CN110189798A - A kind of clustering method and application based on peripheral blood plasma DNA nucleosome footprint difference - Google Patents
A kind of clustering method and application based on peripheral blood plasma DNA nucleosome footprint difference Download PDFInfo
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Abstract
The invention discloses a kind of clustering method and application based on peripheral blood plasma DNA nucleosome footprint difference, the specific method includes: the acquisition of (1) peripheral blood plasma DNA high-flux sequence data；(2) building of standard nucleosome localization region database；(3) each sample sequencing data is compared and analyzed with standard nucleosome localization region database；(4) the coverage data of nucleosome footprint difference are screened and are standardized；(5) clustering is carried out to the data after standardization according to the correlation between sample using hierarchical agglomerate method；Method provided by the invention can effectively avoid dependence of the existing method to tissue or cell, the depth and accuracy of General Promotion high-flux sequence data analysis, the noninvasive Concurrent Chemoradiotherapy Sensitivity prediction to tumor patient is realized, has the characteristics that comprehensive, accurate, coverage is high；Belong to field of biotechnology.
Description
Technical field
The invention discloses a kind of clustering methods based on periphery plasma DNA nucleosome footprint difference, specifically
Ground is said, is the nucleosome footprint difference clustering method based on peripheral blood plasma DNA full-length genome measured data, is belonged to life
Object technical field.
Background technique
Nucleosome is a kind of biology of typical DNA in conjunction with histone as the chromatinic basic unit of eucaryote
Macromolecular is the important content of epigenetics.Under different cell states, nucleosome positioning is dynamic change, position
Change will affect transcription factor and the combination of DNA, so that controlling gene is specific expressed.Therefore, analysis nucleosome footprint is poor
It is different, it is found that the variation of nucleosome footprint is of great significance under different condition.Due to the extreme ring in hypoxemia, highly acidity in tumour
Border, while there are keen competition between tumour cell, apoptosis occurs for a large amount of tumour cell.After apoptosis, cell
DNA in core can gradually be degraded by DNA enzymatic and be released in peripheral blood.And when DNA and protein binding form nucleosome, DNA
The protection of albumen just be will receive without being degraded by enzymes, opposite exposed DNA can be then degraded by enzymes.Due to the expression of gene in cell
Horizontal closely related with the combination degree of nucleosome, the nucleosome combination number of cance high-expression gene is relatively few then relatively easily to be dropped
Solution, the nucleosome combination number of low expression gene is more, is relatively difficult to be degraded.It is carried out by human peripheral blood plasma DNA
High-flux sequence, and to sequencing data depth analysis, nucleosome footprint different information can be found within the scope of full-length genome.
The treatment common method of tumour is surgical operation, chemotherapy and radiation at present.Operation can only cut off visible neoplastic disease
Stove, and the tumorigenic cause of disease cannot be cut off, therefore patients after surgery is easy recurrence；Chemotherapy is comprehensive in malignant tumour
It is still main means in treatment, but the curative effect of current chemotherapy is still undesirable.The reason is that there is heterogeneities for tumour itself, even if
Same histological type, the identical tumour of differentiation degree are different to the sensibility of same drug.Such as single medicine of patients with gastric cancer has
Efficiency is only 15%-30%, and efficient mitomycin (MMC) is 30%, and efficient fluorouracil (5-FU) is 21%, table Ah mould
Plain (EDI) efficient is 19%, and the effective percentage of combined chemotherapy is also only 30%-50%.Due to chemotherapeutics generally all have compared with
Strong toxicity, unsuitable chemotherapy not only caused suffering to patient, but also cannot alleviate the state of an illness, it is often more important that it is possible that inducing multiple
Drug resistance leads to treatment failure.Radiotherapy is that the treatment method of cancer cell is killed using high-energy radiation, and therapeutic domain compares limitation,
Partial controll effect is preferable, but radiotherapy is while inhibition or killing tumor cell, to the toxic effect of organism normal cell,
It is not that each patient is suitable for radiotherapy.Therefore suitable treatment means and drug how are more effectively screened, clinic is instructed to control
It treats and has become the problem of clinical therapy of tumor is attracted attention to improve curative effect.
Summary of the invention
In view of the above-mentioned problems, the purpose of the present invention establishes a kind of gathering for peripheral blood plasma DNA nucleosome footprint difference
Alanysis method, and filter out tumor chemoradiotherapy sensitive patients and insensitive patient in the gene of nucleosome footprint position disparity,
It is poor to nucleosome footprint of the same gene in tumor chemoradiotherapy sensitive patients and insensitive patient using rank sum test method
Allogene carries out clustering, to realize noninvasive tumor chemoradiotherapy sensitivity prediction.
Technical solution provided by the invention is such that
A kind of clustering method and application based on peripheral blood plasma DNA nucleosome footprint difference, the method
Include the following steps:
(1) peripheral blood plasma DNA is subjected to high-flux sequence, obtains the high-flux sequence data of each sample；
(2) according to the annotation information of all human protein coding genes in the RefSeq database of UCSC, each base is obtained
The transcription initiation site (TSSs) of cause and the genomic locations in the region translational termination site (TTSs) upstream and downstream 1Kb construct standard
Nucleosome localization region database；
(3) nucleosome footprint in resulting sequencing data and step (2) is sequenced in each sample using Bowtie software to position
Standard database is compared, and removes PCR repetitive sequence, removal low quality sequence dna fragment, not compare core small for removal
The sequence dna fragment of body footprint localization region compares the sequence dna fragment for arriving multiple positions, and counting statistics is compared to above-mentioned
The reads number of each sample in region, and statistical result is standardized using RPKM method；
(4) rank sum test nonparametric technique is utilized, tumor chemoradiotherapy sensitive patients and insensitive patient's promoter region are calculated
The gene of domain nucleosome footprint position disparity, the variation multiple between two groups | log2Fold change | >=1 and raw P values≤
0.05, original p value is corrected followed by Holm-Bonferroni method, the gene for filtering out value≤0.1 q-value turns
The region initiation site (TSSs) and translational termination site (TTSs) is recorded, they are defined as to the nucleosome region of difference；
(5) discrepant nucleosome area coverage data are standardized using Cluster software, it is poly- using grade
Class method carries out clustering to the data after standardization according to the correlation between sample, and with R language pheatmap packet to data
It is visualized.According to the footprint difference of full-length genome range Natural promoter and terminator nucleosome, sample type cluster
For tumor chemoradiotherapy sensitive patients and insensitive patient.
Further, the above-mentioned clustering method based on peripheral blood plasma DNA nucleosome footprint difference, it is described
Method data source be peripheral blood plasma DNA sequencing data of whole genome, and each sample data amount is no less than
6Million reads, data format include fastq, bam, sam.
Further, the above-mentioned clustering method based on peripheral blood plasma DNA nucleosome footprint difference, it is described
Nucleosome footprint difference refers to that each gene transcription start site and transcription are eventually within the scope of peripheral blood plasma DNA full-length genome
Only the nucleosome of site areas is distributed in the difference in remaining region of gene.
Further, the above-mentioned clustering method based on peripheral blood plasma DNA nucleosome footprint difference, it is described
Full-length genome within the scope of nucleosome footprint different information for clustering chemicotherapy sensitivity tumor patient and chemicotherapy not
Sensitive tumor patient.
Further, the above-mentioned tumor chemoradiotherapy sensibility based on peripheral blood plasma DNA nucleosome footprint difference
Prediction technique, the tumor chemoradiotherapy sensitivity prediction include lung cancer, intestinal cancer.
Compared with prior art, technical solution provided by the invention has following technological merit:
1, depth point of the technical solution provided by the invention for peripheral blood plasma DNA sequencing data of whole genome
Analysis, nucleosome footprint different information can find within the scope of full-length genome, solve conventional method to organize or cell according to
Rely, be a kind of noninvasive nucleosome footprint difference analysis method, has the characteristics that coverage is high, accuracy is good.
2, technical solution provided by the invention is directed to existing tumour chemotherapy drug susceptibility prediction technique ATP method, CD-DST
Method needs the limitations such as fresh tumor tissue or cell, in vitro culture are easy to pollute, complicated for operation, evaluation is inefficient, by swollen
The clustering and depth engineering of nucleosome footprint difference in tumor peripheral blood in patients plasma DNA high-flux sequence data
It practises, realizes the noninvasive Concurrent Chemoradiotherapy Sensitivity prediction of tumour.Therefore the object of the present invention is to provide one kind to be based on peripheral blood plasma free
The tumor chemoradiotherapy sensitivity prediction method of DNA nucleosome footprint difference.
3, technical solution provided by the invention efficiently solves tumor chemoradiotherapy sensitivity Detection materials complexity, detection range
Narrow, the problem of cannot sampling repeatedly, data source of the present invention are peripheral blood plasma DNA sequencing data of whole genome, can
Realize the noninvasive tumor chemoradiotherapy sensitivity predicting method that highly sensitive, non-mutated sites and specific gene rely on.
To sum up, method combination high throughput sequencing technologies provided by the invention, pass through peripheral blood plasma DNA high pass
The clustering for measuring nucleosome footprint difference in sequencing data realizes tumor chemoradiotherapy sensitivity prediction, not only solves existing
Tumor tissues or tumour cell that ATP method, CD-DST method have rely on, it is complicated for operation, tumour cell is easy to pollute, evaluation efficiency not
The features such as high the clinically not high problem of acceptance, and efficiently solve existing gene point mutation detection method to specific base
The dependence of cause and mutational site detection, the depth and accuracy of General Promotion high-flux sequence data analysis, realizes to swollen
The noninvasive Concurrent Chemoradiotherapy Sensitivity of tumor patient predicts there is that comprehensive, accurate, coverage is high.
Detailed description of the invention
Fig. 1 lung cancer chemotherapy sensitivity group and insensitive group of plasma DNA dendrogram；
Fig. 2 intestinal cancer chemosensitivity group and insensitive group of plasma DNA dendrogram；
Specific embodiment
Beneficial effect of the present invention will be described further with specific embodiment below, but the invention is not limited to these
Embodiment.
Embodiment 1: the insensitive group cluster of chemosensitivity group and chemotherapy of lung cancer is analyzed
Peripheral blood plasma DNA high-flux sequence data based on 5 lung cancer chemotherapy sensitivities Yu 6 insensitive patients,
It is discrepant to find that the patient of chemosensitivity has with insensitive patient for the coverage variance analysis for carrying out the region TSSs and TTSs
178, the region TSSs and TTSs (being shown in Table 2), wherein the coverage in 88 regions difference TSSs raises in sensitive patients group, 90
The coverage in the region a difference TSSs is lowered in sensitive patients.By carrying out unsupervised grade using the gene of differential expression
Clustering, as a result, it has been found that sample can be polymerized to sensitive and insensitive 2 kinds of classifications, and two class people based on 178 differential genes
The mode significant difference of the coverage differential gene of group prompts that lung cancer chemotherapy sensitivity prediction can be used for using this method.
Specific implementation step is as follows:
Step 1: high-flux sequence data acquisition: 5 lung cancer chemotherapy sensitivities and the peripheral blood blood plasma of 6 insensitive patients are swum
From DNA high-flux sequence data source in Ion Torrent ProtonTMSequenator sequencing data generated (being shown in Table 1).
Step 2: nucleosome positioning: by the RefSeq database of UCSC, obtaining all human protein coding genes at present
Transcription initiation site (TSSs) and the region translational termination site (TTSs) upstream and downstream 1Kb genomic locations, and construct standard
Nucleosome localization region database.
Step 3: utilizing Bowtie software by nucleosome footprint localization criteria data in each sample sequencing data and step (2)
Library is compared, and removes PCR repetitive sequence, and removal low quality sequence dna fragment, removal do not compare nucleosome footprint and determine
The sequence dna fragment in position region compares the sequence dna fragment for arriving multiple positions, and counting statistics is compared to the every of above-mentioned zone
The reads number of a sample, and statistical result is standardized using RPKM method；
Step 4: utilizing rank sum test nonparametric technique, calculate tumor chemoradiotherapy sensitive patients and insensitive patient's promoter
The gene of region nucleosome footprint position disparity, the variation multiple between two groups | log2Fold change | >=1 and raw P values≤
0.05.Original p value is corrected followed by Holm-Bonferroni method, the gene for filtering out value≤0.1 q-value turns
The region initiation site (TSSs) and translational termination site (TTSs) is recorded, and is defined as the nucleosome region of difference, finds lung cancer
Sensitive group and insensitive group of lung cancer chemotherapy 178, discrepant nucleosome region (being shown in Table 2) are treated, wherein the nucleosome of 88 difference
The coverage in region raises in sensitive patients group, and the coverage in the nucleosome region of 90 difference is lowered in sensitive patients.
Step 5: discrepant nucleosome area coverage data are standardized using Cluster software, using etc.
Grade clustering procedure carries out clustering to the data after standardization according to the correlation between sample.As a result, it has been found that being based on 178 differences
Sample can be polymerized to chemosensitivity group and insensitive group of two categories of chemotherapy by gene, and between branch coverage differential gene mould
Formula significant difference (see Fig. 1).
1 11 Plasma of The Patients With Lung Cancer sample informations of table and sequencing reads number averagely read long message
2. 178 difference coverage analysis regions TSSs and TTSs of table and corresponding list of genes
Embodiment 2: cluster comparative analysis is carried out with insensitive group with the complete incidence graph group of the new chemoradiation therapy of colorectal cancer
Peripheral blood plasma DNA based on 5 Locally Advanced colorectal cancers new chemoradiation therapy complete incidence graph and 4 insensitive patients
High-flux sequence data (are shown in Table 3), carry out the coverage variance analysis in the region TSSs and TTSs, find the patient of chemicotherapy sensitivity
Has discrepant 597, the region TSSs and TTSs (being shown in Table 4) with insensitive patient, wherein the covering in 368 regions difference TSSs
Degree raises in sensitive patients group, and the coverage in 229 regions difference TSSs is lowered in sensitive patients.By utilizing difference table
The gene reached carries out unsupervised hierarchical clustering analysis, as a result, it has been found that can be polymerized to sample completely based on 597 differential genes
Alleviation and insensitive 2 kinds of classifications, and the mode significant difference of the coverage differential gene of two class crowds prompt to utilize this method energy
It is enough in the prediction new chemoradiation therapy sensibility of Locally Advanced colorectal cancer.
Specific implementation step is as follows:
Step 1: high-flux sequence data acquisition: the peripheral blood blood of 5 colorectal carcinoma chemotherapy sensitivities and 4 insensitive patients
Dissociative DNA high-flux sequence data source is starched in Ion Torrent ProtonTMSequenator sequencing data generated (is shown in Table
3)。
Step 2: nucleosome positioning: by the RefSeq database of UCSC, obtaining all human protein coding genes at present
Transcription initiation site (TSSs) and the region translational termination site (TTSs) upstream and downstream 1Kb genomic locations, and construct standard
Nucleosome localization region database.
Step 3: utilizing Bowtie software by nucleosome footprint localization criteria data in each sample sequencing data and step (2)
Library is compared, and removes PCR repetitive sequence, and removal low quality sequence dna fragment, removal do not compare nucleosome footprint and determine
The sequence dna fragment in position region compares the sequence dna fragment for arriving multiple positions, and counting statistics is compared to the every of above-mentioned zone
The reads number of a sample, and statistical result is standardized using RPKM method；
Step 4: utilizing rank sum test nonparametric technique, calculate tumor chemoradiotherapy sensitive patients and insensitive patient's promoter
The gene of region nucleosome footprint position disparity, the variation multiple between two groups | log2Fold change | >=1 and raw P values≤
0.05.Original p value is corrected followed by Holm-Bonferroni method, the gene for filtering out value≤0.1 q-value turns
The region initiation site (TSSs) and translational termination site (TTSs) is recorded, and is defined as the nucleosome region of difference, finds lung cancer
Sensitive group and insensitive group of lung cancer chemotherapy 597, discrepant nucleosome region (being shown in Table 4) are treated, wherein the core of 368 differences is small
Body region coverage raises in sensitive patients group, and the nucleosome area coverage of 229 differences is lowered in sensitive patients.
Step 5: discrepant nucleosome area coverage data are standardized using Cluster software, using etc.
Grade clustering procedure carries out clustering to the data after standardization according to the correlation between sample.As a result, it has been found that being based on 597 differences
Sample can be polymerized to complete incidence graph and insensitive group of two categories by gene, and between branch coverage differential gene mode it is significant
Difference (see Fig. 2).
39 colorectal cancer patients plasma sample information of table and sequencing reads number averagely read long message
4 597 TSSs and TTSs area differentiation list of genes of table
Claims (6)
1. a kind of clustering method based on peripheral blood plasma DNA nucleosome footprint difference, which is characterized in that this method
Include the following steps:
(1) peripheral blood plasma DNA is subjected to high-flux sequence, obtains the high-flux sequence data of each sample；
(2) according to the annotation information of all human protein coding genes in the RefSeq database of UCSC, each gene is obtained
The genomic locations of transcription initiation site (TSSs) and the region translational termination site (TTSs) upstream and downstream 1Kb, building standard core are small
Body localization region database；
(3) resulting sequencing data and step (2) Plays nucleosome localization region is sequenced in each sample using Bowtie software
Database is compared, and removes the PCR repetitive sequence as caused by library construction and high-flux sequence, removes MAPQ=0's
Low quality sequence dna fragment, removal do not compare the sequence dna fragment of nucleosome footprint localization region or compare to multiple positions
The sequence dna fragment set, counting statistics compares the reads number to each sample of above-mentioned zone, and uses statistical result
RPKM method is standardized；
(4) rank sum test nonparametric technique is utilized, tumor chemoradiotherapy sensitive patients and insensitive patient's promoter region core are calculated
The gene of corpusculum footprint position disparity, the variation multiple between two groups | log2Fold change | >=1 and raw P values≤0.05,
Original p value is corrected followed by Holm-Bonferroni method, filters out the genetic transcription starting of value≤0.1 q-value
They, are defined as the nucleosome region of difference by site (TSSs) and the region translational termination site (TTSs)；
(5) using Cluster software to filter out gene transcription start site (TSSs) of the q-value value less than 0.1 and transcription
Termination site (TTSs) area coverage data are standardized, using hierarchical agglomerate method according to the correlation between sample to standard
Data after change carry out clustering, and are visualized with R language pheatmap packet to data, according to full-length genome model
The footprint difference of Natural promoter and terminator nucleosome is enclosed, sample type cluster is the tumor patient and chemicotherapy of chemicotherapy sensitivity
Insensitive tumor patient.
2. a kind of clustering side based on peripheral blood plasma DNA nucleosome footprint difference according to claim 1
Method, which is characterized in that the method data source is in peripheral blood plasma DNA sequencing data of whole genome, and each sample
The data volume of 6Million reads is at least obtained, data format includes fastq, bam, sam.
3. a kind of clustering side based on peripheral blood plasma DNA nucleosome footprint difference according to claim 1
Method, which is characterized in that the method nucleosome footprint localization region is the transcription initiation site of all human protein coding genes
(TSSs) and the genomic locations in the region translational termination site (TTSs) upstream and downstream 1Kb.
4. a kind of clustering side based on peripheral blood plasma DNA nucleosome footprint difference according to claim 1
Method, which is characterized in that the nucleosome footprint difference refers to each gene within the scope of peripheral blood plasma DNA full-length genome
The difference of transcription initiation site TSSs and the nucleosome in the region translational termination site TTSs distribution and remaining region of gene.
5. a kind of application of the clustering based on peripheral blood plasma DNA nucleosome footprint difference, which is characterized in that Quan Ji
Because group within the scope of nucleosome footprint different information cluster analysis result can be used for tumor patient Concurrent Chemoradiotherapy Sensitivity prediction.
6. a kind of clustering based on peripheral blood plasma DNA nucleosome footprint difference according to claim 5 is answered
With, which is characterized in that the tumor chemoradiotherapy sensitivity prediction includes lung cancer, colorectal cancer.
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| 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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