are transferred to be able to breed a healthy child.
    [0017] It should be noted that the DGP has two characteristics that differentiate it from the genetic diagnosis applied to any other field. First, the response time must be much shorter, since, in many cases, it is necessary to obtain results in less than 24 hours to allow the transfer of embryos in the same cycle. Thus, for example, an embryo biopsied on day 3 must be transferred or vitrified on day 5 or 6. On the other hand, normally, each couple produces an average of 6 to 10 embryos, so the cost of the analysis must be low to be able to analyze all the embryos and that this does not suppose a substantial increase of what already costs in itself a cycle of reproduction in vitro.
    [0018]
    [0019] Due to the above, the DGP is performed using multiple and varied techniques, depending on the nature of the alteration studied. Traditionally, methods based on polymerase chain reaction (PCR) and fragment analysis were used for monogenic diseases and, more recently, systems such as Karyomapping based on the use of microarrays applied to the detection of SNPs (for example, as described in document ES2360085T3). Although these are very diverse methods, they all have characteristics in common:
    [0020]
    [0021] First, they require prior amplification. In this case, it works with very little genetic starting material - in many cases, from a single cell - so it is necessary to amplify it. For this, traditionally, a method known as MDA ( Multiple Displacement Amplification) is used that amplifies the genetic material thanks to the Phi29 polymerase at a constant temperature. This method produces long DNA fragments with a low error rate.
    [0022]
    [0023] Second, they have a high Allele-Drop-Out (ADO) rate. The ADO is a frequent artifact in this type of analysis - about 5% of the analyzes have it - which consists in the preferential amplification of one of the alleles. For this reason, if an analysis does not detect mutation, it is possible that it is because the mutated allele has not been amplified.
    [0024]
    [0025] Third, an indirect analysis is performed. As a consequence of the above, an indirect analysis of the mutation is always made. This analysis consists of studying a series of polymorphisms around the mutation - usually STR or Short Tandem Repeats - and determining if the polymorphisms present in the embryo are those associated with the pathological allele or the healthy allele, that is, a linkage analysis is performed .
    [0026] Fourth, they require a study of previous informativity. In order to determine which polymorphisms secrete with the healthy allele and which with the pathological one, it is necessary to conduct a study of previous informativity. This study consists of analyzing 5 to 10 STR near the mutation - located on both sides - in the couple and in other family members. Ideally, a child in common with the mutation, or parents of the couple. Thus, for example, if it is possible to be associated that a certain number of repetitions of a specific STR is always present in relatives with the pathogenic mutation, said polymorphism can be associated with the pathological allele and discard those embryos that possess it.
    [0027]
    [0028] Finally, direct analysis of the mutation is not always possible. Whenever possible, direct analysis of embryo mutation is performed, usually by mini sequencing. However, this is only possible if it is a point mutation. With this type of techniques, it is not possible to detect other types of alterations, such as deletions. For its part, Karyomapping is not able to detect direct mutation in any case.
    [0029]
    [0030] Recently, mass sequencing (NGS) has been incorporated into the DGP as a technique - as described in US20140274741, WO2014082032, US20150038337 or EP2947156-. However, in the state of the art only its application to the detection of aneuploidies (DGP-A) is described.
    [0031]
    [0032] Although technology has evolved in the refinement of these DGP techniques, there are currently certain limitations in the analysis technique. The main techniques and their limitations in DGP are:
    [0033]
    [0034] CGH Microarray (Comparative Genomic Hybridization). This technique is used for the detection of aneuploidies (DGP-A) and unbalanced alterations when one of the parents is a carrier of a balanced disorder. The main limitations of the technique are:
    [0035]
    [0036] It is an expensive technique, so that many of the couples who would really benefit from it - for example, elderly mothers, since a large number of their oocytes will be aneuploid - cannot opt for them.
    [0037] A PCR-based amplification method is used, which has a much higher percentage of ADO than MDA-based methods, which makes integration with techniques for the study of monogenic diseases difficult, as indicated above.
    [0038]
    [0039] It requires specific equipment, such as a microarray scanner.
    [0040]
    [0041] It does not allow the analysis of mutations, so it cannot be used to select embryos free of genetic pathology, when parents are carriers.
    [0042]
    [0043] It does not allow to distinguish between normal embryos and those that carry a balanced translocation.
    [0044]
    [0045] It does not allow to identify those embryos that carry numerical anomalies in mosaic.
    [0046]
    [0047] Mini sequencing It is used for the direct detection of a specific mutation in the study of monogenic diseases in embryos (DGP-M). The main limitations are:
    [0048]
    [0049] It requires the design of specific oligos in a very specific region, which can make analysis difficult.
    [0050]
    [0051] It requires prior amplification by MDA, so it is not easily combinable with aneuploidy screening techniques.
    [0052]
    [0053] Prior knowledge of the mutation to be analyzed, and a long process of tuning is needed.
    [0054]
    [0055] Requires a hair sequencer.
    [0056]
    [0057] It does not allow the detection of structural anomalies of any kind.
    [0058]
    [0059] It is only useful in the case of point mutations.
    [0060] Fragment analysis It is used alone or in conjunction with the previous one, to make the indirect study of the pathologies, so the limitations are the same as in the case of mini-sequencing, in addition to:
    [0061]
    [0062] It requires the design of specific fluorescently labeled oligos to design the study of previous informativity.
    [0063]
    [0064] Occasionally, the informativity study may be extended due to the difficulty of finding informative STRs.
    [0065]
    [0066] Karyomapping It is a technique that analyzes thousands of polymorphisms by microarray, combining aneuploidy analysis and the study of monogenic diseases. The great advantage is that the same microarray is used to analyze different pathologies. Its limitations are as follows:
    [0067]
    [0068] Although it detects aneuploidies, it is not able to detect mitotic errors, which means that it is not able to determine the presence of mosaicism.
    [0069]
    [0070] It requires samples in a trio (father, mother and child with prior affection) to determine the segregation of the alleles. This is because it only makes indirect study.
    [0071]
    [0072] It is not possible to detect the mutation itself in any case, so the risk of recombination is never excluded.
    [0073]
    [0074] It's expensive.
    [0075]
    [0076] The protocol is long and cannot be used for cycles with fresh transfer.
    [0077]
    [0078] Document ES2360085T3 describes that chromosomal analysis by molecular karyotyping (for example, for the detection of trisomy) can be carried out using an analysis of biallelic markers of the complete genome (e.g., biallelic single nucleotide polymorphisms (SNPs)) that are distributed throughout the genome, and that can be easily detected using existing technologies. This discovery is unexpected for several reasons, mainly because a biallelic marker would be assumed a priori (which provides only binary information at a given position on the chromosome) could not positively identify the presence of three or more different chromosomes.
    [0079]
    [0080] However, this document performs a high density analysis of nearby adjacent SNPs is able to positively identify, among others, the presence of two chromosomes derived from a parent and based on well-established assumptions about the frequency and spacing of recombination events between Parental chromosomes during meiosis, this will allow accurate detection of trisomy. In addition, the parental origin of the error is identified in each case, which is not possible by some karyotyping procedures.
    [0081]
    [0082] However, it has not yet been possible to successfully establish a fast, efficient and economical method that allows DGP-A and DGP-M to be combined with a single biopsy. Therefore, the advancement of the technique is in the sense of perfecting the DGP-A and DGP-M tools with a single biopsy through mass sequencing, the main line in the development of this project.
    [0083]
    [0084] EXPLANATION OF THE INVENTION
    [0085]
    [0086] An object of the present invention is a method that combines DGP-A and DGP-M techniques with a single biopsy by mass sequencing. This object is achieved by the method of claim 1. Particular embodiments of the method of the invention are shown in the dependent claims. In other aspects the kit is included which includes an electronic device that executes the method of the invention as well as the software product containing the executable instructions for carrying out the method of the present invention.
    [0087]
    [0088] For the combination of both techniques, the preparation of a library for DGP-A is first performed. Any commercial kit available can be used in the preparation of this library. as, for example, Ion Reproseq ( ThermoFisher), PicoPlex ( Rubicon Genomics), Veríseq ( Illumina) and Repli-G ( Qiagen).
    [0089]
    [0090] Subsequently, an aliquot of that amplified DNA is taken, and a method is applied to enrich the SNPs that are interesting. Preferably, this method is based on multiplex amplification, but capture methods, simple PCR, or any other can also be used. After the amplification of the regions of interest, the preparation is carried out of libraries, adding the necessary adapters and barcodes. Thus, the library for DGP-M will be held.
    [0091]
    [0092] Finally, after the quantification of both libraries, they are combined in certain proportions, and the standard sequencing protocol for the chosen platform is continued. As different library preparation methods are used for both processes, each with its barcode, the sequencer throws the results of DGP-A and DGP-M separately. Thus, the analysis is performed independently for DGP-A, using the appropriate solution according to the library and sequencer preparation method selected, while the DGP-M analysis is performed by a SNP quench, as described below.
    [0093]
    [0094] This protocol is faster than other technologies such as Karyomapping (ES2360085T3) because it only adds four hours (time to prepare the DGP-M library) to the global DGP-A process through mass sequencing. Thus, if, for example, the combination of Ion Rerproseq for DGP-A is used together with the method of the invention, the entire process can be carried out in less than twelve hours, thus being an ideal method to perform biopsy in D-3 and transfer in D-5, but also for biopsy in D-5 and transfer in D-6 and, obviously, for cycles with deferred transfer because in the protocol there are multiple steps where it can be stopped.
    [0095]
    [0096] This method is also cheaper than methods based on karyotyping or karyomaping (ES2360085T3) because the price depends on the cost of library preparation for DGP-A. In addition, it is adaptable to the number of samples that are to be analyzed, while a 12-array slide is used in the karyotype mapping, so the number of samples must be a multiple of 12 to maximize results.
    [0097]
    [0098] For example, a library for DGP-A can be prepared using Ion Reproseq. If the couple has, for example, 8 embryos, 8 different libraries will be prepared with the corresponding barcodes, from 1 to 8. After this library, an aliquot is taken and the corresponding polymorphisms are amplified. If the couple is a carrier, for example, of mutations in the SMN1 gene, a kit that amplifies certain polymorphisms around that mutation will be used. After amplification, the library will be prepared using the corresponding method. One method could be amplification by multiplex PCR using Ampliseq, with its corresponding library preparation kit, and by adding different barcodes to the previous ones (for example, from 9 to 16). Both are quantified libraries, and they are mixed in a 3: 1 ratio, that is, three times more DGP-A library than DGP-M library. After quantification, if the sequencing method selected is, for example, PGM Ion, sequencing is prepared and sequencing itself, using the standard protocol of the equipment manufacturer. Once the sequencing is finished, the sequencer will throw us 16 files, 8 for the DGP-A library and 8 for DGP-M. The files for DGP-A will be analyzed using the equipment manufacturer's software, or any other solution. For the DGP-M analysis, the SNPs will be sampled using the software proposed in the present invention. FIG. 1 shows an outline of the entire process.
    [0099]
    [0100] Thanks to the method thus described, the combination of DGP-A and DGP-M techniques is possible by mass sequencing. In addition, it is considerably faster than karyotyping based technologies or cariomapeado (Karyomapping) as well as being more economical.
    [0101]
    [0102] Throughout the description and the claims, the word "comprises" and its variants are not intended to exclude other technical characteristics, additives, components or steps. For those skilled in the art, other objects, advantages and features of the invention will be derived partly from the invention and partly from the practice of the invention. The following examples and drawings are provided by way of illustration and are not intended to restrict the present invention. In addition, the invention covers all possible combinations of particular and preferred embodiments indicated herein.
    [0103]
    [0104] BRIEF DESCRIPTION OF THE DRAWINGS
    [0105]
    [0106] Next, a series of drawings that help to better understand the invention and that expressly relate to an embodiment of said invention, which is illustrated as a non-limiting example thereof, is described very briefly.
    [0107]
    [0108] FIG. 1 shows a scheme of the method object of the present invention. First, the gene is analyzed with the mutation to be discarded in the embryos and a region around (typically, 4 Mb) is selected. Those polymorphisms that do not meet any exclusion criteria are selected, and those most likely to be informative are sought. On the other hand, those polymorphisms that can be tag are identified by correlation analysis and linkage imbalance. With both, it is done a final panel design, and an in silico validation is done simulating crosslinks between a multitude of individuals whose genomes are deposited in public databases.
    [0109]
    [0110] FIG. 2 shows a diagram of the entire process, including the method of the invention, for a first example of use, starting with the design and synthesis of the panel that will then be used for library amplification for DGP-M. On the one hand, patients and other relatives are analyzed to determine the distribution of polymorphisms in the different alleles. As for the samples of the embryos, after the biopsy, the library for DGP-A is prepared, and with an aliquot of this the library for DGP-M is prepared. All libraries are quantified and mixed, and sequencing is carried out. Finally, the bioinformatic analysis of aneuploidies and monogenic disease is performed independently.
    [0111]
    [0112] FIG. 3 shows an example of SNP fasting, in the case of a trio formed by the couple and an affected child. SNPs are shown before and after fasar, with their distribution in alleles. In addition, which are informative (give information about the phase) and which are not.
    [0113]
    [0114] FIG. 4 shows an example of SNPs fasting with analysis of results in embryos. For simplicity, only those SNPs that are informative are shown. In this case, the couple carries heterozygous mutations in the CEP290 gene , which causes Meckel syndrome. This syndrome is lethal prenatal, so the DNA of a previous fetus was used for the patient. In this case, the panel was designed including the direct analysis of the mutation, which appears shaded.
    [0115]
    [0116] FIG. 5 shows the result of SNPs fasting in an embryo, where different problems and artefacts appear, along with their description. The developed fasting algorithm allows detecting these errors.
    [0117]
    [0118] FIG. 6 shows an example of a couple with a balanced translocation, and the embryos that can be generated as a consequence. 50% of these embryos can inherit an unbalanced alteration with serious consequences (from repeated abortions to children with metal retardation and dysmorphic features). 25% of the embryos will be normal, and the other 25% will have a balanced alteration as one of the parents.
    [0119] EXPLANATION OF A DETAILED MODE OF EMBODIMENT OF THE INVENTION
    [0120]
    [0121] The method for studying embryonic mutations in in vitro reproduction processes,
    [0122] object of the present invention can be divided, in turn, into three sequential and differentiated processes. The method of the invention combines several tagSNPs selection techniques,
    [0123] because it calculates the linkage imbalance correlations for the block of interest (by default, 4 Mb around the mutation, 1 Mb is equal to one million nucleotides). SNPs
    [0124] of that region, in turn, will be considered as a block-free approach of
    [0125] so that all correlations between SNPs are calculated and taken into account in the selection of tagSNPs. In this way the present invention selects polymorphisms
    [0126] with a high probability of being informative, considering the allelic frequencies of the
    [0127] same within the target population and whether or not they are part of the same haploboque
    [0128] (set of SNPs that are inherited together). A tagSNP is that SNP that is considered representative for the entire haploblock, that is, if the tagSNP is in heterozygous,
    [0129] for example, all SNPs belonging to that same haploblock will be in heterozygosis. A tagSNP avoids having to analyze all polymorphisms because knowing how it behaves, it can be deduced how the rest of the haploblock polymorphs do.
    [0130]
    [0131] Therefore, the objective of the method of the invention (FIG. 1) is focused on obtaining a
    [0132] minimum panel of tagSNPs with maximum information capacity, simplifying the subsequent
    [0133] analysis and interpretation of the results of an informativity analysis.
    [0134]
    [0135] More specifically, the method of the invention comprises is divided into two processes
    [0136] basic and a third validation process. The first two processes do not necessarily have to be in this order:
    [0137]
    [0138] (i) A first SNP selection process:
    [0139] to. In this process, the values of the n candidate SNPs (t1 ... tk) of each individual x are taken as input, in a chromosomal region of interest and specifically extracted for the population under study. Those SNPS that are biallelic are selected, so individuals can be represented as haplotypes of length m formed by binary chains {1,0}, with 1 | 0 and 0 | 1 being the values for heterozygous SNPs and 0 | 0 and 1 | 1 values for homozygotes. This is done in the entire chromosomal region of interest that is defined as any position that is
    [0140] find 2 Mb (it is a default value that can be modified) upstream and 2 Mb downstream of the gene / mutation you want to study. b. After obtaining, the n candidate SNPs in the region are analyzed and those that meet any of the following conditions are excluded: i. SNPs with more than one alternative allele (non-biallelic SNPs) ii. SNPs whose alleles are different from a simple nucleotide change (indels, polynucleotide pattern changes, among others)
    [0141] iii. SNPs found in homozygosis in at least 99% of the population of interest
    [0142] iv. Uncommon SNPs, that is, whose allelic frequency is less than 1% c. The next point tries to maximize the situation in which one of the parents presents the value of a SNP in a heterozygous state, while in the other parent it is presented as homozygous, that is, it is informative. This is achieved through the maximization of the value of two functions above a certain threshold value:
    [0143]
    [0144] MaxP: p- (3p2) (4p3) - (2p4)
    [0145] HET rate: 2pq
    [0146]
    [0147] being p and q respectively the allelic frequencies of the reference and alternative alleles for each SNP. These are the Hardy-Weinberg equilibrium equations and their derivative.
    [0148] d. The output of this algorithm will be a panel of z SNPs optimized for both values in the form of matrix M whose columns correspond to the individuals in the population and the rows to the values of each SNP for each individual.
    [0149]
    [0150] (ii) A second SNP selection process:
    [0151] to. Through an exhaustive search, all combinations of SNPs are evaluated to obtain a minimum set t of tagSNPs from the matrix M obtained in point (i).
    [0152] b. First of all, the SNPs of the M matrix of the block-region are organized into high correlation groups based on the criterion of the pairwise R2. For this, the pairwise value r2 is calculated from the allelic frequency calculated for the matrix M. In this way SNPs of different groups will present low correlation, so two SNPs will belong to the same group only when the pairwise r2 between them exceed a certain threshold value (set by the user).
    [0153] c. After this, the selection of tagSNPs within each group is made based on the criterion of LD, starting with k = 1 SNPs and studying all possible kcombinations, organizing the SNPs within each group. d. Assuming two SNPs whose frequencies are p (allele of higher frequency) and q = 1-p. The equations are used:
    [0154]
    [0155] D> 0 ^ Dmax = min (pApb, papB) D = pAB-pApB D '= D / Dmax
    [0156] D <0 ^ Dmax = max-pApB, -papb
    [0157]
    [0158] Being pA and pB the observed probability of the p allele for SNP1 and SNP2 respectively and pa and pb the probability for the minor allele. Finally, pAB is the combined probability of the pair pq. By using these equations, those SNPs whose functional ranges exceed a certain threshold value will be considered tagSNPs.
    [0159]
    [0160] The organization of SNPs within each group based on the criterion of LD allows a selection to be made based on the functional range, ensuring that the first solution found is an optimal solution and considerably reducing the computation time.
    [0161]
    [0162] Finally, if an SNP does not exceed the thresholds of r2 or LD it will be considered in a group only and taken as tagSNP by itself.
    [0163]
    [0164] (iii) A third validation process consisting of an in-silica validation of the tagSNPs panel obtained. To do this and using the 1000Genomes db database [1], individuals are randomly chosen to perform multiple crossings. After this, the number of tagSNPS that were informative of each crossing is counted and the average is provided by way of informational information on the information power of the panel.
    [0165]
    [0166] As indicated, FIG. 2 shows a scheme of the method of the invention, in which first, the gene is analyzed with the mutation to be discarded in the embryos and a region around (typically, 4 Mb) is selected. Those polymorphisms that do not meet any exclusion criteria are selected, and those with higher Probability of being informative. On the other hand, those polymorphisms that can be tag are identified by correlation analysis and linkage imbalance. With both, a final panel design is carried out, and an in silico validation is done simulating cross-linking between a multitude of individuals whose genomes are deposited in public databases.
    [0167]
    [0168] Example 1. Diagnosis of aneuploidies
    [0169]
    [0170] The complete scheme for use in the diagnosis of aneuploidies is shown in FIG. 2. It is considered a European population couple where a member of the couple is a carrier of the autosomal dominant pathogenic variant VHL: c.233A> G p. (Asn78Ser) (chromosomal position chr13: 10183764) causing a condition known as Von Hippel syndrome -Lindau, which has an autosomal dominant mode of inheritance.
    [0171]
    [0172] The software input will be the 69473 SNPs contained in the chr13 block-region: 9181319-11681319. The output of this algorithm will be an M matrix of 1625 candidate SNPs, which will act as input for the SNP selection algorithm, whose output will consist of a panel of 283 tagSNPs. In the validation phase it was obtained that 49% of tagSNPs in the panel was informative on average.
    [0173]
    [0174] Wet lab part. Once the polymorphisms that we want to sequence have been selected, the positions are introduced in the corresponding enrichment platform. Preferably, Ion Ampliseq. This platform designs the oligos necessary to capture the regions. In the IVF laboratory, embryos that biopsy are generated when they reach the blastocyst stage. The biopsy is placed in a PCR tube and sent to the laboratory. In the laboratory, DNA is amplified using, for example, Ion Reproseq, so that, in addition to amplification, the library for DGP-A is made. Following the appropriate protocol, all regions designed with Ampliseq in the previously amplified material are amplified, and the library for DGP-M is produced. Subsequently, we do mass sequencing. It must be taken into account that in order to be able to sequence multiple samples simultaneously, it is necessary to mark the samples with a molecular bar code. Special care should be taken that bar codes do not match between samples.
    [0175]
    [0176] Analysis of data. Once the sequencing is finished, a series of files with readings for the entire embryo (DGP-A) and other files with the detected polymorphisms are obtained (DGP-M). With these files, a bioinformatic analysis should be done. With the former, aneuplodies are determined using the most appropriate software according to the platform. With the latter, the segregation pattern of each polymorphism is determined for the DGP-M analysis. First, the readings obtained are alienated from the reference genome, and polymorphisms are identified in each and every sample, including patients, relatives used as a reference and embryos. In the case of family members, the simplest situation is that in which we have a partner and an affectionate child. For the fasting of SNPs, we must determine which polymorphisms are shared in the trio and in this way find out which ones secrete with the healthy allele and which with the pathogenic. As biallelic SNPs have been selected, each sample can be 0/0, 0/1, 1/1 if they are homozygous for the wild SNP, heterozygous or homozygous for the alternative SNP, respectively. The number 0 is indicating that it is the reference SNP (whatever it may be) while 1 indicates that it is the alternative SNP. This is true for all chromosomes, except sex, in which women can be homozygous or heterozygous, while men are always hemizogotos (0 or 1). With this data, the SNPs fasting is carried out. For this, those SNPs that are informative in the couple are analyzed. Informative SNPs are those in which one of the patients is heterozygous (0/1) and the other is homozygous (0/0 or 1/1). The polymorphism used to marry is one that is different in the heterozygous individual. For example, if we have an individual 0/1 and the other 1/1, the polymorphism that we will use to fasar is 0. By comparison with one or more individuals in the family, it is determined arbitrarily to which allele each one belongs. An example of SNP fasting would be the following:
    [0177]
    [0178] It is considered the situation in which we have a partner with a child, each with their alleles. We consider that the father has the alleles P1 and P2, the mother M1 and M2. Logically, the son will have inherited an allele from each, for example, P1 from the father and M1 from the mother. If, when analyzing polymorphisms, it is obtained that the father is 0/1, the mother 1/1 and the son 0/1, we will determine that the polymorphism 0 belongs to the allele P1, which is shared between the father and the son, given that both present said polymorphism. In another case, we can have father 0/1, mother 1/1 and son 1/1. In that case, polymorphism 0 must necessarily belong to the P2 allele of the father, since it is not shared between father and son. Similarly, we proceed with all polymorphisms that are informative for the mother.
    [0179]
    [0180] Once the haplotypes of the parents have been determined, the embryos are analyzed. To do this, it is about identifying the informative SNP in each of the embryos For example, if polymorphism 0 belongs to the P1 allele, if an embryo exhibits said polymorphism, it means that it has said haplotype. In short, it is about identifying the informative SNPs in the different embryos and thus determining the haplotype of each one of them.
    [0181]
    [0182] An example of the fasting process of SNPs is shown in FIG. 3, where it is also specified whether the SNPs are informative, non-informative or semi-informative. An informative SNP is one that complies with the aforementioned, that is, that it is heterocygous in one of the parents, and homozygous in the other; a non-informative SNP can occur when both parents are homozygous, or both are heterozygous and the child is also homozygous; A semi-informative SNP occurs when both parents are heterozygous and the child is homozygous. This classification can be extended to other family combinations.
    [0183]
    [0184] Once the SNP is done with relatives, the polymorphism pattern must be compared with the sequenced embryos, and in this way we will determine which embryos are carriers and which are normal. FIG. 4 shows an example of SNPs fasting that includes embryo analysis.
    [0185]
    [0186] The SNP fasting algorithm is also able to identify the different possible sources of error and alert the analyst so that he can weigh and analyze them. These sources of error are diverse. The result for an embryo similar to FIG. 4 is shown in FIG. 5, but where the different sources of error are identified and described:
    [0187]
    [0188] For example, we can have an allele-drop-out phenomenon. This phenomenon implies that, in an embryo, only one of the alleles is amplified. So, when sequencing, we can interpret that an embryo is homozygous for a polymorphism, when in fact it is heterozygous. For example, an embryo may be 0/1 but have suffered an ADO phenomenon during amplification and be shown as 1/1 in sequencing. This failure can lead to a misinterpretation of the results, misleading the allele of the embryos. In order to avoid it, it is necessary to distinguish those polymorphisms that, in addition to being informative, are key. The key polymorphisms are what, besides being informative, are heterozygous in the embryo. For example, if we have a 0/1 father and a 1/1 mother, and the embryo at 0/1, polymorphism 0 will be key because it is informative and heterozygous. On the contrary, if the embryo is 1/1, the polymorphism only It will be informative. In the latter case we cannot determine if the embryo is really 1/1, or if we have suffered an allele-drop-out and we are only seeing one of the alleles 1.
    [0189]
    [0190] Another source of error is due to what is called No Call. It occurs when no signal is obtained for any of the alleles for a given polymorphism, so we cannot know even one of them.
    [0191]
    [0192] Finally, another source that can lead to confusion is recombination. A recombination is when the alleles in one of the parents are exchanged, and this is reflected in the embryo. For example, if we analyze 100 polymorphisms in an embryo, it may happen that part of them (for example, 60) belong to the P1 allele and the rest to the P2 allele. In order to identify recombination, it must happen that the change of allele P1 to P2 is sequential. That is, for example, that the first 60 polymorphisms belong to the P1 allele and the following to P2. If the exchange of polymorphisms occurs more or less randomly, that would mean that it is a sequencing error, because statistically it cannot happen that an embryo has more than two recombinations in a space as small as the analyzed fragment (4 Mb)
    [0193]
    [0194] It may also happen that there are sequencing errors or artifacts. These artifacts can be easily identified because they look like recombinations or alleledrop-outs, but they happen sporadically in one or very few positions.
    [0195]
    [0196] Finally, in order to be able to assign the alleles unequivocally, it is required that there be at least three informative polymorphisms and that they are also key on each side of the mutation, consecutively, in addition to at least another 3 more non-key polymorphisms.
    [0197]
    [0198] Example 2. Identification of triploid embryos
    [0199]
    [0200] Triploid embryos are an important problem in any IVF cycle. These account for 15% of spontaneous abortions due to chromosomal abnormalities. Triploid embryos should always be discarded from any in vito fertilization cycle , but it is difficult to identify them because there are no differences in embryonic quality with respect to normal embryos. Sometimes, it is possible to distinguish them because in D + 1 They observe three pronuclei, but it is not always possible. The triploid embryos can be of dysmemic origin (in cases of IVF) or originate from an oocyte failure by not extruding the second polar corpuscle.
    [0201]
    [0202] Triploid embryos cannot be identified by current DGP-A techniques, despite being a numerical anomaly. Sometimes, by visual inspection, it is possible to detect embryos 46, XXY by observing an abnormal distribution of sex chromosome readings, but it is not always possible and requires trained personnel.
    [0203]
    [0204] The method described here can be used to identify this type of embryos. You can select informational polymorphisms throughout the genome and determine if they are triploids by analyzing the present polymorphisms and their frequency. Normally, a heterozygous polymorphism should be found in a proportion around 0.5, because half of the readings will correspond to one allele and half to another. A triploid embryo has three alleles, so this proportion will be diverted. Thus, the result can be three polymorphisms for the same position (if they are multiallelic) or two polymorphs but one of them frequently over 33% and the other over 66%. If all polymorphisms with sufficient readings follow this pattern throughout the entire genome, that means that the embryo is triploid.
    [0205]
    [0206] Example 3. Identification of embryos with balanced translocations
    [0207]
    [0208] Sometimes, some couples decide to go to in vitro fertilization cycles because one of them is a carrier of a balanced translocation. In these cases, these parents have a high reproductive risk, because 50% of their embryos will have an unbalanced translocation as a result of inheriting one of the altered chromosomes. In addition, you will have a 25% chance of generating completely normal embryos, and 25% of generating embryos with balanced alteration. A schematic of the possible embryos generated is shown in FIG. 6. Current techniques allow distinguishing those embryos with unbalanced alterations, most of the time simply using DGP-A. However, it is not possible to differentiate those embryos with balanced alteration from completely normal ones, since no copy number changes occur. Through the present development, it is possible to map the entire chromosome through different polymorphisms and, by studying the distribution of those polymorphisms in the unbalanced embryos, determine which ones are present in the altered chromosome and which in the normal one. In this way, we can know if Embryos without changes in copy number have received the normal or altered chromosome from their parent. This study is possible thanks to the combination of DGP-A and DGP-M.
    权利要求:
    Claims (12)
    [1]
    1. - A method for the study of mutations in embryos in in vitro reproduction processes with the particularity that it combines the techniques of detection of Aneuploidy (DPG-A) and the study of monogenic diseases in embryos (DGP-M) and that It is characterized by comprising, in turn, the processes of:
    a process of selecting SNPs where the values of some are taken as input
    n candidate SNPs (t1 ... tk) of each individual x, in a chromosomal region of interest and specifically extracted for a population under study;
    and where this process is configured to maximize the situation in which one of the parents presents the value of a SNP in a heterozygous state, while in the other parent it is presented as homozygous and obtain a panel of z SNPs optimized for both maximized values in the form of matrix
    M whose columns correspond to the individuals of the population and the rows to the values of each SNP for each individual;
    One selection process is SNPs are evaluated all combinations of SNPs to obtain a minimum set t of tagSNPs from the matrix M obtained in the first selection process is SNPs; Y
    an in-silica validation process of the tagSNPs panel obtained in the second process.
    [2]
    2. - The method according to claim 1 wherein the first SNP selection process comprises the selection of those SNPS that are biallelic, whereby individuals can be represented as length m haplotypes formed by binary chains {1,0 }, being 1 | 0 and 0 | 1 the values for heterozygous SNPs and 0 | 0 and 1 | 1 the values for homozygotes; making this selection throughout the chromosomal region of interest.
    [3]
    3. - The method according to claim 2 wherein the chromosomal region of interest is defined as any position that is two megabases above and two megabases below the gene or mutation under study.
    [4]
    4. - The method according to any one of claims 1 to 3 wherein the first process comprises a step of analyzing the n candidate SNPs in the region and excluding those that meet any of the following conditions: SNPs with more than one alternative allele (Non-biallelic SNPs); SNPs whose alleles are different from the change of a nucleotide simple; SNPs found in homozygosis in at least 99% of the population of interest; and non-common SNPs, that is, whose allelic frequency is less than 1%.
    [5]
    5.
    [6]
    6.
    [7]
    7.
    [8]
    8. - The method according to any one of claims 1 to 7 wherein the selection of tagSNPs within each group is based on the detection limit criterion (LD), starting with k = 1 SNPs and studying all the possible k-combinations, organizing the SNPs within each group.
    [9]
    9.
    [10]
    10.
    [11]
    eleven.
    [12]
    12. software product with instructions configured to be executed by one or more processors that make the electronic device of the kit of claim 11 carry out the method according to any one of claims 1 to 10.
    类似技术:
    公开号 | 公开日 | 专利标题
    Werling et al.2018|An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder
    Gajecka2016|Unrevealed mosaicism in the next-generation sequencing era
    Suchan et al.2016|Hybridization capture using RAD probes |, a new tool for performing genomic analyses on collection specimens
    Henry et al.2014|Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing
    Lindblad-Toh et al.2005|Genome sequence, comparative analysis and haplotype structure of the domestic dog
    CA2731991A1|2010-02-11|Methods for allele calling and ploidy calling
    Calaway et al.2013|Genetic architecture of skewed X inactivation in the laboratory mouse
    Vergult et al.2014|Mate pair sequencing for the detection of chromosomal aberrations in patients with intellectual disability and congenital malformations
    Kim et al.2013|SNP linkage analysis and whole exome sequencing identify a novel POU4F3 mutation in autosomal dominant late-onset nonsyndromic hearing loss |
    Letaief et al.2017|Identification of copy number variation in French dairy and beef breeds using next-generation sequencing
    KR20180054834A|2018-05-24|Molecular quality assurance method for use in sequencing
    US20180260521A1|2018-09-13|Method and apparatus for multiple dot plot analysis
    ES2637292A1|2017-10-11|METHOD OF DETECTION OF THE MARKER NCAPG_c.1754C&gt; T FOR THE EVALUATION OF THE GENETIC MERIT FOR THE CHARACTER WIDTH OF THE GROUP IN SHEEP |
    ES2738176B2|2021-01-11|METHOD FOR THE STUDY OF MUTATIONS IN EMBRYOS IN IN VITRO REPRODUCTION PROCESSES
    Sastre2014|Exome sequencing: what clinicians need to know
    US7303880B2|2007-12-04|Microdissection-based methods for determining genomic features of single chromosomes
    Shi et al.2013|A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera
    Lyu et al.2021|Personalized genome structure via single gamete sequencing
    Urban et al.2021|High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing
    AU2017263319A1|2018-12-13|Methods of determining genomic health risk
    Kessler et al.2022|A robust sequencing assay of a thousand amplicons for the high‐throughput population monitoring of Alpine ibex immunogenetics
    Pfenninger et al.2020|Spontaneous rate of clonal mutations in Daphnia galeata
    Bradley et al.2002|19. The evolutionary genetics and molecular ecology of chimpanzees and bonobos
    Belmont2019|Molecular methods
    Susgun et al.2021|Gene hunting approaches through the combination of linkage analysis with Whole-Exome Sequencing in mendelian diseases: From Darwin to the present day
    同族专利:
    公开号 | 公开日
    EP3825414A1|2021-05-26|
    WO2020016477A1|2020-01-23|
    ES2738176B2|2021-01-11|
    US20210343365A1|2021-11-04|
    引用文献:
    公开号 | 申请日 | 公开日 | 申请人 | 专利标题
    US20130210644A1|2006-06-14|2013-08-15|Roland Stoughton|Fetal aneuploidy detection by sequencing|
    GB0523276D0|2005-11-15|2005-12-21|London Bridge Fertility|Chromosomal analysis by molecular karyotyping|
    ES2675618T3|2012-11-26|2018-07-11|The University Of Toledo|Methods for standardized sequencing of nucleic acids and their uses|
    US20140274741A1|2013-03-15|2014-09-18|The Translational Genomics Research Institute|Methods to capture and sequence large fragments of dna and diagnostic methods for neuromuscular disease|
    US9506053B2|2013-08-01|2016-11-29|Abbvie Inc.|Methods of selecting biologic-producing cell lines by next generation sequencing|
    EP2947156A1|2014-05-22|2015-11-25|Qiagen GmbH|Optimization of sequencing reactions|WO2021180722A1|2020-03-12|2021-09-16|Vrije Universiteit Brussel|Method for the analysis of genetic material|
    法律状态:
    2020-01-20| BA2A| Patent application published|Ref document number: 2738176 Country of ref document: ES Kind code of ref document: A1 Effective date: 20200120 |
    2021-01-11| FG2A| Definitive protection|Ref document number: 2738176 Country of ref document: ES Kind code of ref document: B2 Effective date: 20210111 |
    优先权:
    申请号 | 申请日 | 专利标题
    ES201830731A|ES2738176B2|2018-07-20|2018-07-20|METHOD FOR THE STUDY OF MUTATIONS IN EMBRYOS IN IN VITRO REPRODUCTION PROCESSES|ES201830731A| ES2738176B2|2018-07-20|2018-07-20|METHOD FOR THE STUDY OF MUTATIONS IN EMBRYOS IN IN VITRO REPRODUCTION PROCESSES|
    US17/262,009| US20210343365A1|2018-07-20|2019-07-19|Method for the Study of Embryo Mutations in IN VITRO Reproduction Processes|
    PCT/ES2019/070506| WO2020016477A1|2018-07-20|2019-07-19|Method for the study of embryo mutations in in vitro reproduction processes|
    EP19758787.6A| EP3825414A1|2018-07-20|2019-07-19|Method for the study of embryo mutations in vitro reproduction processes|
    [返回顶部]