CN113969310A - Fetal DNA concentration evaluation method and application - Google Patents
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Abstract
The invention discloses an assessment method and application of fetal DNA concentration, and belongs to the technical field of biological information. The method comprises the following steps: s101: sequencing the polymorphic sites of the father DNA sample, the pregnant woman leukocyte DNA sample and the pregnant woman free DNA sample to respectively obtain DNA data F, M and S; s102: acquiring a site set X' meeting a preset requirement in the S; s103: calculating the probability P of a certain locus in the locus set X' according to a formula I; s104: obtaining p when the cumulative probability h of the point set X' is maximum by adopting a maximum likelihood value methodmax(ii) a S105: concentration of fetal DNA N =2pmax. The method can evaluate the DNA concentration of fetus, and can judge whether the leucocyte of pregnant woman needs to be detected or not and whether the leucocyte needs to be detected or not according to the evaluation value during paternity testNew inspection is carried out; thereby improving the accuracy of paternity test.
Description
Technical Field
The invention belongs to the technical field of biological information analysis, and particularly relates to an assessment method and application of fetal DNA concentration, which are used for performing auxiliary judgment on paternity test.
Background
A gene is a functional fragment carrying genetic information on a DNA molecule, and is a substance for transmitting genetic information by organisms. DNA is increasingly used, for example, for paternity testing. The quality of the DNA sample is directly related to the success or failure of the subsequent experiment.
With the rapid development of high-throughput sequencing technology, Single Nucleotide Polymorphism (SNP) is increasingly becoming the latest detection means for individual and paternity testing as the third generation genetic marker. Compared with STR, SNP has wider distribution and more quantity in chromosome, and the detection method is more convenient and reliable.
When the peripheral blood of a pregnant woman is used for paternity test, if the DNA concentration of a fetus is low, accurate test cannot be usually realized, and the fetus needs to be re-examined; if the fetal DNA concentration is high, accurate identification cannot be achieved generally, and the requirement of matching sequencing of leucocytes of pregnant women increases the cost and the workload. Therefore, it is necessary to evaluate the fetal DNA concentration before paternity testing.
Disclosure of Invention
In one aspect, the embodiments of the present invention provide a method for estimating fetal DNA concentration, the method including the following steps:
s101: sequencing the polymorphic sites of a father DNA sample, a pregnant woman leukocyte DNA sample and a pregnant woman free DNA sample to respectively obtain DNA data F, M and S, wherein the pregnant woman free DNA sample is obtained by separating the peripheral blood of a pregnant woman;
s102: acquiring a site set X' meeting the following requirements in S,
X'＝{xi|nai(F)/ni(F)＜0.1∩nAi(M)/ni(M)＜0.1}∪{xi|nAi(F)/ni(F)＜0.1∩nai(M)/ni(M)＜0.1}，
wherein nA and nA respectively represent observed values of the binary sites A and a, n is nA + nA, and k is nA;
s103: calculating the probability P of a certain locus in the locus set X' according to formula I,
wherein the content of the first and second substances,
0≤p≤0.5，Pm＝0.4；
s104: obtaining p when the cumulative probability h of the point set X' is maximum by adopting a maximum likelihood value methodmax；
S105: fetal DNA concentration N2 pmax。
Wherein, in step S101, the sequencing method comprises:
s1011: constructing a probe;
s1012: extracting DNA in a sample;
s1013: a library of building blocks;
s1014: performing hybridization capture and sequencing on the library target region by adopting the probe of the step S1011;
s1015: and splitting and filtering the sequencing data by the quality value to obtain the sequencing data.
Wherein the polymorphic locus is selected from SNP locus, INDEL locus and/or STR locus, and the population frequency of the polymorphic locus is 0.05-0.95.
Specifically, in the SNP site, A represents a wild-type site and a represents a mutant site.
Preferably, the number of said dynodes is greater than 1000.
Wherein, in step S104: calculating the cumulative probability h of all the sites in the site set X' according to a formula II, calculating the cumulative probability h by taking the value of p at preset intervals, and determining the value of p as p when h takes the maximum valuemax；
Preferably, the predetermined interval is 0.0001.
On the other hand, the embodiment of the invention also provides the application of the fetal DNA concentration evaluation method, when N is more than or equal to 0.4, and paternity test is carried out, sequencing is carried out on leucocytes of a pregnant woman; when N is more than 0.004 and less than 0.4, paternity test is carried out according to a second generation DNA paternity test method; when N is less than or equal to 0.004, performing paternity test, and if all loci are matched with the male parent, judging the parent as a new parent; if the locus is not matched and the fetus is a male fetus, judging according to the matching condition of the Y chromosome, and judging that the fetus is a non-father if a mismatch exists; if the loci are not matched and the fetus is a female fetus, the paternity can not be judged, and the free DNA sample of the pregnant woman needs to be collected again.
The evaluation method provided by the invention can evaluate the DNA concentration of the fetus, and during paternity test, whether leucocytes of a pregnant woman need to be detected or not can be judged according to the evaluation value, whether the leucocytes need to be re-checked or not can be judged, and paternity test can be carried out by adopting a conventional second-generation DNA paternity test method within an empirical value range (N is more than 0.004 and less than 0.4); thereby improving the accuracy of paternity test.
Drawings
FIG. 1 is a flow chart of a method for assessing fetal DNA concentration according to an embodiment of the present invention;
fig. 2 is a flowchart of step S101;
FIG. 3 is a graph of cumulative probability h and P values;
FIG. 4 is a linear distribution diagram of N-N in example 3;
FIG. 5 is a linear distribution graph of N-N in example 4.
Detailed Description
In order to make the objects, technical solutions and advantages of the present invention more apparent, the present invention will be described in further detail with reference to the accompanying drawings.
Example 1
Example 1 provides a method for assessing fetal DNA concentration, comprising the steps of:
s101: sequencing the polymorphic sites of a father DNA sample, a pregnant woman leucocyte DNA sample (which is the DNA of a pregnant woman) and a pregnant woman free DNA sample (which is the mixed signal of the DNA of the pregnant woman and the DNA of a fetus) to respectively obtain DNA data F, M and S; wherein, the free DNA sample of the pregnant woman is obtained by separating the peripheral blood of the pregnant woman (containing fetal DNA). Among them, the DNA data F, M and S in this example were obtained by the second generation sequencing technique.
S102: acquiring a site set X' meeting the following requirements in S,
X'＝{xi|nai(F)/ni(F)＜0.1∩nAi(M)/ni(M)＜0.1}∪{xi|nAi(F)/ni(F)＜0.1∩nai(M)/ni(M)＜0.1}，
wherein nA and nA respectively represent observed values of the binary sites A and a, n is nA + nA, and k is nA; the value requirements of F and M indicate that the same point positions on the data S, F and M are in line with the value requirements.
S103: calculating the probability P of a certain locus in the locus set X' according to formula I,
wherein the content of the first and second substances,
p is more than or equal to 0 and less than or equal to 0.5, and Pm is 0.4; specifically, p is discretely valued at predetermined intervals starting from 0.
S104: obtaining p when the cumulative probability h of the point set X' is maximum by adopting a maximum likelihood value methodmax。
S105: fetal DNA concentration N2 pmax。
Wherein, in step S101, a conventional second-generation sequencing technology is adopted, and the sequencing method comprises:
s1011: constructing a probe, wherein the probe is designed as required.
S1012: extracting DNA from the sample.
S1013: a library of building blocks.
S1014: and (4) performing hybridization capture and sequencing on the target region of the library by using the probe of the step S1011.
S1015: and splitting and filtering the sequencing data by the quality value to obtain the sequencing data.
Wherein the polymorphic locus is selected from SNP locus, INDEL locus and/or STR locus, etc., and the population frequency of the polymorphic locus is 0.05-0.95.
Among the SNP sites, A represents a wild-type site and a represents a mutant site. Specifically, the site is aligned with a human genome reference sequence, and the site aligned with the reference genome is called as a wild type, whereas the site aligned with the reference genome is called as a mutant type, and the site aligned with the reference genome is called as a mutant type.
Preferably, to ensure accuracy, the number of binary sites is greater than 1000, e.g., 2693.
Wherein, in step S104: calculating the cumulative probability h of all the sites in the site set X' according to a formula II, calculating the cumulative probability h by taking the value of p at preset intervals (from 0 to 0.5), and determining the value of p as p when h takes the maximum valuemax；
Preferably, to ensure accuracy, the predetermined interval is 0.0001; of course, other values, such as 0.001, may be used as desired.
Example 2
The embodiment of the invention also provides application of the fetal DNA concentration evaluation method disclosed in the embodiment 1, and when N is more than or equal to 0.4 and paternity test is carried out, leucocytes of a pregnant woman need to be sequenced to obtain the SNP locus genotype of the pregnant woman. And (3) when N is more than 0.004 and less than 0.4, performing paternity test according to a conventional second-generation DNA paternity test method. When N is less than or equal to 0.004, performing paternity test, and if all loci are matched with the male parent, judging the parent as a new parent; if the locus is not matched and the fetus is a male fetus, judging according to the matching condition of the Y chromosome, and judging that the fetus is a non-father if a mismatch exists; if the loci are not matched and the fetus is a female fetus, the relationship between the parent and the child cannot be judged, and the sample is required to be sent again.
Example 3
The method comprises the steps of randomly generating a father DNA sample F and a mother DNA sample M through Chinese population frequency, generating a child Z through Mendel' S genetic law, mixing samples at intervals of 0.01 from 0 to 0.4, mixing the child Z and the mother M to obtain a simulated pregnant woman free DNA sample S, mixing 10 samples in each proportion, and obtaining the number of the S sample set as 400. Of these, F, M and S sample sets contained dyadic types including SNPs and INDELs.
Obtaining a partial subset of the Chinese population polymorphic sites as a detection site set X, wherein the number of the adopted population frequency binary SNP sites is more than 1000, and the number of the adopted population frequency binary SNP sites is 0.05-0.95. And obtaining the polymorphism distribution of each site xi of the detection site set X of the sample F, M and S.
The fetal concentration in the S sample was calculated from the set of test sites of samples F, M and S according to the method of example 1. Taking the analog concentration as 0.1 as an example, the obtained relation graph of the cumulative probability h and the p value is shown in fig. 3, and it can be seen from the graph that when p is at a certain value (0.05), h can take the maximum value, and the p value at the moment is just 1/2 of the analog concentration after verification. The simulated concentration N is taken as an X axis, the calculated N (p3) is taken as a Y axis to be plotted, and N-N is taken as a linear distribution diagram, wherein p3 is N +0.0030, and r is20.9966969, the profile is shown in fig. 4. The lower oblique line is the actual simulated concentration, and the upper oblique line is the value calculated by the method of the patent. As can be seen from the figure, the difference between the concentration calculated by the method of the present invention and the simulated concentration is very small, i.e. the evaluation method of the present invention has very high accuracy.
Example 4
And obtaining the polymorphic sites of the father DNA sample F, the mother DNA sample M and the offspring DNA sample Z through experimental sequencing analysis. A sample of mock maternal free DNA sample S was obtained by mixing samples of Z and M in known proportions p as in example 3. The fetal concentration in the S sample was calculated from the set of test sites of samples F, M and S according to the method of example 1. The simulated concentration N is used as an X axis, the calculated N (p3) is used as a Y axis to be plotted, and N-N is obtained as a linear distribution diagram, wherein p3 is 1.014062X N, and r is20.9996, the profile is shown in fig. 5. It is composed ofThe lower slope is the actual simulated concentration, and the upper slope is the value calculated by the method of this patent. As can be seen from the figure, the difference between the concentration calculated by the method of the present invention and the simulated concentration is very small, i.e. the evaluation method of the present invention has very high accuracy.
The above description is only for the purpose of illustrating the preferred embodiments of the present invention and is not to be construed as limiting the invention, and any modifications, equivalents, improvements and the like that fall within the spirit and principle of the present invention are intended to be included therein.
Claims (8)
1. A method for assessing fetal DNA concentration, the method comprising the steps of:
s101: sequencing the polymorphic sites of a father DNA sample, a pregnant woman leukocyte DNA sample and a pregnant woman free DNA sample to respectively obtain DNA data F, M and S, wherein the pregnant woman free DNA sample is obtained by separating the peripheral blood of a pregnant woman;
s102: acquiring a site set X' meeting the following requirements in S,
X'＝{xi|nai(F)/ni(F)＜0.1∩nAi(M)/ni(M)＜0.1}∪{xi|nAi(F)/ni(F)＜0.1∩nai(M)/ni(M)＜0.1}，
wherein nA and nA respectively represent observed values of the binary sites A and a, n is nA + nA, and k is nA;
s103: calculating the probability P of a certain locus in the locus set X' according to formula I,
wherein the content of the first and second substances,
0≤p≤0.5，Pm＝0.4；
s104: obtaining p when the cumulative probability h of the point set X' is maximum by adopting a maximum likelihood value methodmax；
S105: fetal DNA concentration N2 pmax。
2. The method for assessing fetal DNA concentration according to claim 1, wherein in step S101, the sequencing method comprises:
s1011: constructing a probe;
s1012: extracting DNA in a sample;
s1013: a library of building blocks;
s1014: performing hybridization capture and sequencing on the library target region by adopting the probe of the step S1011;
s1015: and splitting and filtering the sequencing data by the quality value to obtain the sequencing data.
3. The method for assessing fetal DNA concentration according to claim 1, wherein the polymorphic sites are selected from SNP sites, INDEL sites and/or STR sites, and the population frequency of the polymorphic sites is 0.05-0.95.
4. The method for evaluating a fetal DNA concentration according to claim 3, wherein in the SNP site, A represents a wild type site and a represents a mutant type site.
5. The method of claim 3, wherein the number of the polymorphic sites is greater than 1000.
6. The method for evaluating the fetal DNA concentration according to claim 1, wherein in step S104: calculating the cumulative probability h of all the sites in the site set X' according to a formula II, calculating the cumulative probability h by taking the value of p at preset intervals, and determining the value of p as p when h takes the maximum valuemax；
7. The method of claim 6, wherein the predetermined interval is 0.0001.
8. Use of the method for fetal DNA concentration assessment according to any one of claims 1-7 wherein, for paternity testing at N.gtoreq.0.4, sequencing of the leukocytes of pregnant women is required; when N is more than 0.004 and less than 0.4, paternity test is carried out according to a second generation DNA paternity test method; when N is less than or equal to 0.004, performing paternity test, and if all loci are matched with the male parent, judging the parent as a new parent; if the locus is not matched and the fetus is a male fetus, judging according to the matching condition of the Y chromosome, and judging that the fetus is a non-father if a mismatch exists; if the loci are not matched and the fetus is a female fetus, the paternity can not be judged, and the free DNA sample of the pregnant woman needs to be collected again.
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