A method, system and electronic device for detecting a homozygous region of a chromosome

Abstract

The application provides a method and system for detecting a homozygous region of a chromosome and an electronic device, and relates to the technical field of prenatal detection. The method comprises the following steps: dividing chromosomes of a sample to be tested into a plurality of chromosome regions according to a preset step length and selecting a target chromosome region; constructing a background joint probability distribution model and a target joint probability distribution model; determining a background parameter according to the background joint probability distribution model; determining a joint distribution likelihood value of an SNP site in the target chromosome region according to the target joint probability distribution model and the background parameter; and determining a homozygous condition of the target chromosome region according to the joint distribution likelihood value of the SNP site in the target chromosome region. The application can determine whether a fetus has a homozygous region of a chromosome based on non-invasive sampling and deduce a genetic source of the fetus by constructing the background joint probability distribution model and the target joint probability distribution model, thereby reducing the cost of detection and improving the safety of detection.

Description

TECHNICAL FIELD

[0001] The present application relates to the technical field of prenatal detection, in particular to a method and system for detecting a chromosome homozygous region and an electronic device. BACKGROUND

[0002] A chromosome homozygous region (ROH) refers to a region on the genome of an individual in which all loci are homozygous, also known as a homozygous fragment. A continuous chromosome homozygous region reaching a certain length may affect the expression of imprinting genes (including the relationship between parents, mitotic recombination errors, meiotic errors, or complex chromosomal rearrangements based on replication). ROH is an important chromosomal abnormality, and the genomic location is crucial for the study of imprinting gene expression and recessive homozygous mutations. As more and more ROH cases are reported, it is found that ROH reaching a certain length is enriched for deleterious homozygous variants, and high levels of ROH increase various risks. Therefore, the detection of ROH has important value.

[0003] The detection of chromosome homozygous regions has been valued by professional groups in recent years. In 2021, the American College of Medical Genetics and Genomics (ACMG) issued a statement on ROH or uniparental disomy (UPD) and expressed support for the importance of its detection; the same year, China also issued an expert consensus on the importance of ROH or UPD detection. Current methods for prenatal detection of fetal ROH or UPD include invasive sampling such as chorionic villus sampling (CVS) and amniocentesis. For invasive samples, existing detection techniques are divided into two categories: one is specific to target ROH or UPD detection, mainly including short tandem repeat typing and methylation-specific detection, which has the limitation of only being suitable for the detection of a specific UPD suspected based on clinical phenotypes; the other is comprehensive detection of UPD in the whole genome, mainly including single nucleotide polymorphism chip (SNP array) and high-throughput sequencing, which often refers to conventional deep sequencing, not low-depth whole genome sequencing. The following details the existing technical means:

[0004] (1) Short tandem repeat sequence typing (STR) is a simple repeat sequence uniformly distributed in the genome of eukaryotes, which is composed of 2 to 6 nucleotide tandem repeat fragments. Due to the high variability of the number of repeat units between individuals and the high heterozygosity of the markers in the whole genome, it can reflect the difference in allele frequency in the population. Main defects: need invasive sampling, and can only detect a certain pre-set target ROH or UPD; in addition, STR has a high mutation rate, which causes confusion in judgment; and due to the limitation of collection sites, the sample requirements are high.

[0005] (2) Chromosome microarray analysis technology (CMA), due to different probe designs, is divided into microarray-based comparative genomic hybridization (aCGH) technology and single nucleotide polymorphism microarray (SNP array) technology. Among them, SNP array can identify the genotype of each SNP corresponding to the probe, thereby detecting UPD in the whole genome. The main defects of SNP array: need invasive sampling; and the detection range is easily affected by probe preference; at the same time, the chip has much higher requirements for sample DNA starting amount and quality than sequencing; the detection cost of the chip is several times higher than that of whole genome low-depth sequencing.

[0006] (3) Whole exome sequencing (WES), this method is to capture fetal genomic DNA by custom probe mixture, enrich exonic region DNA and perform whole exome sequencing, and then analyze and compare the data to determine the genotype state of each SNP to estimate whether UPD exists. Main defects: need invasive sampling; can only detect exonic regions, and cannot effectively detect regions outside the exons; need high sequencing depth, and the detection cost is high.

[0007] (4) Low-depth whole genome sequencing (CNV-seq) is a chromosomal analysis technology based on whole genome sequencing method of second-generation sequencing technology to detect genomic copy number variation. This method is to extract genomic DNA from chorionic membrane, amniotic fluid or umbilical cord blood, perform low-depth sequencing on whole genome DNA library, and detect copy number abnormalities. The CNV-seq method before 2021 was considered to be able to only detect copy number abnormalities, and until 2021, a literature confirmed that the CNV-seq technology can detect fetal UPD by inferring B allele frequency at 4x sequencing depth. Main defects: need invasive sampling; need 4x sequencing depth, which is higher than the sequencing depth of conventional CNV-seq (the sequencing depth of conventional CNV-seq is less than 1x).

[0008] (5) Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), a key feature of imprinting genes is the presence of parent-specific methylation, such methods are by extracting fetal genomic DNA, then designing probes to hybridize with target sequences, adding restriction endonuclease to recognize non-methylated sites for cutting, then amplifying methylated DNA and analyzing its methylation status, and then judging the possibility of UPD. Main defects: need for invasive sampling; this method is limited by the recognition of restriction enzyme sites in the probe ligation site, and the reaction temperature of the enzyme used needs to be considered, the experimental requirements are high; only a certain pre-set target ROH or UPD can be detected. Methylation-specific PCR (MS-PCR), such methods are by extracting fetal and parental DNA samples, then designing primers to amplify bisulfite-treated DNA, analyzing the differential methylation region and imprinting center methylation status, and then judging the possibility of ROH or UPD. Main limitations: need for invasive sampling; primer design and bisulfite treatment are also critical, and incomplete treatment may lead to false positives; only a certain pre-set target UPD can be detected. SUMMARY

[0009] The purpose of the present application is to provide a chromosome homozygous region detection method, system and electronic equipment, which can determine whether the test sample contains a chromosome homozygous region based on non-invasive sampling, and infer the chromosome source of the homozygous region, thereby reducing the cost of detection while improving the safety of detection.

[0010] To achieve the above purpose, the present application provides the following solutions:

[0011] A chromosome homozygous region detection method, comprising:

[0012] Divide the chromosomes of the test sample into a plurality of chromosome regions according to a preset step size; the test sample is free DNA in the peripheral blood plasma of a pregnant woman; the free DNA is a mixture of maternal DNA and fetal DNA;

[0013] Select any chromosome region as a target chromosome region;

[0014] Construct a background joint probability distribution model and a target joint probability distribution model; the background joint probability distribution model is a statistical model constructed according to the sequencing data of the test sample genome except the sequencing data in the target chromosome region; the target joint probability distribution model is a statistical model constructed according to the sequencing data in the target chromosome region;

[0015] Determine the background parameters according to the background joint probability distribution model;

[0016] determining a joint distribution likelihood value of the SNP sites in the target chromosome region according to the target joint probability distribution model and the background parameter;

[0017] determining a homozygous status of the target chromosome region according to the joint distribution likelihood value of the SNP sites in the target chromosome region; the homozygous status comprises whether the target chromosome region is a chromosome homozygous region and a genetic source when the target chromosome region is the chromosome homozygous region.

[0018] Optionally, after the determining of the homozygous status of the target chromosome region according to the joint distribution likelihood value of the SNP sites in the target chromosome region, the method comprises:

[0019] judging whether to traverse the chromosome region to obtain a first judgment result;

[0020] if the first judgment result is no, updating the target chromosome region and returning to the step of constructing the background joint probability distribution model and the target joint probability distribution model;

[0021] if the first judgment result is yes, judging whether the number of the chromosome homozygous regions is greater than 0 to obtain a second judgment result;

[0022] if the second judgment result is no, determining that the test sample does not exist the chromosome homozygous region;

[0023] if the second judgment result is yes, determining that the test sample exists the chromosome homozygous region.

[0024] Optionally, after the determining of the test sample existing the chromosome homozygous region, the method comprises:

[0025] judging whether the number of the chromosome homozygous regions is equal to 1 to obtain a third judgment result;

[0026] if the third judgment result is yes, reporting the position and the genetic source of the chromosome homozygous region;

[0027] if the third judgment result is no, merging the chromosome homozygous regions meeting a merging condition in the plurality of chromosome homozygous regions and reporting the position and the genetic source of all the chromosome homozygous regions after the merging; the merging condition is that the chromosome homozygous regions are adjacent to each other and the genetic sources are consistent.

[0028] Optionally, the determining of the joint distribution likelihood value of the SNP sites in the target chromosome region according to the target joint probability distribution model and the background parameter comprises:

[0029] determining a plurality of target SNP sites in the target chromosome region; the target SNP sites are covered by a plurality of reads;

[0030] determining any target SNP site as a current target SNP site;

[0031] determining the number of times that the current target SNP site is covered by alleles as a first current number and a second current number;

[0032] determining an edge likelihood value of the current target SNP site according to the first current number, the second current number and the background parameter; the edge likelihood value comprises a fetal normal edge likelihood value, a maternal UPD edge likelihood value and a paternal UPD edge likelihood value;

[0033] determining a product of edge likelihoods of the plurality of target SNP sites in the current sequencing data in a model that the fetus is normal as a first joint distribution likelihood value;

[0034] determining a product of edge likelihoods of the plurality of target SNP sites in the current sequencing data in a model that the fetus is maternal UPD as a second joint distribution likelihood value;

[0035] determining a product of edge likelihoods of the plurality of target SNP sites in the current sequencing data in a model that the fetus is paternal UPD as a third joint distribution likelihood value;

[0036] determining the first joint distribution likelihood value, the second joint distribution likelihood value and the third joint distribution likelihood value as a SNP joint distribution likelihood value of the current sequencing data.

[0037] Optionally, the determining the edge likelihood value of the current target SNP site according to the first current number, the second current number and the background parameter comprises:

[0038] determining a binomial distribution likelihood value of the target SNP site for each genotype according to the first current number, the second current number, the background parameter and the allele frequency;

[0039] performing weighted summation on the binomial distribution likelihood values of the plurality of genotypes corresponding to the fetal normal state with the probabilities of the plurality of genotypes corresponding to the fetal normal state as weights to obtain the fetal normal edge likelihood value of the current target SNP site;

[0040] performing weighted summation on the binomial distribution likelihood values of the plurality of genotypes corresponding to the maternal UPD state with the probabilities of the plurality of genotypes corresponding to the maternal UPD state as weights to obtain the maternal UPD edge likelihood value of the current target SNP site;

[0041] performing weighted summation on the binomial distribution likelihood values of the plurality of genotypes corresponding to the paternal UPD state with the probabilities of the plurality of genotypes corresponding to the paternal UPD state as weights to obtain the paternal UPD edge likelihood value of the current target SNP site.

[0042] Optionally, the determining the homozygosity of the target chromosome region according to the SNP site joint distribution likelihood value in the target chromosome region comprises:

[0043] determining a maternal determination parameter according to the first joint distribution likelihood value and the second joint distribution likelihood value;

[0044] determining a paternal determination parameter according to the first joint distribution likelihood value and the third joint distribution likelihood value;

[0045] determining the homozygosity of the target chromosome region according to the maternal determination parameter and the paternal determination parameter.

[0046] Optionally, the maternal determination parameter is:

[0047] the paternal determination parameter is:

[0048] wherein, LLR1 is the maternal determination parameter; LN(h, F1, F2, e) is the first joint distribution likelihood value; MAt(h, F1, F2, e) is the second joint distribution likelihood value; LPat(h, F1, F2, e) is the third joint distribution likelihood value; LLR2 is the paternal determination parameter; F1 is the maternal inbreeding coefficient; h is the fetal proportion; F2 is the fetal inbreeding coefficient; and e is the sequencing error rate; the maternal inbreeding coefficient, the fetal proportion, the fetal inbreeding coefficient and the sequencing error rate are all background parameters.

[0049] Optionally, the determining the homozygosity of the target chromosome region according to the maternal determination parameter and the paternal determination parameter comprises:

[0050] determining whether the maternal determination parameter is greater than a maternal determination parameter threshold value to obtain a fourth determination result;

[0051] if the fourth determination result is yes, determining that the target chromosome region is a chromosome homozygous region and is caused by maternal UPD;

[0052] if the fourth determination result is no, determining whether the paternal determination parameter is greater than a paternal determination parameter threshold value to obtain a fifth determination result;

[0053] if the fifth determination result is yes, determining that the target chromosome region is a chromosome homozygous region and is caused by paternal UPD;

[0054] if the fifth determination result is no, determining that the target chromosome region is not a chromosome homozygous region.

[0055] A system for detecting a chromosome homozygous region comprises:

[0056] The chromosome region division module is configured to divide chromosomes of a to-be-tested sample into a plurality of chromosome regions according to a preset step length; the to-be-tested sample is free DNA in peripheral blood plasma of a pregnant woman; and the free DNA is a mixture of maternal DNA and fetal DNA.

[0057] The target chromosome region determination module is configured to select any chromosome region as a target chromosome region.

[0058] The distribution model construction module is configured to construct a background joint probability distribution model and a target joint probability distribution model; the background joint probability distribution model is a statistical model constructed according to sequencing data in the to-be-tested sample except for sequencing data in the target chromosome region; and the target joint probability distribution model is a statistical model constructed according to sequencing data in the target chromosome region.

[0059] The background parameter determination module is configured to determine a background parameter according to the background joint probability distribution model.

[0060] The SNP site joint distribution likelihood value determination module is configured to determine a SNP site joint distribution likelihood value in the target chromosome region according to the target joint probability distribution model and the background parameter.

[0061] The homozygous state determination module is configured to determine a homozygous state of the target chromosome region according to the SNP site joint distribution likelihood value in the target chromosome region; and the homozygous state includes whether the target chromosome region is a chromosome homozygous region and a genetic source when the target chromosome region is the chromosome homozygous region.

[0062] An electronic device includes a memory and a processor, the memory is used to store a computer program, and the processor runs the computer program to make the electronic device execute the chromosome homozygous region detection method.

[0063] According to the embodiments of the present application, the following technical effects are provided.

[0064] The application provides a chromosome homozygous region detection method, system and electronic equipment, the method comprising: dividing chromosomes of a sample to be detected into a plurality of chromosome regions according to a preset step size and selecting a target chromosome region; constructing a background joint probability distribution model and a target joint probability distribution model; determining a background parameter according to the background joint probability distribution model; determining a SNP site joint distribution likelihood value in the target chromosome region according to the target joint probability distribution model and the background parameter; and determining a homozygous condition of the target chromosome region according to the SNP site joint distribution likelihood value in the target chromosome region. The background joint probability distribution model and the target joint probability distribution model are constructed, the presence of a chromosome homozygous region in a fetus can be determined based on non-invasive sampling, and the genetic source of the chromosome homozygous region can be inferred, thereby reducing the cost of detection and improving the safety of detection. BRIEF DESCRIPTION OF DRAWINGS

[0065] In order to more clearly illustrate the technical solutions in the embodiments of the present application or the prior art, the drawings needed in the embodiments will be briefly introduced as follows. Obviously, the drawings in the following description are only some embodiments of the present application, and other drawings can be obtained by those skilled in the art without creative labor.

[0066] Figure 1 A flow chart of a chromosome homozygous region detection method in Embodiment 1 of the present application;

[0067] Figure 2 A principle diagram of a chromosome homozygous region detection method in Embodiment 1 of the present application. DETAILED DESCRIPTION

[0068] The technical solutions in the embodiments of the present application will be described clearly and completely with reference to the drawings in the embodiments of the present application. Obviously, the described embodiments are only some embodiments of the present application, rather than all the embodiments. Based on the embodiments in the present application, all other embodiments obtained by those skilled in the art without creative labor are within the scope of protection of the present application.

[0069] The present application aims to provide a chromosome homozygous region detection method, system and electronic equipment, which can determine whether a sample to be detected has a chromosome homozygous region based on non-invasive sampling, and infer the chromosome source of the homozygous region, thereby reducing the cost of detection and improving the safety of detection.

[0070] In order to make the above-mentioned purposes, features and advantages of the present application more apparent and easy to understand, the present application will be further described in detail below with reference to the drawings and specific embodiments.

[0071] Terminology explanation:

[0072] Uniparental disomy (UPD) refers to two copies of homologous chromosomes or chromosomal fragments derived from one parent, and its pathogenic mechanism includes imprinting gene disorder and recessive homozygous mutation.

[0073] Noninvasive prenatal testing (NIPT): Through the collection of maternal peripheral blood, the extraction of free DNA in plasma, the use of next-generation high-throughput sequencing technology, and the combination of bioinformatics analysis, the detection of fetal chromosomal aneuploidy diseases. This technology has been widely used in clinical first-line, but conventional NIPT cannot detect UPD.

[0074] Cell-free DNA (cfDNA): refers to DNA fragments derived from cell apoptosis or necrosis and free in the extracellular space, which widely exists in human serum, plasma, cerebrospinal fluid, urine or saliva. The cfDNA in the plasma of maternal peripheral blood is a mixture of DNA from the fetus and the DNA from the pregnant woman herself (wherein the maternal DNA accounts for the majority, and the fetal DNA accounts for only a small part), and since the cfDNA in the maternal peripheral blood contains the genetic material of the fetus, it has been used as a biomarker for clinical prenatal diagnosis of pregnant women.

[0075] Fetal proportion: the proportion of free DNA from the fetus in the plasma of maternal peripheral blood, which usually reaches 10% at about 12 weeks.

[0076] Read heterozygosity: a concept defined by the author, if a SNP site can be covered by more than one read, and if the bases measured at the site by these reads are different, it is recorded as read heterozygosity.

[0077] Read homozygosity: a concept defined by the author, if a SNP site can be covered by more than one read, and if the bases measured at the site by these reads are the same, it is recorded as read homozygosity.

[0078] Combined genotype: the combination of the genotype of the fetus and the genotype of the mother.

[0079] Imprinted gene: homologous gene expression from only one parent, while the other parent does not express;

[0080] Homozygous recessive mutation: after allelic mutation, it becomes a recessive homozygote, which may cause some recessive genetic diseases.

[0081] Region of homozygosity (ROH): A region of an individual's genome in which all sites within the region are homozygous is called a segment of homozygosity. UPD can cause regions of homozygosity.

[0082] Embodiment 1

[0083] As shown in Figure 1 and Figure 2 The embodiment provides a method for detecting a region of homozygosity, comprising:

[0084] Step 101: dividing chromosomes of a to-be-tested sample into a plurality of chromosome regions according to a preset step length; the to-be-tested sample is free DNA in peripheral blood plasma of a pregnant woman; the free DNA is a mixture of maternal DNA and fetal DNA.

[0085] Step 102: selecting any chromosome region as a target chromosome region.

[0086] Step 103: constructing a background joint probability distribution model and a target joint probability distribution model; the background joint probability distribution model is a statistical model constructed according to sequencing data of the to-be-tested sample except for sequencing data in the target chromosome region; and the target joint probability distribution model is a statistical model constructed according to sequencing data in the target chromosome region.

[0087] The joint probability distribution model is obtained by statistical fitting using sequencing data of the to-be-tested sample; the joint probability distribution model of the mother-fetal genotype includes a plurality of factors of heterozygosity, and the factors include one or more of a coefficient of inbreeding of the mother, a coefficient of inbreeding of the fetus, a sequencing error rate and an allele frequency of a population, and the heterozygosity is a proportion of SNP homozygous site numbers to total site numbers in the sequencing data. The joint probability distribution model of the mother-fetal genotype includes: a joint genotype distribution probability of a plurality of genotypes at any SNP site in a chromosome segment and a frequency of an allele when the fetus is normal, a joint genotype distribution probability of a plurality of genotypes at any SNP site in the chromosome segment and a frequency of the allele when the maternal UPD occurs, and a joint genotype distribution probability of a plurality of genotypes at any SNP site in the chromosome segment and a frequency of the allele when the paternal UPD occurs.

[0088] Although the NIPT is 0.1x-1x low-depth sequencing, there are still enough SNP sites in the sample that can be covered by more than 1 read, as shown in Table 1. For any SNP site with coverage greater than 1, the site can be defined as read homozygous or read heterozygous.

[0089] Table 1: Coverage of SNP sites in NIPT samples of low-depth sequencing

[0090]

[0091] The number of SNPs in the NIPT sample that can be covered by 1, 2, 3 reads, respectively, under the sequencing depth of 0.1x, 0.2x, 0.5x and 1x. Even if the sequencing depth is less than 1x, there are still enough SNP sites in the sample that can be covered by more than 1 read.

[0092] In actual cases, other factors that affect read heterozygosity also need to be considered: the inbreeding coefficient of the mother F1, the inbreeding coefficient of the fetus F2 and the sequencing error rate e. For a SNP site with two alleles, the inbreeding coefficient F directly affects the probabilities of genotypes AA, BB and AB:

[0093] AA ~ p 2 + p(1-p)F;

[0094] AB ~ 2p(1-p)(1-F);

[0095] BB ~ (1-p) 2 + p(1-p)F;

[0096] The joint genotype distribution probability and the frequency of allele A at any SNP site in the chromosome fragment under the conditions of normal fetus, maternal UPD and paternal UPD are shown in Tables 2-4, respectively. For the sake of neatness of the table, (1-p) is denoted as q.

[0097] Table 2 Genotype (MMFF) probability distribution (Prob) and frequency of allele A (F A ) Table

[0098]

[0099]

[0100] Table 3 Genotype probability distribution and frequency of allele A of SNP sites in maternal UPD region

[0101]

[0102] Table 4 Genotype probability distribution and frequency of allele A of SNP sites in paternal UPD region

[0103]

[0104]

[0105] Step 104: Determine the background parameters according to the background joint probability distribution model.

[0106] (i) The maternal inbreeding coefficient F1 and the fetal proportion h: The fetal proportion can be calculated using the fetal proportion inference model published in 2020 (the model is disclosed in the patent entitled "Fetal cell-free DNA concentration acquisition method and device", application number 201811162012.9). It is worth noting that the model should use SNP site data in the whole genome range except chromosome segment R to set the initial value of F1, and through iteration, obtain F1 and h that make the likelihood function take the maximum value.

[0107] (ii) The fetal inbreeding coefficient F2: Due to the low fetal proportion, the influence of F2 can be ignored, and it is set to 0.

[0108] (iii) The sequencing error rate e: It can be estimated using all non-polymorphic sites covered by only one read in the sample. On non-polymorphic sites, the read measured base is inconsistent with the reference genome, which is an error.

[0109] (iv) The population allele frequency p: The population allele frequency at each SNP site can be obtained from the population allele frequency data of the East Asian population of the 1000 Genomes Project.

[0110] Step 105: Determine the joint distribution likelihood value of the SNP sites in the target chromosome region according to the target joint probability distribution model and the background parameters.

[0111] For example, step 105 includes:

[0112] Step 1051: Determine a plurality of target SNP sites in the target chromosome region; the target SNP sites are covered by a plurality of reads.

[0113] Step 1052: Determine that any target SNP site is a current target SNP site.

[0114] Step 1053: Determine that the number of times the current target SNP site is covered by an allele is a first current number and a second current number.

[0115] Step 1054: Determine the marginal likelihood value of the current target SNP site according to the first current number, the second current number, and the background parameters; the marginal likelihood value includes a fetal normal marginal likelihood value, a maternal UPD marginal likelihood value, and a paternal UPD marginal likelihood value.

[0116] For example, step 1054 includes:

[0117] Step 10541: Determine the binomial distribution likelihood value of the target SNP site for each genotype according to the first current number, the second current number, the background parameters, and the allele frequency.

[0118] Step 10542: Weighted sum of the binomial distribution likelihood values of the multiple genotypes corresponding to the fetus being normal is performed with the probabilities of the multiple genotypes as the weights to obtain a fetal normal edge likelihood value of the current target SNP site.

[0119] Step 10543: Weighted sum of the binomial distribution likelihood values of the multiple genotypes corresponding to the fetus being maternal UPD is performed with the probabilities of the multiple genotypes as the weights to obtain a maternal UPD edge likelihood value of the current target SNP site.

[0120] Step 10544: Weighted sum of the binomial distribution likelihood values of the multiple genotypes corresponding to the fetus being paternal UPD is performed with the probabilities of the multiple genotypes as the weights to obtain a paternal UPD edge likelihood value of the current target SNP site.

[0121] Based on the three models corresponding to steps 10542, 10543 and 10544, the likelihood function analysis process is introduced. For any SNP site i covered by more than one read, the number of times that the two alleles A and B are covered by reads is denoted as C i i A i B , and let x be the frequency of allele A. The binomial distribution likelihood value is obtained as follows:

[0122]

[0123] For each SNP site i, the binomial distribution likelihood value corresponding to each genotype j is first calculated, and then the edge likelihood value is calculated with the probability of the genotype j as the weight:

[0124]

[0125] The edge likelihood values of all SNP sites in the chromosome fragment R are multiplied to obtain the joint distribution likelihood value of the SNP sites in the region: L(h, F1, F2, e) = ΠM(h, F1, F2, e).

[0126] Step 1055: The product of the edge likelihoods of the multiple target SNP sites in the current sequencing data in the model of the fetus being normal is determined as a first joint distribution likelihood value.

[0127] Step 1056: The product of the edge likelihoods of the multiple target SNP sites in the current sequencing data in the model of the fetus being maternal UPD is determined as a second joint distribution likelihood value.

[0128] ​​Step 1057: determining that the product of the marginal likelihoods of the plurality of target SNP loci in the current sequencing data in the model of paternal UPD of the fetus is a third joint distribution likelihood value.

[0129] Step 1058: determining that the first joint distribution likelihood value, the second joint distribution likelihood value and the third joint distribution likelihood value are the SNP loci joint distribution likelihood values of the current sequencing data.

[0130] According to the joint genotype probability distribution and the A allele frequency in Table 2, Table 3 and Table 4, the SNP loci joint distribution likelihood values in the chromosome fragment R in the three cases can be written into the above formula.

[0131] To solve L N (h, F1, F2, e), L Mat (h, F1, F2, e) and L Pat The numerical value of (h, F1, F2, e) requires the values of the parameters F1, F2, e, h and the population allele frequency p to be known, and the numerical value of the background parameter is obtained from step 104.

[0132] Step 106: determining the homozygosity of the target chromosome region according to the SNP loci joint distribution likelihood values in the target chromosome region; the homozygosity includes whether the target chromosome region is a chromosome homozygosity region, and the genetic source when the target chromosome region is a chromosome homozygosity region.

[0133] For example, step 106 includes:

[0134] Step 1061: determining a maternal determination parameter according to the first joint distribution likelihood value and the second joint distribution likelihood value; the maternal determination parameter is:

[0135] Step 1062: determining a paternal determination parameter according to the first joint distribution likelihood value and the third joint distribution likelihood value; the paternal determination parameter is:

[0136] Wherein, LLR1 is the maternal determination parameter; LN(h, F1, F2, e) is the first joint distribution likelihood value; MAt(h, F1, F2, e) is the second joint distribution likelihood value; LPat(h, F1, F2, e) is the third joint distribution likelihood value; LLR2 is the paternal determination parameter; F1 is the mother inbreeding coefficient; h is the fetal proportion; F2 is the fetal inbreeding coefficient; e is the sequencing error rate; the mother inbreeding coefficient, the fetal proportion, the fetal inbreeding coefficient and the sequencing error rate are all background parameters.

[0137] Step 1063: determining the homozygosity of the target chromosome region according to the maternal determination parameter and the paternal determination parameter.

[0138] For example, step 1063 comprises:

[0139] Step 10631: determining whether the maternal determination parameter is greater than the maternal determination parameter threshold value, to obtain a fourth determination result; if the fourth determination result is yes, executing step 10632; if the fourth determination result is no, executing step 10633.

[0140] Step 10632: determining that the target chromosomal region is a chromosomal homozygous region and is caused by maternal UPD.

[0141] Step 10633: determining whether the paternal determination parameter is greater than the paternal determination parameter threshold value, to obtain a fifth determination result; if the fifth determination result is yes, executing step 10634; if the fifth determination result is no, executing step 10635.

[0142] Step 10634: determining that the target chromosomal region is a chromosomal homozygous region and is caused by paternal UPD.

[0143] Step 10635: determining that the target chromosomal region is not a chromosomal homozygous region.

[0144] Step 107: determining whether the chromosomal region is traversed, to obtain a first determination result; if the first determination result is no, executing step 108; if the first determination result is yes, executing step 109.

[0145] Step 108: updating the target chromosomal region and returning to step 103.

[0146] Step 109: determining whether the number of chromosomal homozygous regions is greater than 0, to obtain a second determination result; if the second determination result is no, executing step 1010; if the second determination result is yes, executing step 1011.

[0147] Step 1010: determining that the sample to be tested does not exist a chromosomal homozygous region.

[0148] Step 1011: determining that the sample to be tested exists a chromosomal homozygous region.

[0149] Step 1012: determining whether the number of chromosomal homozygous regions is equal to 1, to obtain a third determination result; if the third determination result is yes, executing step 1013; if the third determination result is no, executing step 1014.

[0150] Step 1013: reporting the location and genetic source of the chromosomal homozygous region.

[0151] Step 1014: merging the chromosomal homozygous regions meeting the merging condition in the plurality of chromosomal homozygous regions, and reporting the positions and genetic sources of the chromosomal homozygous regions after the merging; the merging condition is that the chromosomal homozygous regions are adjacent to each other and have consistent genetic sources.

[0152] The method can not only detect fetal UPD, but also infer the parental origin thereof. By using genomic data, gene number SRR707167, etc., model data is generated to test and verify the performance of the method.

[0153] Embodiment 2

[0154] In order to perform the method corresponding to the above-mentioned embodiment one, to realize the corresponding functions and technical effects, the following provides a chromosomal homozygous region detection system, comprising:

[0155] The chromosomal region division module is configured to divide the chromosomes of the to-be-tested sample into a plurality of chromosomal regions according to a preset step length; the to-be-tested sample is free DNA in the peripheral blood plasma of a pregnant woman; and the free DNA is a mixture of maternal DNA and fetal DNA.

[0156] The target chromosomal region determination module is configured to select any chromosomal region as a target chromosomal region.

[0157] The distribution model construction module is configured to construct a background joint probability distribution model and a target joint probability distribution model; the background joint probability distribution model is a statistical model constructed according to sequencing data of the to-be-tested sample except for sequencing data in the target chromosomal region; and the target joint probability distribution model is a statistical model constructed according to the sequencing data in the target chromosomal region.

[0158] The background parameter determination module is configured to determine a background parameter according to the background joint probability distribution model.

[0159] The SNP site joint distribution likelihood value determination module is configured to determine a SNP site joint distribution likelihood value in the target chromosomal region according to the target joint probability distribution model and the background parameter.

[0160] The homozygous condition determination module is configured to determine a homozygous condition of the target chromosomal region according to the SNP site joint distribution likelihood value in the target chromosomal region; the homozygous condition includes whether the target chromosomal region is a chromosomal homozygous region and a genetic source when the target chromosomal region is the chromosomal homozygous region.

[0161] Embodiment 3

[0162] The embodiment provides an electronic device, comprising a memory and a processor, the memory is used for storing a computer program, and the processor runs the computer program to enable the electronic device to execute the chromosome homozygous region detection method in the embodiment 1. The memory is a readable storage medium.

[0163] The embodiments in the specification are described in a progressive manner, and each embodiment focuses on the difference from other embodiments. The same or similar parts of each embodiment can be referred to each other. For the system disclosed in the embodiments, since it corresponds to the method disclosed in the embodiments, the description is relatively simple, and the related parts can be referred to the method part.

[0164] The principles and implementation manners of the present application are described by using specific examples in the present application. The above embodiment is only used to help understand the method and core idea of the present application. Meanwhile, for the general technical personnel in the art, the specific implementation manner and application range can be changed according to the idea of the present application. In conclusion, the content of the specification should not be understood as the limitation of the present application.

Claims

1. A method for detecting a homozygous region of a chromosome, characterized by, The method comprises the following steps: dividing the chromosome of the sample to be tested into a plurality of chromosome regions according to a preset step size; the sample to be tested is free DNA in the plasma of peripheral blood of a pregnant woman; the free DNA is a mixture of maternal DNA and fetal DNA; selecting any chromosome region as a target chromosome region; constructing a background joint probability distribution model and a target joint probability distribution model; the background joint probability distribution model is a statistical model constructed according to the sequencing data of the whole genome of the sample to be tested except the sequencing data in the target chromosome region; the target joint probability distribution model is a statistical model constructed according to the sequencing data in the target chromosome region; determining a background parameter according to the background joint probability distribution model; determining a SNP site joint distribution likelihood value in the target chromosome region according to the target joint probability distribution model and the background parameter, which comprises the following steps: determining a plurality of target SNP sites in the target chromosome region; a plurality of reads are covered on the target SNP sites; determining any target SNP site as a current target SNP site; determining a first current number and a second current number of times that the current target SNP site is covered by alleles; determining an edge likelihood value of the current target SNP site according to the first current number, the second current number and the background parameter; the edge likelihood value comprises a fetal normal edge likelihood value, a maternal UPD edge likelihood value and a paternal UPD edge likelihood value; determining a first joint distribution likelihood value of the edge likelihoods of the plurality of target SNP sites in the current sequencing data in the model of fetal normal; determining a second joint distribution likelihood value of the edge likelihoods of the plurality of target SNP sites in the current sequencing data in the model of fetal maternal UPD; determining a third joint distribution likelihood value of the edge likelihoods of the plurality of target SNP sites in the current sequencing data in the model of fetal paternal UPD; and determining the first joint distribution likelihood value, the second joint distribution likelihood value and the third joint distribution likelihood value as the SNP site joint distribution likelihood value of the current sequencing data; determining a homozygous condition of the target chromosome region according to the SNP site joint distribution likelihood value in the target chromosome region; the homozygous condition comprises whether the target chromosome region is a chromosome homozygous region and a genetic source when the target chromosome region is a chromosome homozygous region; the determination of the homozygous condition of the target chromosome region according to the SNP site joint distribution likelihood value in the target chromosome region comprises: determining a parent determination parameter based on the first joint distribution likelihood value and the second joint distribution likelihood value; the parent determination parameter is: wherein LLR1 is the parent determination parameter; L N (h, F1, F2, e) is the first joint distribution likelihood value; L Mat (h, F1, F2, e) is the second joint distribution likelihood value; L Pat (h, F1, F2, e) is the third joint distribution likelihood value; determining a parent determination parameter based on the first joint distribution likelihood value and the third joint distribution likelihood value; the parent determination parameter is: wherein, LLR2 is the parent determination parameter; F1 is a maternal inbreeding coefficient; h is a fetal proportion; F2 is a fetal inbreeding coefficient; e is a sequencing error rate; the maternal inbreeding coefficient, the fetal proportion, the fetal inbreeding coefficient and the sequencing error rate are all background parameters; According to the maternal determination parameter and the paternal determination parameter, the homozygosity of the target chromosome region is determined, including: determining whether the maternal determination parameter is greater than a maternal determination parameter threshold to obtain a fourth determination result; if the fourth determination result is yes, determining that the target chromosome region is a chromosome homozygous region and is caused by maternal UPD; if the fourth determination result is no, determining whether the paternal determination parameter is greater than a paternal determination parameter threshold to obtain a fifth determination result; if the fifth determination result is yes, determining that the target chromosome region is a chromosome homozygous region and is caused by paternal UPD; if the fifth determination result is no, determining that the target chromosome region is not a chromosome homozygous region.

2. The method of detecting a homozygous chromosomal region according to claim 1, wherein, After the homozygosity of the target chromosome region is determined according to the joint distribution likelihood values of the SNP sites in the target chromosome region, the method further includes: determining whether the chromosome region is traversed to obtain a first determination result; if the first determination result is no, updating the target chromosome region and returning to the step of constructing the background joint probability distribution model and the target joint probability distribution model; if the first determination result is yes, determining whether the number of chromosome homozygous regions is greater than 0 to obtain a second determination result; if the second determination result is no, determining that the test sample does not have a chromosome homozygous region; if the second determination result is yes, determining that the test sample has a chromosome homozygous region.

3. The method of detecting a chromosomally homozygous region according to claim 2, wherein After it is determined that the test sample has a chromosome homozygous region, the method further includes: determining whether the number of chromosome homozygous regions is equal to 1 to obtain a third determination result; if the third determination result is yes, reporting the location and genetic source of the chromosome homozygous region; if the third determination result is no, merging the chromosome homozygous regions that meet the merging condition in the plurality of chromosome homozygous regions, and reporting the location and genetic source of the merged chromosome homozygous regions; the merging condition is that the chromosome homozygous regions are adjacent to each other and have the same genetic source.

4. The method of detecting a homozygous chromosomal region according to claim 1, wherein The determination of the marginal likelihood value of the current target SNP site according to the first current number, the second current number and the background parameter includes: determining the binomial distribution likelihood value of the target SNP site for each genotype according to the first current number, the second current number, the background parameter and the allele frequency; weighting and summing the binomial distribution likelihood values of the multiple genotypes corresponding to the fetus when the fetus is normal to obtain the fetal normal marginal likelihood value of the current target SNP site, with the probabilities of the multiple genotypes corresponding to the fetus when the fetus is normal as the weights; weighting and summing the binomial distribution likelihood values of the multiple genotypes corresponding to the fetus when the fetus is maternal UPD to obtain the maternal UPD marginal likelihood value of the current target SNP site, with the probabilities of the multiple genotypes corresponding to the fetus when the fetus is maternal UPD as the weights; weighting and summing the binomial distribution likelihood values of the multiple genotypes corresponding to the fetus when the fetus is paternal UPD to obtain the paternal UPD marginal likelihood value of the current target SNP site, with the probabilities of the multiple genotypes corresponding to the fetus when the fetus is paternal UPD as the weights.

5. A system for detecting a homozygous region of a chromosome, characterized by, The detection system of the chromosome homozygous region comprises the detection method of the chromosome homozygous region according to any one of claims 1-4. The chromosome region division module is configured to divide the chromosomes of the to-be-tested sample into a plurality of chromosome regions according to a preset step length; the to-be-tested sample is free DNA in peripheral blood plasma of a pregnant woman; and the free DNA is a mixture of maternal DNA and fetal DNA. The target chromosome region determination module is configured to select any chromosome region as a target chromosome region. The distribution model construction module is configured to construct a background joint probability distribution model and a target joint probability distribution model; the background joint probability distribution model is a statistical model constructed according to sequencing data of the to-be-tested sample except for sequencing data in the target chromosome region; and the target joint probability distribution model is a statistical model constructed according to the sequencing data in the target chromosome region. The background parameter determination module is configured to determine a background parameter according to the background joint probability distribution model. The SNP site joint distribution likelihood value determination module is configured to determine a SNP site joint distribution likelihood value in the target chromosome region according to the target joint probability distribution model and the background parameter. The homozygous condition determination module is configured to determine a homozygous condition of the target chromosome region according to the SNP site joint distribution likelihood value in the target chromosome region; the homozygous condition comprises whether the target chromosome region is a chromosome homozygous region and a genetic source when the target chromosome region is the chromosome homozygous region.

6. An electronic device, comprising: The electronic device comprises a memory and a processor; the memory is configured to store a computer program; and the processor is configured to run the computer program to enable the electronic device to perform the detection method of the chromosome homozygous region according to any one of claims 1-4.

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