CN110305954A - A kind of early stage accurately detects the prediction model of pre-eclampsia - Google Patents
A kind of early stage accurately detects the prediction model of pre-eclampsia Download PDFInfo
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Abstract
The prediction model of pre-eclampsia is accurately detected the invention discloses a kind of early stage.The research of the invention finds that, distribution situation of the peripheral blood dissociative DNA in gene transcription start site region can react the physiological status of pregnant woman and fetus, based on the free serum DNA abundance in gene transcription start site region, there are significant differences in preeclamptic patients and healthy pregnant women, after carrying out homogenization correction to dissociative DNA abundance, use machine learning algorithm, by the preferred combination of different differential genes, the morbidity of pre-eclampsia can be effectively predicted.Therefore the screening prediction model of the pre-eclampsia based on the prediction of peripheral blood dissociative DNA is constructed, and the target gene combination of optimization, it prediction pre-eclampsia can fall ill before the appearance of pre-eclampsia clinical symptoms, it is a kind of method of relative noninvasive, economic convenient early stage pre-eclampsia prediction, is had a good application prospect in terms of the prediction screening product of exploitation pre-eclampsia.
Description
Technical field
The invention belongs to disease detection product technical fields.Pre-eclampsia is accurately detected more particularly, to a kind of early stage
Prediction model.
Background technique
Pre-eclampsia (preeclampsia), also known as preeclampsia are a kind of common gestational period multisystem disease, morbidity
Rate is about 3~8%.Pre-eclampsia is mainly characterized by pregnant woman's hypertension and albuminuria, and severe patient damages with whole body multiple organ
Harmful or functional failure, serious person may occur in which pregnant woman's twitch, stupor, even death, and accounting for about leads to the direct or indirect of pregnant woman's death
The 10~15% of reason.Although the cause of disease of pre-eclampsia is simultaneously indefinite, and has no effective treatment method in addition to terminal pregnancy, if
It can find as early as possible, intervene in time, injury of the related complication to pregnant woman can be effectively reduced, so that effectively prevention pre-eclampsia is led
The pregnant woman of cause is dead.
Studies have shown that the morbidity of pre-eclampsia is related with a series of high risk factors, including hypertension, hyperlipidemia, Yun Fugao
Age, albuminuria etc.；In addition, a series of biochemical indicators, such as placenta growth factor (PLGF), Pregnancy-associated plasma A in serum
(PAPP-A), soluble vascular endothelial growth factor receptor1 (sFlt-1) etc., being also found the morbidity with pre-eclampsia has centainly
Correlation.Benefit from the discovery of the above high risk factor, whole world difference research group reports a series of to be referred to based on Physiology and biochemistry
Target omen eclampsia prediction technique, but these methods do not use independent pregnant woman's data to carry out verifying assessment mostly, it is a small number of
Several methods by verifying assessment, result is also not fully up to expectations.This may be since these physiological and biochemical indexs are by more
The influence of kind physiologic factor, it is not strong enough with the relevance of pre-eclampsia, it cannot reflect pre-eclampsia bring physiological change completely,
Accuracy so as to cause prediction is insufficient.
It can accurate, early detection pre-eclampsia prediction screening technology it would therefore be highly desirable to research and develop.
Summary of the invention
The technical problem to be solved by the present invention is to overcome existing pre-eclampsia screenings, the defect and deficiency of Predicting Technique, mention
For a kind of technology for predicting pre-eclampsia by peripheral blood dissociative DNA high-flux sequence.The present invention constructs one kind first
It detects to predict the prediction model of pre-eclampsia based on peripheral blood dissociative DNA, and has obtained one group and be suitable for based on peripheral blood
Dissociative DNA predicts the target gene combination of screening pre-eclampsia, optimizes prediction model.The technology of the present invention can face in pre-eclampsia
Prediction pre-eclampsia morbidity before bed symptom occurs is a kind of relative noninvasive, economical convenient and earlier than the tendency of existing method
The method of epilepsy prediction.
The object of the present invention is to provide a kind of suitable for the target gene group based on peripheral blood dissociative DNA prediction pre-eclampsia
It closes.
It is a further object of the present invention to provide a kind of prediction models of pre-eclampsia based on the detection of peripheral blood dissociative DNA.
Above-mentioned purpose of the present invention is achieved through the following technical solutions:
The research of the invention finds that distribution situation of the peripheral blood dissociative DNA in gene transcription start site region can react
The physiological status of pregnant woman and fetus, although that is, preeclamptic patients in pregnancy clinical symptoms not yet occur in 12~20 weeks, at this time
Patient and the distribution of healthy pregnant women free serum DNA on chromosome are existing dramatically different, portion gene transcription initiation site
There are significant differences in preeclamptic patients and healthy pregnant women for the free serum DNA abundance in region.The present invention is to free simultaneously
It, can be effective by the preferred combination of different differential genes using machine learning algorithm after DNA abundance carries out homogenization correction
Predict the morbidity of pre-eclampsia.Pre-eclampsia can be predicted by maternal blood dissociative DNA high-flux sequence based on this, it can
Effective method is provided with the early prediction for pre-eclampsia.
Mould is predicted in the screening for providing the pre-eclampsia based on the detection of peripheral blood dissociative DNA the present invention is based on result of study
Type, while optimizing the associated target assortment of genes.
A kind of target gene combination predicted suitable for the pre-eclampsia detected based on peripheral blood dissociative DNA, specifically
It is any several in NFKB2, EHBP1L1, AMOTL1, VSIG10, USP10, ZSWIM4, ZNF565, BZW1, ATP6V1E2, CDX1
Kind.
The target gene combines the application in terms of as the marker of screening pre-eclampsia, and in preparation tendency
Epilepsy predicts the application in screening product, also should be within protection scope of the present invention.
In addition, a kind of prediction model of the pre-eclampsia based on the detection of peripheral blood dissociative DNA is (i.e. free based on peripheral blood
The method of DNA prediction pre-eclampsia), high-flux sequence (high-flux sequence method is carried out to gestational period peripheral blood dissociative DNA to be measured
Can be both-end sequencing or single-ended sequencing), the sequencing result of peripheral blood dissociative DNA and genomic sequence map are compared
It is right, it then calculates from test gene transcript initiation site region DNA fragment quantity in same sample, then according to formula 1
After being corrected with formula 2 to DNA sequence dna sum, calculates and export pregnant woman's pre-eclampsia illness prediction result to be checked.
Wherein, the testing gene is the difference obtained after high-flux sequence result is compared with genomic sequence map
Allogene combination.Preferably above-mentioned target gene combination.
Specifically, the prediction model of the pre-eclampsia based on the detection of peripheral blood dissociative DNA includes three modules:
(1) module of high-flux sequence and analysis is carried out to sample to be tested peripheral blood dissociative DNA:
Sample to be tested peripheral blood dissociative DNA carries out high-flux sequence, and sequencing result and genomic sequence map are carried out
It compares, is calculated in same sample from test gene transcript initiation site region DNA fragment quantity；
(2) formula 1:
In formula, total aligned sequences number refers to the total sequence number for comparing in high-flux sequence data and arriving human chromosomal group sequence；
Formula 1 is used to be corrected test gene transcript initiation site region DNA fragment quantity obtained by step (1)；
The present invention counts the open journey of quantity survey (surveying) chromosome of free serum DNA sequence in gene transcription start site region
Degree；
(3) formula 2:
In formula, xiFor the gene transcription start site region DNA fragment quantity after gene i correction, βiFor the coefficient of gene i
β；C is constant；
Formula 2 is for calculating and exporting pregnant woman's pre-eclampsia illness prediction result to be checked.
Further, the prediction standard of the screening prediction model is as follows:
It brings the calculated result of formula 2 into formula 3 and calculates Y value:
Logit (Y)=ln (Y/ (1-Y)) (formula 3)
Y value is compared with preeclampsia risk threshold value P, when sample values Y is greater than threshold value P, then sample is judged as
Pre-eclampsia is high-risk；When sample values Y is less than threshold value P, then sample is judged as the low danger of pre-eclampsia.
Preferably, the preeclampsia risk threshold value P is 0.258.
Furthermore it is preferred that the c constant is -0.655 in formula 2.
Preferably, in formula 2, the coefficient of correspondence β of the gene i is respectively as follows:
Preferably, in formula 1, the transcription initiation site area size of gene is upstream region of gene 1000bp to downstream 1000bp
Region.
The invention has the following advantages:
The research of the invention finds that although not yet there are clinical symptoms in 12~20 weeks in pregnancy in preeclamptic patients, at this time
Patient and the distribution of healthy pregnant women free serum DNA on chromosome are existing dramatically different, portion gene transcription initiation site
There are significant differences in preeclamptic patients and healthy pregnant women for the free serum DNA abundance in region.Dissociative DNA abundance is carried out
After homogenization correction, pre-eclampsia can be effectively predicted by the preferred combination of different differential genes using machine learning algorithm
Morbidity.Therefore the screening prediction model of the pre-eclampsia based on the detection of peripheral blood dissociative DNA, and the target of optimization are constructed
The assortment of genes.
The technology of the present invention prediction pre-eclampsia can fall ill before the appearance of pre-eclampsia clinical symptoms, be a kind of opposite nothing
Wound, economic convenient and earlier than the prediction of the pre-eclampsia of existing method method, can mention for the early prediction screening of pre-eclampsia
For effective method, had a good application prospect in terms of the screening prediction Related product of exploitation pre-eclampsia.
Detailed description of the invention
Fig. 1 is the preeclamptic pregnancies not yet fallen ill and healthy pregnant women free serum DNA in gene transcription start site area
Domain coverage compares, there are significant differences for the chromosome degree of opening of portion gene position, and can effectively distinguish and not yet fall ill
Preeclamptic pregnancies and healthy pregnant women.
Fig. 2 is that the present invention in training group and validation group judges the ROC curve of preeclamptic patients.
Specific embodiment
Further illustrate the present invention below in conjunction with specific embodiment, but embodiment the present invention is not done it is any type of
It limits.Unless stated otherwise, the present invention uses reagent, method and apparatus is the art conventional reagents, method and apparatus.
Unless stated otherwise, following embodiment agents useful for same and material are commercially available.
Explanation of nouns herein: both-end sequencing refers to that test respectively is located at the sequence at sequence both ends.Single-ended sequencing refers to survey
Examination is located at the sequence of sequence one end.
Model method of the embodiment 1 based on peripheral blood dissociative DNA prediction pre-eclampsia
The present invention is based on the methods of peripheral blood dissociative DNA prediction pre-eclampsia are as follows: by the sequencing result of peripheral blood dissociative DNA
It is compared, is then calculated in same sample from test gene transcript initiation site region with genomic sequence map
DNA fragmentation quantity is corrected according to DNA sequence dna sum, after carrying out homogenization correction to dissociative DNA abundance, uses engineering
It practises algorithm and calculates and export pregnant woman's pre-eclampsia illness prediction result to be checked by the preferred combination of different differential genes, it can
The morbidity of pre-eclampsia is effectively predicted.
Specifically, method and step is as follows:
Step 1: determining specific location of the DNA fragmentation in blood plasma on chromosome
Be diagnosed as preeclamptic pregnancies before the onset of sample and healthy sample carry out comparative study, to two kinds of samples
Peripheral blood dissociative DNA carries out high-throughput both-end sequencing (alternatively, it is also possible to being single-ended sequencing).
After carrying out the sequencing of peripheral blood dissociative DNA high throughput both-end, by the sequence at this both ends and human genome standard sequence
Column 37.1 compare (http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
Data/? build=37) (database is also referred to as hg19), it is determined that the position of the sequence at this both ends respectively on chromosome, it should
The distance between two terminal sequences are exactly the length of the DNA fragmentation, while the chromosome location where two terminal sequence has determined
Which chromosome the DNA fragmentation comes from.
Although the results show that not yet there are clinical symptoms in 12 weeks in pregnancy in preeclamptic patients, at this time patient with it is healthy
The distribution of pregnancy serum dissociative DNA on chromosome is existing dramatically different, the serum in portion gene transcription initiation site region
There are significant difference (as shown in Figure 1) in preeclamptic patients and healthy pregnant women for dissociative DNA abundance.
Grope by numerous studies, it is determined that a kind of testing gene combination of optimization, as shown in table 1:
1 testing gene of table
It should be noted that in the case of no contradiction, the combination of differential gene shown in the table 1 in the application only represents certain
Preferred combination under one reagent, instrument platform, the present invention does not limit inventor, and it is preferable to use it under other instruments, reagent conditions
He predicts in differential gene combination.
Step 2: determining the DNA fragmentation abundance in test gene transcript initiation site region
The total aligned sequences number of statistical sample (total aligned sequences number point of two samples in the present embodiment, sample 1 and sample 2
It Wei 63486 and 51100).Calculate the number of the DNA fragmentation in test gene transcript initiation site region in same sample
Amount, is corrected DNA fragmentation abundance using formula 1.
Table 2 is the example that the DNA fragmentation abundance in two sample test gene transcript initiation site regions calculates:
Table 2
Step 3: according to testing gene expression, calculating onset risk
The onset risk of pre-eclampsia is calculated using formula 2:
In formula, xiFor the gene transcription start site region DNA fragment quantity after gene i correction, βiFor the coefficient of gene i
β；C is constant, c value -0.655.
The gene and its coefficient of correspondence β are as shown in table 3:
Table 3
Y value is calculated further according to formula 3:
Logit (Y)=ln (Y/ (1-Y)) (formula 3)
Preeclampsia risk threshold value P is 0.258, and when sample values Y is greater than threshold value P, then sample is judged as pre-eclampsia
It is high-risk；When sample values Y is less than threshold value P, then sample is judged as the low danger of pre-eclampsia.
In conclusion the present invention is based on the model (prediction technique) of peripheral blood dissociative DNA prediction pre-eclampsia, including three
Module:
(1) high-flux sequence and analysis are carried out to sample to be tested peripheral blood dissociative DNA:
Sample to be tested peripheral blood dissociative DNA carries out high-flux sequence, and sequencing result is compared with genomic sequence map
It is right, it is calculated in same sample from test gene transcript initiation site region DNA fragment quantity；
(2) test gene transcript initiation site region DNA fragment quantity obtained by step (1) is corrected according to formula 1；
(3) it is calculated according to formula 2 and formula 3 and exports pregnant woman's pre-eclampsia illness prediction result to be checked.
2 pattern detection example of embodiment
1, experiment sample:
Training group includes 60 pre-eclampsia samples, 378 normal healthy controls；
Validation group includes 44 pre-eclampsia samples, 162 normal healthy controls.
It operates according to the method for embodiment 1.The accuracy of statistical calculation method, sensibility and specificity.
2, the results show that method model of the invention can effectively judge before the onset of early stage in training group and validation group
Preeclamptic patients (table 4 and Fig. 2).
Table 4
Wherein, calculated result example is as follows:
Sample 1 (sample before the onset for having made a definite diagnosis preeclamptic pregnancies):
Logit (Y)=- 0.655-1.146 × NFKB2+1.350 × EHBP1L1-1.371 × AMOTL1-0.784 ×
VSIG10–1.047×USP10–1.226×ZSWIM4+1.242×ZNF565–0.983×BZW1+0.761×ATP6V1E2+
1.842 × CDX1=0.439
Y=0.608
Sample values are greater than pre-eclampsia threshold value P (0.258), are judged as the high-risk sample of pre-eclampsia.As a result accurate.
Sample 2 (healthy sample):
Logit (Y)=- 0.655-1.146 × NFKB2+1.350 × EHBP1L1-1.371 × AMOTL1-0.784 ×
VSIG10–1.047×USP10–1.226×ZSWIM4+1.242×ZNF565–0.983×BZW1+0.761×ATP6V1E2+
1.842 × CDX1=-4.911
Y=0.007
Sample values are less than threshold value P (0.258), are judged as the low danger sample of pre-eclampsia.As a result accurate.
The above embodiment is a preferred embodiment of the present invention, but embodiments of the present invention are not by above-described embodiment
Limitation, other any changes, modifications, substitutions, combinations, simplifications made without departing from the spirit and principles of the present invention,
It should be equivalent substitute mode, be included within the scope of the present invention.
Claims (10)
1. a kind of suitable for the target gene combination based on peripheral blood dissociative DNA prediction pre-eclampsia, which is characterized in that the target
The mark assortment of genes be NFKB2, EHBP1L1, AMOTL1, VSIG10, USP10, ZSWIM4, ZNF565, BZW1, ATP6V1E2,
It is any several in CDX1.
2. target gene described in claim 1 combines the application in terms of as the marker of screening pre-eclampsia.
3. the combination of target gene described in claim 1 or its detection reagent answering in preparation pre-eclampsia prediction screening product
With.
4. a kind of pre-eclampsia screening prediction model based on the detection of peripheral blood dissociative DNA, which is characterized in that including three moulds
Block:
(1) module of high-flux sequence and analysis is carried out to sample to be tested peripheral blood dissociative DNA:
Sample to be tested peripheral blood dissociative DNA carries out high-flux sequence, and sequencing result is compared with genomic sequence map,
It is calculated in same sample from test gene transcript initiation site region DNA fragment quantity；The testing gene is high pass
The differential gene that amount sequencing result obtains after being compared with genomic sequence map combines；
(2) formula 1:
In formula, total aligned sequences number refers to the total sequence number for comparing in high-flux sequence data and arriving human chromosomal group sequence；
Formula 1 is used to be corrected test gene transcript initiation site region DNA fragment quantity obtained by step (1)；
(3) formula 2:
In formula, xiFor the gene transcription start site region DNA fragment quantity after gene i correction, βiFor the factor beta of gene i；C is
Constant；
Formula 2 is for calculating and exporting pregnant woman's pre-eclampsia illness prediction result to be checked.
5. screening prediction model according to claim 4, which is characterized in that prediction standard is as follows:
It brings the calculated result of formula 2 into formula 3:logit (Y)=ln (Y/ (1-Y)), calculates Y value；By Y value and tendency
Epilepsy risk threshold value P is compared, and when sample values Y is greater than threshold value P, then sample is judged as that pre-eclampsia is high-risk；Work as sample number
When value Y is less than threshold value P, then sample is judged as the low danger of pre-eclampsia.
6. screening prediction model according to claim 4, which is characterized in that the testing gene is target described in claim 1
Mark the assortment of genes.
7. screening prediction model according to claim 4, which is characterized in that in formula 1, the transcription initiation site region of gene
Size is upstream region of gene 1000bp to the region of downstream 1000bp.
8. screening prediction model according to claim 4, which is characterized in that in formula 2, the c constant is -0.655, described
Gene and its coefficient of correspondence β are respectively as follows: that factor beta that the factor beta of NFKB2 is -1.146, EHBP1L1 is 1.350, AMOTL1 is
The factor beta that the factor beta that the factor beta that number β are -1.371, VSIG10 is -0.784, USP10 is -1.047, ZSWIM4 is -1.226,
The factor beta that the factor beta that the factor beta of ZNF565 is 1.242, the factor beta of BZW1 is -0.983, ATP6V1E2 is 0.761, CDX1 is
1.842。
9. screening prediction model according to claim 8, which is characterized in that prediction standard is as follows:
It brings the calculated result of formula 2 into following formula 3 and calculates Y value:
Logit (Y)=ln (Y/ (1-Y))
Preeclampsia risk threshold value P is 0.258, and when sample values Y is greater than threshold value P, then sample is judged as that pre-eclampsia is high-risk；
When sample values Y is less than threshold value P, then sample is judged as the low danger of pre-eclampsia.
10. screening prediction model according to claim 4, which is characterized in that sequencing is single-ended sequencing or both-end sequencing.
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| CN114822682A (en) * | 2022-04-12 | 2022-07-29 | 苏州市立医院 | Target gene combination related to early-onset severe preeclampsia and application thereof |
| CN115019888A (en) * | 2022-07-14 | 2022-09-06 | 苏州贝康医疗器械有限公司 | Screening system of tissue specific gene marker based on peripheral blood free DNA high-throughput sequencing and application thereof |
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