WO2021232388A1 - Procédé pour déterminer un type de base d'un site prédéterminé dans un chromosome de cellule embryonnaire, et son application - Google Patents

Procédé pour déterminer un type de base d'un site prédéterminé dans un chromosome de cellule embryonnaire, et son application Download PDF

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WO2021232388A1
WO2021232388A1 PCT/CN2020/091702 CN2020091702W WO2021232388A1 WO 2021232388 A1 WO2021232388 A1 WO 2021232388A1 CN 2020091702 W CN2020091702 W CN 2020091702W WO 2021232388 A1 WO2021232388 A1 WO 2021232388A1
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predetermined site
embryonic
sequencing
genome
determining
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PCT/CN2020/091702
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English (en)
Chinese (zh)
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夏军
程小芳
刘萍
陈丹
曹磊
严会娟
邹艳
龙舟
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深圳华大智造科技有限公司
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Priority to CN202080095705.XA priority Critical patent/CN115052994A/zh
Priority to PCT/CN2020/091702 priority patent/WO2021232388A1/fr
Publication of WO2021232388A1 publication Critical patent/WO2021232388A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/06—Biochemical methods, e.g. using enzymes or whole viable microorganisms

Definitions

  • the present invention relates to the field of biological information, in particular, to a method, device and application for determining the base type of a predetermined site in an embryonic cell chromosome.
  • PTT Preimplantation Genetic Testing
  • Monogenic disease is a genetic disease caused by mutations of a pair of alleles (genes that control relative traits at the same position on a pair of homologous chromosomes), and its transmission mode follows Mendel's law of inheritance.
  • WHO World Health Organization
  • monogenic diseases there are currently more than 10,000 known monogenic diseases, and the global prevalence of all monogenic diseases at birth is about 10/1000.
  • the existing technical methods lack effective treatments for most single-gene diseases, so it is quite necessary to effectively adopt detection methods to avoid pregnancy and birth of children with single-gene diseases.
  • Preimplantation single-gene disease detection can detect embryos, so as to screen embryos that are not diseased for transfer, which can block the inheritance of single-gene diseases.
  • the single nucleotide polymorphism (SNP)-based haplotype analysis method is now the most commonly used method to determine whether an embryo has inherited a single-gene disease.
  • the SNP-based haplotype linkage analysis technique includes the capture and sequencing of the target region Obtain the method of haploid linkage analysis and karyotype mapping technology (Karyomapping) near the SNP site of the pathogenic gene, in addition to the linkage analysis method based on STR, but it requires pre-experiment to screen the relevant marker sites, the whole process consumes It takes a long time and the experimental operation is complicated, and it is no longer widely used as a mainstream method.
  • Target region-based capture sequencing and haploid linkage analysis technology is to obtain haploid linkage analysis by obtaining SNP sites within the pathogenic gene and upstream and downstream sequences through target region capture and sequencing.
  • the karyotype mapping technology uses microarray chips to obtain genome-wide SNP sites, uses these SNP sites to construct haplotypes, and then performs haplotype linkage analysis to determine whether the embryo has inherited pathogenic sites.
  • Target region capture sequencing and haploid linkage analysis technology can only detect specific monogenic diseases, but cannot detect chromosomal abnormalities in embryos. Karyomapping can only rely on haplotypes and cannot directly detect disease-causing sites, and can only detect non-whole embryos, and cannot detect small copy number variations.
  • the above-mentioned techniques need to be achieved through the linkage analysis of a relatively complete family sample (Figure 1), where the family sample includes but is not limited to 1) both spouses and their children, and the children are the probands ( The first person to be found to be diseased) or does not carry the pathogenic gene at all; 2) Both spouses and their father or mother, their parents carry the pathogenic gene or are probands; 3) Both spouses and their siblings, siblings carry the pathogenic genes
  • the disease gene may be a proband.
  • the present invention has developed a method for determining the base type of a predetermined site in the embryonic cell chromosome.
  • the single-tube long fragment reading technology (stLFR) used in the present invention can co-mark the long fragment DNA. After sequencing, the short read length information is restored back to the corresponding long fragment DNA information by using the marker, and the read long fragment information , You can directly perform haplotype typing on a single sample.
  • the present invention aims to develop an efficient and practical universal type Single-gene genetic disease diagnosis method for preimplantation embryos.
  • the present invention creatively uses the single tube long fragment reading (stLFR) technology to perform whole-genome sequencing on the genomic DNA samples of the couples undergoing preimplantation diagnosis, obtain the haplotype information of the parents, and then analyze the pathogenicity carried by the couples
  • the haplotype of the locus can directly determine the linkage relationship between the haplotype and the pathogenic locus, without the need for whole genome sequencing information of other family samples or proband samples.
  • the embryo biopsy cell samples are subjected to ordinary whole-genome sequencing, and the haplotype linkage analysis is used to determine whether the embryo has inherited the pathogenic site (the analysis process is shown in Figure 2).
  • This method can be used to detect the specified single-gene disease and other existing diseases. Accurate diagnosis of all known monogenic diseases can be completed, and embryonic chromosomal abnormalities and gene copy number variation (CNV) can also be accurately detected.
  • CNV gene copy number variation
  • the present invention proposes a method for determining the base type of a predetermined site in the embryonic cell chromosome.
  • the method includes: (1) Based on the sequencing result of the embryo parent, the linked haplotype block at the predetermined site is determined, and the linked haplotype block includes the predetermined site and the predetermined site linked site is in the parent (2) Based on the sequencing result of the embryonic cells, determine the sequence information of at least a part of the embryonic genome, at least a part of the embryonic genome including the predetermined site; and (3) based on the predetermined The linked haplotype block of the site is corrected for the base type of the predetermined site in the embryo cell, so as to obtain the base type of the predetermined site.
  • the haploid information of the parent can be directly determined, and all the genes of the monogenic disease in the whole genome can be completed without the family and proband samples.
  • Site mutation information inspection and data collection and can detect all single-gene genetic disease base information within the entire embryo's genome, without the need to develop new methods for specific diseases, thereby reducing the difficulty of operation and reducing the complexity of the process , Reduce the difficulty of collecting samples, improve the detection efficiency, and prepare for scientific research.
  • the above method may further include at least one of the following additional technical features:
  • the embryo cell is in the blastocyst stage, and the embryo parent includes at least one of the mother and father of the embryo.
  • the embryo's parent includes at least one of the mother and father of the embryo.
  • only the genome sequencing data of the embryo's parent can complete the mutation information inspection and data collection of all the monogenic disease gene loci in the whole genome of the embryo, and the family and proband samples are not required, which reduces It is difficult to collect samples, and then it can realize the diagnosis of some serious lethal single-gene genetic diseases or the collection of some serious lethal single-gene information, and at the same time, the embryo can be used to detect chromosomal abnormalities based on the embryo's genome information.
  • the sequencing result of the embryonic cells in step (2) comes from the sequencing of 1-10 cells.
  • the sequencing result of the embryonic parent is obtained by long-range sequencing.
  • the sequencing read length of the long-sequence sequencing is PE100 and/or PE150.
  • the sequenced fragment length of the embryonic cell sequencing result is PE100 and/or PE150.
  • the method can be performed on the embryo's target cell stage or blastocyst stage for 3 or 5 days after embryos are cultured in vitro, with one to two blastomeres or three to eight outer trophoblast cells Detection.
  • the method only requires a small amount of embryonic cells for detection, and performs ordinary whole-genome sequencing on embryonic cells, does not require whole-genome amplification, reduces the probability of allele decoupling, and reduces the occurrence of data errors.
  • the step (1) further includes: (1-1) performing genome single-tube long fragment reading technology (stLFR) sequencing on the blood sample of the embryo parent; (1-2) based on The sequencing result is compared with the reference genome sequence, and the GATK software is used to determine the mutation information, the mutation information includes at least one of SNP and indel markers (Indel); (1-3) Hapcut2 software is used, based on step (1 -2) the mutation information obtained in assembling the haplotype of the embryonic parent; and (1-4) selecting the linked haplotype block on the haplotype based on the predetermined site
  • the corresponding length of the linked haplotype block on the reference genome is 10,000 to 90 trillion.
  • the stLFR technology is used to perform whole-genome sequencing on the genomic DNA samples of the parents to obtain the haplotype information of the father and mother, and then analyze the pathogenic sites carried by both parents, and then directly Determine the linkage relationship between the haplotype and the pathogenic site, and correct the subsequent embryo sequencing results to determine whether the embryo inherits a haplotype linked to the pathogenic site, without the need for other samples or whole genome sequencing information of the proband sample , Which simplifies the operation process and improves the detection efficiency.
  • the predetermined site is located in the COL1A1 gene.
  • the present invention proposes a method for determining CNV variant regions based on the embryonic genome.
  • the embryonic genome reference sequence is divided into multiple windows, and statistics fall into The number of sequencing reads in each window; (2) For each window, the start or end of the window is used as a dividing point, based on two values composed of the number of sequencing reads in the window on both sides of the dividing point Determine multiple initial breakpoints based on the differences of the set; (3) Based on the multiple initial breakpoints, determine multiple secondary windows in the embryo genome reference sequence, and determine the multiple secondary windows The number of sequencing reads for each; (4) Based on the difference between the two numerical sets composed of the number of sequencing reads in the secondary window on both sides of the initial breakpoint, determine the final breakpoint position to determine the CNV variation area.
  • the merging of windows is not limited to the second round of statistics, that is: after determining the secondary window, the difference statistics of the sequencing read values are still performed according to the two windows on the left and right ends of the endpoint, and the statistical values are significantly different Determine whether it is a real breakpoint, judge whether it is missing or repeated according to the value of the reading segment in the window interval, and judge the detection accuracy according to the window size.
  • the method can not only detect the base information of all single-gene genetic diseases in the whole embryo genome, but does not need to develop new methods specifically for specific diseases, and reduces the difficulty of operation.
  • the present invention proposes a device for determining the base type of a predetermined site in the chromosome of an embryonic cell.
  • the linked haplotype block at the predetermined site is determined, and the linked haplotype block includes the positioning point and the linkage site of the predetermined site in the parent Base type; embryonic cell sequence information determining module, the embryonic cell sequence information determining module is connected to the linked haplotype block determining module, and is used to determine at least a part of the embryonic genome based on the sequencing result of the embryonic cell At least a part of the embryonic genome includes the predetermined site; and a predetermined site correction module, the predetermined site correction module and the embryonic cell sequence information determination module are configured to perform data based on the predetermined site In the linked haplotype block, the base type at the predetermined site in the embryonic cell is corrected to obtain the base type at the predetermined site.
  • the device for determining the base type of the predetermined site in the embryonic cell chromosome is suitable for performing the aforementioned method for determining the base type of the predetermined site in the embryonic cell chromosome, so as to effectively determine whether the embryo carries
  • the above-mentioned device may also have the following additional technical features:
  • the linked haplotype block determination module further includes: a long-sequence sequencing unit, configured to perform genomic stLFR sequencing on the blood sample of the embryonic parent; and a comparison unit, configured based on the sequencing The result is compared with the reference genome sequence, and the GATK software is used to determine the mutation information.
  • the mutation information includes at least one of SNP and Indel.
  • the haploid type of the embryo parent; and a linked haploid block determining unit for selecting the linked haploid block on the haploid based on the predetermined site, optionally, the The corresponding length of the linked haplotype block on the reference genome is 10,000 to 90 trillion.
  • the present invention proposes an apparatus for determining CNV variant regions based on the embryonic genome.
  • the apparatus includes: a window division module for dividing the genome reference sequence into multiple Window, counting the number of sequencing reads that fall into each window; an initial breakpoint determination module, which is connected to the window division module, and is used for each window based on the start or end of the window As a demarcation point, a plurality of initial breakpoints are determined based on the difference between two numerical sets composed of the numerical values of the number of sequencing reads of the window on both sides of the demarcation point; a secondary window division module, the secondary window division The module is connected to the initial breakpoint determining module, and is configured to determine multiple secondary windows in the genome reference sequence based on the multiple initial breakpoints, and determine the value of each of the multiple secondary windows The number of sequencing reads; a CNV variation area determination module, which is connected to the secondary window division module, and is configured to be composed of the number of sequencing reads
  • the present invention proposes a computer-readable storage medium on which a computer program is stored, and when the program is executed by a processor, the steps of the method for determining the base type of the predetermined site in the embryonic cell chromosome are realized .
  • the method for determining the base type of the predetermined site in the embryonic cell chromosome described above can be effectively implemented, so that it can be effectively determined whether the embryo carries the genetic information characteristics of a single-gene genetic disease and whether it carries the chromosomal abnormal characteristics.
  • the present invention provides a computer device, including a processor and a memory; wherein the processor reads the executable program code stored in the memory to run and the executable program The program corresponding to the code is used to implement the method for determining the base type of the predetermined site in the embryonic cell chromosome.
  • the present invention provides a computer program product, when the instructions in the computer program product are executed by a processor, the method for determining the base type of a predetermined site in the embryonic cell chromosome is executed .
  • Figure 1 shows the inferred haplotype linked to the pathogenic locus based on family samples according to an embodiment of the present invention
  • Fig. 2 is a pre-implantation diagnostic test flow for embryos without family samples or proband samples according to an embodiment of the present invention
  • FIG. 3 is a schematic flow chart of a method for determining the base type of a predetermined site in a chromosome of an embryonic cell according to an embodiment of the present invention
  • FIG. 4 is a schematic flowchart of a method for determining a linked haplotype block at the predetermined site according to an embodiment of the present invention
  • FIG. 5 is a schematic flowchart of a method for determining CNV variant regions based on the embryonic genome according to an embodiment of the present invention
  • Fig. 6 is a block diagram of an apparatus for a predetermined site base type in a chromosome of an embryonic cell according to an embodiment of the present invention
  • Fig. 7 is a block diagram of a chain haplotype block determining module according to an embodiment of the present invention.
  • Fig. 8 is a block diagram of an apparatus for determining CNV variant regions based on the embryonic genome according to an embodiment of the present invention.
  • the terms “installed”, “connected”, “connected”, “fixed” and other terms should be understood in a broad sense, for example, it can be a fixed connection or a detachable connection. , Or integrated; it can be mechanically connected or electrically connected; it can be directly connected or indirectly connected through an intermediary, it can be the internal connection of two components or the interaction relationship between two components, unless otherwise specified The limit.
  • installed can be a fixed connection or a detachable connection. , Or integrated; it can be mechanically connected or electrically connected; it can be directly connected or indirectly connected through an intermediary, it can be the internal connection of two components or the interaction relationship between two components, unless otherwise specified The limit.
  • the specific meanings of the above-mentioned terms in the present invention can be understood according to specific circumstances.
  • single nucleotide polymorphism refers to a DNA sequence polymorphism caused by a single nucleotide variation at the genome level.
  • the indel marker (Indel) used in this article refers to the difference in the whole genome of the two parents. Compared with the other parent, one of the parents has a certain number of nucleotides in the genome. Insertion or deletion.
  • CNV analysis used in this article includes chromosome microduplication/microdeletion, aneuploidy, polyploidy, uniparental diploidy, mosaicism, and family linkage analysis, especially focusing on molecular genetics. Perform detection and interpretation of complex chromosomal diseases/genomic diseases and discover the relationship between copy number abnormalities and phenotypes.
  • the present invention provides a method for determining the base type of a predetermined site in the chromosome of an embryonic cell. According to an embodiment of the present invention, referring to FIG. 3, the method includes:
  • the sequencing results are filtered and the data are compared to obtain SNP/Indel information, and the SNP/Indel information is used for haploid assembly to determine the parental list.
  • Ploidy information according to the sequencing result of the embryo, the sequencing result is filtered, chromosome splitting and single chromosome correction, based on the comparison result of the sequencing result and the reference genome sequence, the mutation detection of SNP and Indel is performed, and the comparison result Annotate, extract the SNP information of the target area and its upstream and downstream, and generate haplotype results based on family information.
  • the haploid type linked to the pathogenic site is inherited to determine whether the embryo inherits the pathogenic site.
  • the embryo cell is in the blastocyst stage, and the embryo parent includes at least one of the mother and father of the embryo.
  • the embryonic cell may be a blastomere stage cell or a blastocyst stage trophoblast cell; the sample of the embryonic parent is taken from blood samples of the embryo's father and mother, and long genomic DNA is extracted.
  • the sequencing result of the embryonic cells in step (2) comes from the sequencing of 1-10 cells, the sequencing result of the embryo parent is obtained by long-sequence sequencing, The sequencing read length is PE100 and/or PE150, and the sequenced fragment length of the embryonic cell sequencing result is PE100 and/or PE150.
  • the step S100 further includes:
  • step S130 using Hapcut2 software, based on the mutation information obtained in step S120, assembling the haploid type of the embryonic parent;
  • the linked haplotype block Based on the predetermined site, select the linked haplotype block on the haplotype.
  • the linked haplotype block has a corresponding length of 10,000 to 9 on the reference genome. Ten trillion.
  • the stLFR technology is used to construct a library of the extracted genomic long fragment DNA.
  • the main step is to use transposase to fragment the DNA, add a linker, and then combine with the labeled magnetic beads. Connect the tag to the DNA, add another adapter, and perform PCR amplification to obtain a library of long fragments read in a special single tube, and sequence the built library.
  • split the molecular tags use SOAPnuke software to filter the original data with sequencing adapters, the proportion of N bases is too high, the proportion of A bases is too high, and the sequencing quality is low, and the basic data are counted.
  • the predetermined site is located in the COL1A1 gene.
  • the present invention proposes a method for determining CNV variant regions based on the embryonic genome.
  • the method includes:
  • S4000 Determine a final breakpoint position based on the difference between two numerical sets composed of the number of sequencing reads in the secondary window on both sides of the initial breakpoint, so as to determine the CNV variation region.
  • chromosomal abnormality analysis is performed on the whole genome sequencing data of embryos.
  • the sequencing data is filtered by SOAPnuke software, and then the BWA software is used for comparison, and the only aligned sequence is selected from the comparison results.
  • the reference genome is randomly interrupted according to the length of the measured sequence, and then the simulated offline sample data is generated and re-aligned to the reference genome to ensure that each window contains 100K read, and the overlapping area between adjacent windows contains 20K read, and finally
  • the whole genome is divided into 131290 windows, and other window lengths can also be selected according to the difference in the number of reads falling into the window.
  • a certain breakpoint For points perform statistical tests on the left and right breakpoint intervals, delete insignificant breakpoints in the loop, and obtain the average of the P value and depth value of each breakpoint interval. Finally, it is judged whether it is a true breakpoint based on the significance of the P value of the breakpoint, whether it is missing or repeated based on the depth value, and the detection accuracy is judged based on the size of the breakpoint interval.
  • the P value is 1e-10
  • the deletion threshold is 0.7
  • the duplication threshold is 1.3.
  • the interval greater than 16M is selected as the final copy number variation interval.
  • the present invention provides a device for determining the base type of a predetermined site in the embryonic cell chromosome, which is used to implement a method for determining the base type of the predetermined site in the embryonic cell chromosome.
  • the device includes: a linked haplotype block determining module 100, configured to determine the linked haplotype block at the predetermined site based on the sequencing result of the embryo parent, and the linked haploid block includes the The base type of the site linked to the anchor point and the predetermined site in the parent; embryonic cell sequence information determining module 200, the linked haplotype block determining module 100 and the embryonic cell sequence information determining module 200 is connected to determine the sequence information of at least a part of the embryonic genome based on the sequencing result of the embryonic cell, at least a part of the embryonic genome includes the predetermined site; and a predetermined site correction module 300, the embryonic cell
  • the sequence information determining module 200 is connected to the predetermined site correction module 300, and is configured to perform a calculation of the base type at the predetermined site in the embryo cell based on the linked haplotype block at the predetermined site. Correction to obtain the base type of the predetermined site.
  • the linked haplotype block determination module 100 further includes: a long-segment sequencing unit 110, configured to perform genomic stLFR sequencing on the blood sample of the embryo parent; and a comparison unit 120
  • the long-sequence sequencing unit 110 is connected to the comparison unit 120, and is used to determine mutation information based on the comparison of the sequencing result with the reference genome sequence and using GATK software.
  • the mutation information includes at least SNP and Indel.
  • the haploid construction unit 130, the comparison unit 120 is connected to the haploid construction unit 130, and is used to use the Hapcut2 software to assemble the haploid of the embryo parent based on the mutation information; and
  • the linked haplotype block determining unit 140, the haplotype constructing unit 130 is connected to the linked haplotype block determining unit 140, and is configured to select all the haplotypes on the haplotype based on the predetermined site.
  • the linked haplotype block corresponds to a length of 10,000 to 90 trillion on the reference genome.
  • the present invention proposes a device for determining CNV variant regions based on the embryonic genome.
  • the device includes: a window The dividing module 1000 is configured to divide the genome reference sequence into multiple windows and count the number of sequencing reads that fall into each window; an initial breakpoint determination module 2000, the initial breakpoint determination module 2000 is connected to the window division module 1000 , For each window, using the start or end point of the window as the dividing point, and determining multiple sets of values based on the difference between the two numerical values of the number of sequencing reads in the window on both sides of the dividing point Initial breakpoint; a secondary window division module 3000, the secondary window division module 3000 is connected to the initial breakpoint determination module 2000, and is configured to determine in the genome reference sequence based on the multiple initial breakpoints Multiple secondary windows, and determine the number of sequencing reads in each of the multiple secondary windows; a CNV variation region determination module 4000, the C
  • the present invention proposes a computer-readable storage medium on which a computer program is stored.
  • a method for determining the base type of a predetermined site in a chromosome of an embryonic cell and a method based on The steps of the method for determining the CNV variation region in the embryonic genome.
  • the method for determining the base type of the predetermined site in the embryonic cell chromosome described above can be effectively implemented, so that it can be effectively determined whether the embryo carries the genetic information characteristics of a single-gene genetic disease and whether it carries the chromosomal abnormal characteristics.
  • the present invention provides a computer device, including a processor and a memory; wherein the processor reads the executable program code stored in the memory to run and the executable program
  • the program corresponding to the code is used to implement the method for determining the base type of the predetermined site in the embryonic cell chromosome and the method for determining the CNV mutation region based on the embryonic genome.
  • the present invention provides a computer program product.
  • the instructions in the computer program product are executed by a processor, the method for determining the base type of a predetermined site in the embryonic cell chromosome is executed.
  • stLFR high-throughput sequencing reagent kit
  • the low-quality reads are filtered through data filtering (according to two indicators: the average quality value of the bases in the sequence and the proportion of the number of N bases contained in the sequence, and the base quality value of read is less than or equal to 20", "N base number is greater than or equal to 5", the two meet one or both are filtered out), the filtered sequence is compared with BWA, after the comparison is completed, use GATK for SNP/Indel detection , SNP and Indel information is used for haplotype linkage analysis.

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Abstract

L'invention concerne également un procédé de détermination d'un type de base d'un site prédéterminé dans un chromosome de cellule embryonnaire. Le procédé de détermination d'un type de base d'un site prédéterminé dans un chromosome de cellule embryonnaire comprend les étapes suivantes : (1) détermination d'un bloc d'haplotype lié du site prédéterminé sur la base d'un résultat de séquençage du parent embryonnaire, le bloc d'haplotype lié comprenant les types de base du site prédéterminé et un site de liaison du site prédéterminé dans le parent ; (2) détermination des informations de séquence d'au moins une partie du génome embryonnaire sur la base du résultat de séquençage de la cellule embryonnaire, la au moins une partie du génome embryonnaire comprenant le site prédéterminé ; (3) réalisation d'une correction pour le type de base du site prédéterminé dans la cellule embryonnaire sur la base du bloc d'haplotype lié du site prédéterminé, de manière à obtenir le type de base du site prédéterminé ; et (4) détermination si le génome embryonnaire présente une anomalie chromosomique sur la base du résultat du séquençage de la cellule embryonnaire.
PCT/CN2020/091702 2020-05-22 2020-05-22 Procédé pour déterminer un type de base d'un site prédéterminé dans un chromosome de cellule embryonnaire, et son application WO2021232388A1 (fr)

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CN202080095705.XA CN115052994A (zh) 2020-05-22 2020-05-22 确定胚胎细胞染色体中预定位点碱基类型的方法及其应用
PCT/CN2020/091702 WO2021232388A1 (fr) 2020-05-22 2020-05-22 Procédé pour déterminer un type de base d'un site prédéterminé dans un chromosome de cellule embryonnaire, et son application

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CN115631789A (zh) * 2022-10-25 2023-01-20 哈尔滨工业大学 一种基于泛基因组的群体联合变异检测方法
CN116343919A (zh) * 2023-04-11 2023-06-27 天津大学四川创新研究院 一种全基因组图谱绘制测序方法
CN116646010A (zh) * 2023-07-27 2023-08-25 深圳赛陆医疗科技有限公司 人源性病毒检测方法及装置、设备、存储介质
CN117116344A (zh) * 2023-10-25 2023-11-24 北京大学第三医院（北京大学第三临床医学院） 一种单细胞水平pmp22重复变异的检测系统和方法
CN117116348A (zh) * 2023-02-07 2023-11-24 杭州联川基因诊断技术有限公司 针对靶向测序数据的mTag序列进行修正的方法、设备和介质
WO2024027569A1 (fr) * 2022-08-05 2024-02-08 苏州贝康医疗器械有限公司 Procédé de construction d'haplotype indépendant d'une probande

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WO2024027569A1 (fr) * 2022-08-05 2024-02-08 苏州贝康医疗器械有限公司 Procédé de construction d'haplotype indépendant d'une probande
CN115631789A (zh) * 2022-10-25 2023-01-20 哈尔滨工业大学 一种基于泛基因组的群体联合变异检测方法
CN115631789B (zh) * 2022-10-25 2023-08-15 哈尔滨工业大学 一种基于泛基因组的群体联合变异检测方法
CN117116348A (zh) * 2023-02-07 2023-11-24 杭州联川基因诊断技术有限公司 针对靶向测序数据的mTag序列进行修正的方法、设备和介质
CN116343919A (zh) * 2023-04-11 2023-06-27 天津大学四川创新研究院 一种全基因组图谱绘制测序方法
CN116343919B (zh) * 2023-04-11 2023-12-08 天津大学四川创新研究院 一种全基因组图谱绘制测序方法
CN116646010A (zh) * 2023-07-27 2023-08-25 深圳赛陆医疗科技有限公司 人源性病毒检测方法及装置、设备、存储介质
CN116646010B (zh) * 2023-07-27 2024-03-29 深圳赛陆医疗科技有限公司 人源性病毒检测方法及装置、设备、存储介质
CN117116344A (zh) * 2023-10-25 2023-11-24 北京大学第三医院（北京大学第三临床医学院） 一种单细胞水平pmp22重复变异的检测系统和方法

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