CN109321641B - A kind of antenatal noninvasive fetal chromosomal detection system based on DNA fragmentation enrichment and sequencing technologies - Google Patents
A kind of antenatal noninvasive fetal chromosomal detection system based on DNA fragmentation enrichment and sequencing technologies Download PDFInfo
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Abstract
The invention discloses a kind of methods based on DNA fragmentation specific enrichment detection prenatal foetal chromosome abnormality, this method is by obtaining maternal blood and obtaining dissociative DNA by DNA beneficiation technologies, the enrichment method of probe hybrid capture is used in enrichment DNA operation, the specific fragment of the enrichment method Sync enrichment mother and fetus, without being only enriched with to foetal DNA, the detection method not only realizes the detection of fetus whole chromosome content, also achieve the detection of fetus part chromosome content, it is high that this method is applied to pregnant woman blood plasma dissociative DNA detection fetal chromosomal abnormalities accuracy.
Description
Technical field
The present invention relates to chromosome abnormality detection systems, and concretely, the present invention relates to one kind based on DNA fragmentation specificity
The antenatal noninvasive fetal chromosomal detection system of enrichment and second generation sequencing technologies.
Background technique
In human genetic diseases, chromosomal disorders are the most common genopathies of the mankind, are caused at present because chromosome is abnormal
About more than 300 kinds of disease, the cell chromosome of this kind of patient all has certain numerical abnormality or textural anomaly.For by dyeing
Effective treatment means are often not present in genetic disease caused by body variation, therefore people whether there is dye to newborn fetus
Colour solid makes a variation and the attention degree with ancestor genetic diseases is gradually increased.With free fetal dna in maternal blood
It was found that noninvasive prenatal foetal DNA detection technique, which effectively reduces high risk pregnant woman, to be caused due to false positive by invasive diagnosis
The risk of normal fetus miscarriage or infection.However, traditionally noninvasive prenatal foetal DNA detection technique has relatively large office
It is sex-limited.
Chromosome abnormality is the main reason for causing a large amount of birth defects (including mental retardation).Abnormal general table
Now for chromosomal DNA repeat or lack and chromosomal aneuploidy, the latter refer to complete chromosome anomaly exist or
Missing.When organism having less than or more than normal diploid chromosome quantitative when, will generate a large amount of off-notes and because
This variety of syndrome.Down syndrome, also known as trisomy 21 syndrome, are the most common examples of chromosomal aneuploidy, including one
No. 21 additional chromosomes of item.Other common chromosomal aneuploidies have Patau syndrome, Edwards syndrome, Tener comprehensive
Simulator sickness and Crane Fei Erte syndrome (Klinefelter ˊ s Syndrome).
Down syndrome is a kind of relatively common genetic block, suffers from this for about one in every 800 life birth babies
Syndrome.The syndrome is caused by the presence by additional whole chromosome 21 (trisomy 21, T21), or less typically, by volume
Caused by the most presence of the outer chromosome, it is related to other autosomal trisomys (i.e. T13 or T18) and also occurs in work
It produces in baby, but rarer than T21.Usually there is the disease of the fetus aneuploidy caused by extra-chromosome or chromosome deficiency
Disease generates imbalance in the foetal DNA molecular population in parent cell-free plasma DNA, this is detectable.Exploitation is used for tire
The reliable method of the pre-natal diagnosis of youngster's chromosome abnormality is a long term object in reproductive health care, gives and passes through amniocentesis
With chorionic villus sampling and the method that obtains fetal material is invasive, and there is very important wind for gestation
Danger, even in experienced clinician's hand also so.In current practice, the method for such invasive diagnosis has
It is well used in the case where the sign for increasing Tang Shi gestation chance.
21, the disease incidence about 1/500 of 13,18 chromosome aneuploid fetuses, carry the children of these diseases in the future to
Family and society bring heavy burden, and the selection of detection antenatal for chromosome abnormality is limited primarily to invasive method, these
Method has the risk for causing fetal loss.The abnormal method of most common detection is amniocentesis.However, since amnion is worn
Piercing art is invasive method, therefore is generally only used for elderly parturient women, because the wind of chromosome abnormality occurs in the fetus of elderly parturient women
Danger increased.Existing methods for prenatal diagnosis processing sampling procedure is invasive, operation also time and effort consuming.For example, Jim
Sa decoration method is most widely used technology, and when this method requires experiment, cell is in metaphase in cell division or is dividing
It splits, characteristic oolemma will not caught to chromosome or blanking bar is composed.In this way, all chromosome can be by one by one
It distinguishes and is easy anomalous property show in any structure or quantitative.Giemsa staining method can not detect fine
Chromosomal rearrangement.If suspecting chromosomal rearrangement, but it can't detect in this way, further detailed analysis can be used glimmering
Light in situ hybridization or map karyotyping carry out.With Giemsa staining method, test result needed for one to two weeks.
Therefore, current noninvasive antenatal detection very useful for the non invasive method of fetal chromosomal abnormalities diagnosis is established
Technology application, accuracy are up to 99.9%, and most chromosome aneuploid fetuses can be detected
Come.However pointed out in " the Birth Defects In China prevention and treatment report 2012 " issued according to the Ministry of Public Health, the Fetal Birth Defect in China occurs
Rate and the average level of medium input country, the world are close, and about 5.6%, increase birth defect number about 900,000 newly every year, hence it is evident that
Visible birth defect about 250,000, account for about baby's ratio 1.5%, 19.1% is that birth defect directly results in infant mortality cause.
And the chromosome aneuploid of most serious only accounts for extremely and is evident that the 13% of birth defect, and other 87% serious births
There is presently no effective detection methods for defect.
A kind of Noninvasive prenatal gene point of fetus sex chromosome is disclosed in Chinese patent application 2012800108284
Type, the invention provides for analyzing maternal sample, so that it is determined that the X whether male fetus of pregnant woman inherits mother is chain prominent
Method, instrument and the system of change.The percentage of foetal DNA in sample is obtained, and determines that (fetus inherits mutation to two kinds of possibilities
Allele or normal allele) cutoff value.Then, by mutation allele on X chromosome relative to normal equipotential
The ratio of gene is compared with cutoff value, to make the classification for inheriting which allele.It is alternatively possible to will be dyed by X
The quantity for the allele that target area on body obtains is compared with the quantity of the allele of the reference area on X chromosome
Compared with to identify missing or amplification.It can be reacted by counting with the distinctive allele of fetus, and correct quantity to illustrate
Statistical distribution in reaction calculates the percentage of foetal DNA.But this application discloses prenatal gene parting and is mainly used for examining
Survey whether fetus inherits the X linked mutation of mother, be to the selection of DNA fragmentation in the detection process entirely it is random, cover
Lid depth is low, and for some specific region on chromosome, not can guarantee centainly has DNA fragmentation to be detected and have sufficient amount full
Sufficient subsequent analysis, in this way can not accurate detection small fragment chromosome abnormality.
Therefore, it is abnormal to be badly in need of a kind of fetus whole chromosome that not only can detecte, local piece on chromosome can also be detected
The amplification and missing of section, for supplementing the Genetic Detection system of birth defect.
Summary of the invention
In order to solve above-mentioned the technical issues of facing, the present invention is intended to provide it is a kind of based on DNA fragmentation specific enrichment and
Method, instrument and the system of the antenatal noninvasive fetal chromosomal detection of second generation sequencing technologies, the detection system can not only be examined
The exception for surveying fetus whole chromosome, can also detect the repetition and missing of more small fragment on chromosome.The present invention uses
Plasma sample derived from pregnant woman, not only fetal cell and small percentage containing less percentage in Maternal plasma
Foetal DNA.
A method of prenatal foetal chromosome abnormality is detected based on DNA fragmentation specific enrichment, this method comprises:
(1) maternal blood sample, the plasma DNA in separating sample are obtained；
(2) plasma DNA obtained using the DNA probe of human genome whole exon or primer pair step (1)
It is enriched with, obtains DNA fragmentation；
(3) DNA fragmentation being enriched to step (2) is sequenced；
(4) sequencing result obtained according to step (3), each DNA sequence dna that identification sequencing obtains is in the mankind with reference to gene
Position in group, for the mankind with reference to each target rich region on genome, by the DNA sequence dna meter in the region recognized
Number, for N number of nonoverlapping target rich region, obtains N number of counting, refers to the position on genome for N number of number according to the mankind
Line up a vector A；
(5) it by the peripheral blood sample of the pregnant woman of dye-free body exception, is calculated simultaneously according to step (1)-(4) same procedure
The mean value for calculating the sequence number of all samples of each target rich region, obtains outgoing vector B；
(6) vector C=(C is obtained with the following methodi), wherein AiIt is i-th of element of vector A, BiIt is the i-th of vector B
A element；CiIt is i-th of element of vector C；
Ci=Ai/Bi
Enrichment described in above-mentioned steps (2) is the enrichment method of probe hybrid capture, and the enrichment method Sync enrichment is female
The specific fragment of affine fetus.
Sequencing described in above-mentioned steps (3), average sequencing depth are greater than 100X, that is, the genome sequence for needing to be enriched with
Averagely there are 100 or more DNA fragmentations to cover on position.
The width of each target rich region described in above-mentioned steps (4) is 50-500 base.
Preferably, the width of each target rich region described in above-mentioned steps (4) is 100-400 base.
The present invention also provides a kind of antenatal noninvasive fetus based on DNA fragmentation specific enrichment and second generation sequencing technologies
Chromosome detection system, including four modules:
Module one, obtains maternal blood sample, the plasma DNA in separation and Extraction sample, this module is a set of DNA
Extraction element；
Module two, the blood plasma obtained using the DNA probe or primer pair module one of specific positions some on human genome
Dissociative DNA is enriched with, and DNA fragmentation is obtained, this module is a set of DNA enriching apparatus；
Module three carries out sequencing detection to the DNA fragmentation that module two is enriched to, obtains the DNA sequence dna detected, this mould
Block is a second generation DNA sequencer；
Module four carries out data processing to the DNA sequence dna that module three has detected, this includes a computer and 9 calculating
Program:
Program one, this program are a sequence alignment program, and sequence is positioned in long sequence, suitable position, people are found
Genoid group is 24 long sequences, and the DNA sequence dna detected is millions of short sequences；
Program two, caller two carry out gender calculating using the DNA quantity being positioned on human genome；
Program three, if it is male fetus, caller three is to the DNA fragmentation content quantitative on each chromosome；
Program four, if it is male fetus, caller four is in megabase length areas every on each chromosome
DNA fragmentation content quantitative；
Program five, if it is male fetus, base of the caller five to target rich region on each chromosome of fetus
Sizing；
Program six, if it is female child, caller six is to the DNA fragmentation content quantitative on each chromosome；
Program seven, if it is female child, caller seven is in megabase length areas every on each chromosome
DNA fragmentation content quantitative；
Program eight, if it is female child, base of the caller eight to target rich region on each chromosome of fetus
Sizing；
Program nine, caller nine are formed to the base of target rich region on each chromosome of parent.
In a specific embodiment, it provides a kind of based on DNA fragmentation specific enrichment detection prenatal foetal chromosome
Abnormal method, this method comprises:
(1) it obtains maternal blood sample and separates and extracts peripheral blood sample using the DNA extraction element in module one
In plasma DNA, obtain plasma DNA；
(2) using the DNA enriching apparatus in module two and DNA probe or primer pair step (1) on human genome
Obtained in plasma DNA be enriched with, obtain DNA fragmentation；
(3) DNA fragmentation obtained in step (2) is sequenced using the second generation DNA sequencer in module three, is obtained
The DNA sequence dna detected；
(4) data processing is carried out to the DNA sequence dna detected obtained in step (3) using computer and 9 programs:
Program one, this program are a sequence alignment program, and the DNA sequence detected obtained in module three is positioned at
On human genome, the DNA sequence dna detected is millions of short sequences；
Program two, caller two carry out gender calculating using the DNA quantity being positioned on human genome；
Program three, if it is male fetus, caller three is to the DNA fragmentation content quantitative on each chromosome；
Program four, if it is male fetus, caller four is in megabase length areas every on each chromosome
DNA fragmentation content quantitative；
Program five, if it is male fetus, base of the caller five to target rich region on each chromosome of fetus
Sizing；
Program six, if it is female child, caller six is to the DNA fragmentation content quantitative on each chromosome；
Program seven, if it is female child, caller seven is in megabase length areas every on each chromosome
DNA fragmentation content quantitative；
Program eight, if it is female child, base of the caller eight to target rich region on each chromosome of fetus
Sizing；
Program nine, caller nine are formed to the base of target rich region on each chromosome of parent.
DNA probe described in above-mentioned steps (2) is the probe in EXOME, by the sequencing data of EXOME, carries out tire
The calculating of the gene copy number variation (CNV) of larger segment in youngster's genome；
The calculating of gene copy number variation (CNV) further includes 13,18 and No. 21 chromosome trisomies in above-mentioned Fetal genome
The calculating of probability.
The capture region of above-mentioned DNA probe further includes the region ENCODE, the region TFBS and the region ncRNA&siRNA.
The length of above-mentioned DNA probe is the sequence of the encoded protein products of ten thousand genes of 1-3.
The present invention, in order to accurately detect gene copy number variation, can select in implementation process in any range of genome
A certain number of probes can preferably select a certain number of probes in genome in the fixed area of 1-10M；Further preferably it is
A certain number of probes are selected in the fixed area of 1M, 2M, 3M, 5M and 10M in genome.
Enrichment described in above-mentioned steps (2) is the enrichment method of probe hybrid capture, and the enrichment method Sync enrichment is female
The specific fragment of affine fetus.
Sequencing described in step (3) uses second generation high throughput sequencing technologies, and average sequencing depth is greater than 100X.
The chromosome abnormality is that DNA is repeated or DNA is lacked.
Wherein, the chromosome abnormality is aneuploidy；The aneuploidy is trisomy 21,18 three-bodies or 13 3
Body.
In a specific embodiment, it provides a kind of based on DNA fragmentation specific enrichment detection prenatal foetal chromosome
Abnormal method, this method comprises:
Module one:
A, the blood 5mL of pregnant 12 weeks pregnant woman to be measured is acquired with the Cell-Free DNA BCT test tube of STRECK company；
B, using the QIAamp Circulating Nucleic Acid Kit kit extraction step a of QIAGEN company
Acquire the dissociative DNA in blood plasma；
C, the blood that step b is extracted using the KAPA Hyper Prep Kit kit of KAPA biosystems company
It starches dissociative DNA and constructs library；
Module two:
Kit enrichment mode is captured using the SeqCap EZ Human Exome Probes v3.0 DNA of Roche company
People's exon sequence in the DNA library that block one obtains；
Module three:
Using Illumina company Nextseq500 model high-flux sequence instrument in module two be enriched with after people outside
The data of aobvious subsequence measurement 32G base, DNA sequence dna length is 150 length of both-end, obtains DNA sequence dna；
Module four:
A, module three obtained DNA sequence dna is detected using one BWA software of program to be positioned on human genome hg19；
B, sex of foetus male is obtained as a result, calculate sex of foetus using program two and program one；
C, be calculated using the result of program three, four, five, nine and program one that fetal chromosomal is integrally quantitative, contaminates
Colour solid regional area is quantitative, target rich region foetal DNA base is formed, the sizing of target rich region mother body D NA base.
Compared with prior art, the present invention beneficial effect is:
(1) this application discloses one kind to be based on DNA fragmentation specific enrichment and prenatal foetal chromosome abnormality detection system,
DNA beneficiation technologies are used in this application, and the technical application is accurate to pregnant woman blood plasma dissociative DNA detection fetal chromosomal abnormalities
Degree is high.
(2) detection system disclosed herein, enrichment DNA operation in use probe hybrid capture enrichment method, should
The specific fragment of enrichment method Sync enrichment mother and fetus, without being only enriched with to foetal DNA.
(3) detection system provided by the present application not only realizes the detection of fetus whole chromosome content, also achieves tire
The detection of youngster part chromosome content.
(4) detection system provided by the invention realizes while detecting the inspection of foetal DNA base type and mother body D NA base type
It surveys.
Detailed description of the invention
Fig. 1 is disclosed by the invention based on DNA fragmentation enrichment and fetal chromosomal detection system flow chart.
Specific embodiment
A kind of method based on DNA fragmentation specific enrichment detection prenatal foetal chromosome abnormality of embodiment 1, this method packet
It includes:
(1) maternal blood sample, the plasma DNA in separating sample are obtained；
(2) plasma DNA obtained using the DNA probe of human genome whole exon or primer pair step (1)
The enrichment of probe hybrid capture is carried out, Sync enrichment obtains the DNA fragmentation of mother and fetus；
(3) DNA fragmentation being enriched to step (2) is sequenced, and average sequencing depth is greater than 100X, that is, needs to be enriched with
Genome sequence column position on averagely there are 100 or more DNA fragmentations to cover；
(4) sequencing result obtained according to step (3), each DNA sequence dna that identification sequencing obtains is in the mankind with reference to gene
Position in group, for the mankind with reference to each target rich region on genome, by the DNA sequence dna meter in the region recognized
Number, for N number of nonoverlapping target rich region, obtains N number of counting, refers to the position on genome for N number of number according to the mankind
Line up a vector A；
(5) it by the peripheral blood sample of the pregnant woman of dye-free body exception, is calculated simultaneously according to step (1)-(4) same procedure
The mean value for calculating the sequence number of all samples of each target rich region, obtains outgoing vector B；
(6) vector C=(C is obtained with the following methodi), wherein AiIt is i-th of element of vector A, BiIt is the i-th of vector B
A element；CiIt is i-th of element of vector C；
Ci=Ai/Bi
The width of each target rich region described in above-mentioned steps (4) is 50-500 base.
A kind of antenatal noninvasive fetal chromosomal based on DNA fragmentation specific enrichment and second generation sequencing technologies of embodiment 2
Detection system, including four modules:
Module one, obtains maternal blood sample, the plasma DNA in separation and Extraction sample, this module is a set of DNA
Extraction element；
Module two, the blood plasma obtained using the DNA probe or primer pair module one of specific positions some on human genome
Dissociative DNA is enriched with, and DNA fragmentation is obtained, this module is a set of DNA enriching apparatus；
Module three carries out sequencing detection to the DNA fragmentation that module two is enriched to, obtains the DNA sequence dna detected, this mould
Block is a second generation DNA sequencer；
Module four carries out data processing to the DNA sequence dna that module three has detected, this includes a computer and 9 calculating
Program:
Program one, this program are a sequence alignment program, and sequence is positioned in long sequence, suitable position, people are found
Genoid group is 24 long sequences, and the DNA sequence dna detected is millions of short sequences；
Program two, caller two carry out gender calculating using the DNA quantity being positioned on human genome；
Program three, if it is male fetus, caller three is to the DNA fragmentation content quantitative on each chromosome；
Program four, if it is male fetus, caller four is in megabase length areas every on each chromosome
DNA fragmentation content quantitative；
Program five, if it is male fetus, base of the caller five to target rich region on each chromosome of fetus
Sizing；
Program six, if it is female child, caller six is to the DNA fragmentation content quantitative on each chromosome；
Program seven, if it is female child, caller seven is in megabase length areas every on each chromosome
DNA fragmentation content quantitative；
Program eight, if it is female child, base of the caller eight to target rich region on each chromosome of fetus
Sizing；
Program nine, caller nine are formed to the base of target rich region on each chromosome of parent.
A kind of method based on DNA fragmentation specific enrichment detection prenatal foetal chromosome abnormality of embodiment 3, this method packet
It includes:
(1) it obtains maternal blood sample and separates and extracts peripheral blood sample using the DNA extraction element in module one
In plasma DNA, obtain plasma DNA；
(2) using the DNA enriching apparatus in module two and DNA probe or primer pair step (1) on human genome
Obtained in plasma DNA be enriched with, obtain DNA fragmentation；
(3) DNA fragmentation obtained in step (2) is sequenced using the second generation DNA sequencer in module three, is obtained
The DNA sequence dna detected；
(4) data processing is carried out to the DNA sequence dna detected obtained in step (3) using computer and 9 programs:
Program one, this program are a sequence alignment program, and the DNA sequence detected obtained in module three is positioned at
On human genome, the DNA sequence dna detected is millions of short sequences；
Program two, caller two carry out gender calculating using the DNA quantity being positioned on human genome；
Program three, if it is male fetus, caller three is to the DNA fragmentation content quantitative on each chromosome；
Program four, if it is male fetus, caller four is in megabase length areas every on each chromosome
DNA fragmentation content quantitative；
Program five, if it is male fetus, base of the caller five to target rich region on each chromosome of fetus
Sizing；
Program six, if it is female child, caller six is to the DNA fragmentation content quantitative on each chromosome；
Program seven, if it is female child, caller seven is in megabase length areas every on each chromosome
DNA fragmentation content quantitative；
Program eight, if it is female child, base of the caller eight to target rich region on each chromosome of fetus
Sizing；
Program nine, caller nine are formed to the base of target rich region on each chromosome of parent.
DNA probe described in above-mentioned steps (2) is the probe in EXOME, by the sequencing data of EXOME, carries out tire
The calculating of the gene copy number variation (CNV) of larger segment in youngster's genome；
The capture region of above-mentioned DNA probe further includes the region ENCODE, the region TFBS and the region ncRNA&siRNA.
The length of above-mentioned DNA probe is the sequence of the encoded protein products of ten thousand genes of 1-3.
Enrichment described in above-mentioned steps (2) is the enrichment method of probe hybrid capture, and the enrichment method Sync enrichment is female
The specific fragment of affine fetus.
A kind of method based on DNA fragmentation specific enrichment detection prenatal foetal chromosome abnormality of embodiment 4, this method packet
It includes:
Module one:
A, the blood 5mL of pregnant 12 weeks pregnant woman to be measured is acquired with the Cell-Free DNA BCT test tube of STRECK company；
B, using the QIAamp Circulating Nucleic Acid Kit kit extraction step a of QIAGEN company
Acquire the dissociative DNA in blood plasma；
C, the blood that step b is extracted using the KAPA Hyper Prep Kit kit of KAPA biosystems company
It starches dissociative DNA and constructs library；
Module two:
Kit enrichment mode is captured using the SeqCap EZ Human Exome Probes v3.0 DNA of Roche company
People's exon sequence in the DNA library that block one obtains；
Module three:
Using Illumina company Nextseq500 model high-flux sequence instrument in module two be enriched with after people outside
The data of aobvious subsequence measurement 32G base, DNA sequence dna length is 150 length of both-end, obtains DNA sequence dna；
Module four:
A, module three obtained DNA sequence dna is detected using one BWA software of program to be positioned on human genome hg19；
B, sex of foetus male is obtained as a result, calculate sex of foetus using program two and program one；
C, be calculated using the result of program three, four, five, nine and program one that fetal chromosomal is integrally quantitative, contaminates
Colour solid regional area is quantitative, target rich region foetal DNA base is formed, the sizing of target rich region mother body D NA base.
Claims (5)
1. a kind of antenatal noninvasive fetal chromosomal detection system based on DNA fragmentation specific enrichment and second generation sequencing technologies,
It is characterized by: the module is software for carrying out enrichment detection prenatal foetal chromosome the system comprises four modules
Abnormal method, this method comprises:
(1) maternal blood sample, the plasma DNA in separating sample are obtained；
(2) the plasma DNA progress probe obtained using the DNA probe of human genome whole exon to step (1) is miscellaneous
Capture enrichment is handed over, the specific fragment of Sync enrichment mother and fetus obtain DNA fragmentation；
(3) DNA fragmentation being enriched to step (2) is sequenced, and average sequencing depth is greater than 100X；
(4) sequencing result obtained according to step (3), each DNA sequence dna that identification sequencing obtains is in the mankind with reference on genome
Position the DNA sequence dna in the region recognized is counted for the mankind with reference to each target rich region on genome, it is right
It is 50-500 base in the width of N number of nonoverlapping target rich region, each target rich region, obtains N number of counting, according to
N number of number is lined up a vector A with reference to the position on genome by the mankind；
(5) by the peripheral blood sample of the pregnant woman of dye-free body exception, each target is calculated according to step (1)-(4) same procedure
The mean value of the sequence number of all samples of rich region, obtains outgoing vector B；
(6) vector C=(C is obtained with the following methodi), wherein AiIt is i-th of element of vector A, BiIt is i-th yuan of vector B
Element；CiIt is i-th of element of vector C；
Ci=Ai/Bi。
2. system according to claim 1, it is characterised in that: four modules are as follows:
Module one, obtains maternal blood sample, the plasma DNA in separation and Extraction sample, this module is a set of DNA extraction
Device；
Module two carries out the plasma DNA that module one obtains using the DNA probe of human genome whole exon rich
Collection, obtains DNA fragmentation, this module is a set of DNA enriching apparatus；
Module three carries out sequencing detection to the DNA fragmentation that module two is enriched to, obtains the DNA sequence dna detected, this module is one
Platform second generation DNA sequencer；
Module four carries out data processing to the DNA sequence dna that module three has detected, this includes a computer and 9 calculation procedures:
Program one, this program are a sequence alignment program, and sequence is positioned in long sequence, suitable position, Ren Leiji are found
Because group is 24 long sequences, the DNA sequence dna detected is millions of short sequences；
Program two, caller two carry out gender calculating using the DNA quantity being positioned on human genome；
Program three, if it is male fetus, caller three is to the DNA fragmentation content quantitative on each chromosome；
Program four, if it is male fetus, caller four is to the DNA piece in megabase length areas every on each chromosome
Section content quantitative；
Program five, if it is male fetus, caller five is formed to the base of target rich region on each chromosome of fetus；
Program six, if it is female child, caller six is to the DNA fragmentation content quantitative on each chromosome；
Program seven, if it is female child, caller seven is to the DNA piece in megabase length areas every on each chromosome
Section content quantitative；
Program eight, if it is female child, caller eight is formed to the base of target rich region on each chromosome of fetus；
Program nine, caller nine are formed to the base of target rich region on each chromosome of parent.
3. system according to claim 2, it is characterised in that: using the side of the system detection prenatal foetal chromosome abnormality
Method, this method comprises:
(1) maternal blood sample is obtained to separate and extract in peripheral blood sample using the DNA extraction element in module one
Plasma DNA obtains plasma DNA；
(2) it uses and is obtained in the DNA enriching apparatus in module two and the DNA probe on human genome or primer pair step (1)
To plasma DNA be enriched with, obtain DNA fragmentation；
(3) DNA fragmentation obtained in step (2) is sequenced using the second generation DNA sequencer in module three, is detected
Good DNA sequence dna；
(4) data processing is carried out to the DNA sequence dna detected obtained in step (3) using computer and 9 programs:
Program one, this program are a sequence alignment program, and the DNA sequence dna detected obtained in module three is positioned at mankind's base
Because the DNA sequence dna in group, detected is millions of short sequences；
Program two, caller two carry out gender calculating using the DNA quantity being positioned on human genome；
Program three, if it is male fetus, caller three is to the DNA fragmentation content quantitative on each chromosome；
Program four, if it is male fetus, caller four is to the DNA piece in megabase length areas every on each chromosome
Section content quantitative；
Program five, if it is male fetus, caller five is formed to the base of target rich region on each chromosome of fetus；
Program six, if it is female child, caller six is to the DNA fragmentation content quantitative on each chromosome；
Program seven, if it is female child, caller seven is to the DNA piece in megabase length areas every on each chromosome
Section content quantitative；
Program eight, if it is female child, caller eight is formed to the base of target rich region on each chromosome of fetus；
Program nine, caller nine are formed to the base of target rich region on each chromosome of parent.
4. system according to claim 3, it is characterised in that: DNA probe described in step (2) is Roche company
SeqCapEZ Human Exome Probes v3.0 DNA captures the probe in kit.
5. system according to claim 3, it is characterised in that: the capture region of the DNA probe further includes ENCODE
Region, the region TFBS and the region ncRNA&siRNA.
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| CN103946394A (en) * | 2011-10-18 | 2014-07-23 | 姆提普力科姆公司 | Fetal chromosomal aneuploidy diagnosis |
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