CN105354443A - Noninvasive prenatal gene testing and analyzing software - Google Patents
Noninvasive prenatal gene testing and analyzing software Download PDFInfo
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- CN105354443A CN105354443A CN201510925363.0A CN201510925363A CN105354443A CN 105354443 A CN105354443 A CN 105354443A CN 201510925363 A CN201510925363 A CN 201510925363A CN 105354443 A CN105354443 A CN 105354443A
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Abstract
The invention discloses noninvasive prenatal gene testing and analyzing software. The software comprises a data quality control module, a data comparison module, a noninvasive prenatal analysis module, a data statistics module and a report generating module which are connected in sequence, and finally an analysis can be obtained, wherein the noninvasive prenatal analysis module comprises a GC correction module. The software is installed and used simply, is higher in accuracy compared with a conventional testing method and can analyze 23 pairs of karyotypes.
Description
Technical field
The invention belongs to field of gene detection, particularly for a kind of software that pregnant front fetus chromosomal disorders detect, be particularly related to a kind of without wound prenatal gene detection analysis software.
Background technology
Chromosomal disorder is the abbreviation of chromosome disorder.Mainly because of the main carriers of inhereditary material in cell---the disease that chromosomal number or form, textural anomaly cause.Usually autosomal disease and the large class of sex chromosomal disease two is divided into.Autosomal disease is caused by autosomal abnormalities, clinical manifestation congenital mental retardation, grows delayed and Poly-monstrosity.Sex chromosomal disease do as one likes chromosome abnormality causes, clinical manifestation sexual dyspenesis, feeblemindedness, Poly-monstrosity etc.In spontaneous abortion fetus, have 20 ~ 50% to be caused by chromosome abnormality; In new life baby, the incidence of chromosome abnormality is 0.5 ~ 1%.Chromosomal disorder patient lacks self care ability usually, and namely some patients died young in childhood, so chromosomal disorder is one of main research becoming clinical genetics.
At present for reducing the birth rate having chromosomal disorders fetus, usually analyze by carrying out antenatal detection.The detection mode of conventional prenatal chromosome disease has Tang Shi examination, amniocentesis, fine hair inspection and detecting without wound DNA.
Tang Shi examination, by the blood of chemical examination pregnant woman, detects the concentration of A type fetoprotein and chorionic gonadotropin in maternal serum, and in conjunction with expected date of childbirth of pregnant woman, the age, body weight and blood sampling time pregnant week etc., calculate the detection method bearing the danger coefficient of Tang Shi.Tang's sieve checks and screening can go out the Down Syndrome infant of 60--70%, and accuracy rate is low.Amniocentesis, fine hair checks that Detection accuracy is higher than 99%, but has certain risk of miscarriage.
And only need extract maternal blood without creating antenatal DNA detection, carry out DNA and detect just whether to be changed chromosomal disorders, nothing creates and accuracy is high.And along with the development of high throughput sequencing technologies, order-checking price reduces again and again, and DNA sequencing analytical technology (DNA-seq) instead of old Sanger sequencing technologies, becomes the conventional means in DNA research direction.Along with two generation sequencing technologies development, this technology has been used to the inspection (namely detecting without the antenatal fund of wound) of fetal chromosomal times type.But for the technology that this is emerging, normalized analysis flow process also ununified so far.And adopt standardized analysis process to be conducive to detecting without the antenatal fund of wound the industrialization of analytical technology.And the current characteristic reckoning without human chromosome GC skewness without wound prenatal Ultrasound software, qualification result usually can be affected, and causes the sensitivity of software on the low side.In addition, software only designs for professional, do not take into full account the installation and deployment of software and simple ease for use, the biological information personnel of specialty are needed to dispose before using, the installation specification of software is high, only have professional to use, and 13,18 and 21 3 chromosomal times of type information can only be evaluated.
Inspection DNA Analysis of test results software installation difficulty is produced without wound for existing, reckon without the properties influence detection accuracy of human chromosome GC skewness, and the problem of 13,18,21 3 chromosomes times type information can only be analyzed, the invention provides a kind of without wound prenatal gene detection analysis software.
Summary of the invention
Existing without wound product inspection DNA Analysis of test results software installation difficulty in order to overcome, and reckon without the properties influence detection accuracy of human chromosome GC skewness, and the problem of 13,18,21 3 chromosomes times type information can only be analyzed, the object of this invention is to provide a kind of nothing wound prenatal gene that can solve the problem and detect analysis software.
Object of the present invention is achieved through the following technical solutions:
A kind of without wound prenatal gene detection analysis software, comprise data Quality Control module, comparing module, nothing wound prenatal Ultrasound module, data statistics module and report generation module, it is characterized in that, each module connects transmission data successively, wherein comprises GC rectification module without wound prenatal Ultrasound module.Data Quality Control module is used for carrying out Quality Control to maternal blood genetic test data; Be used for being analyzed and format transformation the data after Quality Control without wound prenatal Ultrasound module; Data statistics module is used for correcting GC distribution situation, and calculates each chromosomal Z value; The Z value that data statistics module is used for coming without wound prenatal Ultrasound module transfer is added up; The data genaration final report that data statistics module transmission comes by report generation module, makes result present.
Further, described data Quality Control module carries out the Quality Control of genetic test data by fastx algorithm.
Further, described comparing module is compared by the data of bwa and samtools algorithm to Quality Control module transfer.
Further, the bwa algorithm of the sequencing data comparison use of described comparing module, samtools and the picardtools algorithm that Data Format Transform uses.
Further, described nothing wound prenatal Ultrasound module comprises GC rectification module and Z value computing module.
Further, described GC rectification module use formula is: RCGC=RCraw X F, wherein
Further, the computing formula of Z value computing module is:
chrN's
The implication of symbology in table 1. formula
Further, described data statistics module carries out assessment statistics to the chromosomal Z value of every bar.
The invention also discloses the use flow process detecting analysis software without wound prenatal gene, be specially:
1) data Quality Control module utilizes fastx algorithm to carry out Quality Control to the genetic test data obtained;
2) comparing module utilizes the data of bwa algorithm to data Quality Control module transfer to compare, and the rear samtools of utilization and picardtools algorithm are changed data layout;
3) carry out GC rectification without the data of wound prenatal Ultrasound module to the corresponding form that data comparing module transmits, and calculate often pair of chromosomal Z value;
4) data statistics module is added up the Z value of coming without wound prenatal Ultrasound module transfer;
5) data that data statistics module obtains are transferred to report generation module and produce final test results report.
Beneficial effect of the present invention is: this software utilizes bioinformatics method to incorporate many algorithms and by its procedure, Software deployment does not need compiling, complete greenization is installed, be not only applicable to the librarian use being engaged in biological information work, be equally applicable to the non-librarian use being engaged in the work of biological information system, and all chromosomal times of type information can be evaluated, greatly simplify the work of researchist when analyzing fetal chromosomal times type, having the advantages that to use simple, procedure, be easy to safeguard, show visual result.This software is by processing the maternal blood DNA sequencing data comprising Fetal genome sequence, can cross and obtain the chromosomal Z value of every bar, thus for the Down's syndrome examination of fetus, and result is accurate, false positive and false negative are extremely low, and detect and only use a small amount of in vitro peripheral blood sample, significantly reduce misery and the risk of pregnant woman, there is good application prospect.
Accompanying drawing explanation
Fig. 1 process flow diagram of the present invention
In figure 1, data Quality Control module; 2, comparing module; 3, without wound prenatal Ultrasound module; 4, data statistics module; 5, report generation module.
Embodiment
Embodiment 1 one kinds detects analysis software without wound prenatal gene
A kind of without wound prenatal gene detection analysis software, comprise data Quality Control module 1, comparing module 2, without wound prenatal Ultrasound module 3, data statistics module 4 and report generation module 5, each module connects transmission data successively.Data Quality Control module 1 is for carrying out Quality Control to maternal blood genetic test data; Without wound prenatal Ultrasound module 3 for being analyzed the data after Quality Control and format transformation; Data statistics module 4 for correcting GC distribution situation, and calculates each chromosomal Z value; Data statistics module 4 is for adding up the Z value transmitted without wound prenatal Ultrasound module 3; Data statistics module 4 is transmitted the data genaration final report come by report generation module 5, and result is presented.
Data Quality Control module 1 carries out the Quality Control of genetic test data by fastx algorithm.Comparing module 2 is compared by the data of bwa and samtools algorithm to Quality Control module transfer.The bwa algorithm of the sequencing data comparison use of comparing module 2, samtools and the picardtools algorithm that Data Format Transform uses.GC rectification module and Z value computing module is comprised without wound prenatal Ultrasound module 3.GC rectification module uses formula to be RCGC=RCraw X F, wherein
the computing formula of Z value computing module is
chrN's
data statistics module 4 carries out assessment statistics to the chromosomal Z value of every bar.
In embodiment in formula the implication of symbol with reference to table 1.
Embodiment 2 one kinds detects the use flow process of analysis software without wound prenatal gene
The invention also discloses the use flow process detecting analysis software without wound prenatal gene, be specially:
1) the genetic test data of the maternal blood obtained are transferred to data Quality Control module 1;
2) data Quality Control module 1 utilizes fastx algorithm to carry out Quality Control to the genetic test data obtained;
3) comparing module 2 utilizes bwa algorithm to compare to the data that data Quality Control module 1 is transmitted, and the rear samtools of utilization and picardtools algorithm are changed data layout;
4) carry out GC rectification without the data creating the corresponding form that prenatal Ultrasound module 3 pairs of data comparing module 2 transmit, and calculate often pair of chromosomal Z value;
5) data statistics module 4 is added up the Z value transmitted without wound prenatal Ultrasound module 3;
6) data that data statistics module 4 obtains are transferred to report generation module 5 and produce final test results report.
7) output detections report, provides analysis result information clearly.
The explanation of above-described embodiment is just for understanding the present invention.It should be pointed out that for the person of ordinary skill of the art, under the premise without departing from the principles of the invention, can also carry out some improvement to the present invention, these improvement also will fall in the protection domain of the claims in the present invention.
Claims (9)
1. one kind is detected analysis software without wound prenatal gene, comprise data Quality Control module, comparing module, nothing wound prenatal Ultrasound module, data statistics module and report generation module, it is characterized in that, each module connects transmission data successively, wherein comprises GC rectification module without wound prenatal Ultrasound module.
2. according to claim 1 without wound prenatal gene detection analysis software, it is characterized in that, described data Quality Control module carries out the Quality Control of genetic test data by fastx algorithm.
3. according to claim 1 without wound prenatal gene detection analysis software, it is characterized in that, described comparing module is compared by the data of bwa and samtools algorithm to Quality Control module transfer.
4. nothing wound prenatal gene according to claim 3 detects analysis software, it is characterized in that, the bwa algorithm of the sequencing data comparison use of described comparing module, samtools and the picardtools algorithm that Data Format Transform uses.
5. nothing wound prenatal gene according to claim 1 detects analysis software, it is characterized in that, described nothing wound prenatal Ultrasound module comprises GC rectification module and Z value computing module.
6. nothing wound prenatal gene according to claim 5 detects analysis software, it is characterized in that, described GC rectification module use formula is: RCGC=RCraw × F, wherein
7. according to claim 1 without wound prenatal gene detection analysis software, it is characterized in that, the computing formula of Z value computing module is:
chrN's
8. according to claim 1 without wound prenatal gene detection analysis software, it is characterized in that, described data statistics module is assessed the chromosomal Z value of every bar.
9. described in claim 1 without the use flow process of wound prenatal gene detection analysis software be,
1) data Quality Control module carries out Quality Control to the genetic test data obtained;
2) data of comparing module to data Quality Control module transfer are compared, and change data layout afterwards;
3) carry out GC rectification without the data of wound prenatal Ultrasound module to the corresponding form that data comparing module transmits, and calculate the chromosomal Z value of every bar;
4) data statistics module is added up the Z value of coming without wound prenatal Ultrasound module transfer;
5) data that data statistics module obtains are transferred to report generation module and produce final test results report.
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| CN106096330A (en) * | 2016-05-31 | 2016-11-09 | 北京百迈客医学检验所有限公司 | A kind of noninvasive antenatal biological information determination method |
| CN108315240A (en) * | 2018-01-19 | 2018-07-24 | 武汉永瑞康华医学检验所有限公司 | A kind of flow quality control standard technology can be used for gene sequencing |
| CN108388770A (en) * | 2018-03-01 | 2018-08-10 | 北京乐普基因科技股份有限公司 | The noninvasive antenatal bioinformatics detecting system of one kind and its methods and applications |
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| CN108315240A (en) * | 2018-01-19 | 2018-07-24 | 武汉永瑞康华医学检验所有限公司 | A kind of flow quality control standard technology can be used for gene sequencing |
| CN108388770A (en) * | 2018-03-01 | 2018-08-10 | 北京乐普基因科技股份有限公司 | The noninvasive antenatal bioinformatics detecting system of one kind and its methods and applications |
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