CN106916881A - Kit and application thereof - Google Patents
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- CN106916881A CN106916881A CN201511016867.7A CN201511016867A CN106916881A CN 106916881 A CN106916881 A CN 106916881A CN 201511016867 A CN201511016867 A CN 201511016867A CN 106916881 A CN106916881 A CN 106916881A
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- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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Abstract
The invention discloses a kind of kit, it includes probe, and probe is fixed on solid-phase matrix or is free in solution, at least a portion region of each gene in 17 genes that alleged probe can be in specific recognition table 1.The present invention also provides purposes, a kind of method of structure target area sequencing library, a kind of sequence measurement, a kind of method of detection target area variation, a kind of device of detection target area variation of kit.Using kit of the invention and/or the method for the present invention or device, it is capable of the related gene sequence of disposable, simple and convenient and high specific acquisition stomach cancer, these related gene sequences can be accurately tested and analyzed, detection and analysis result is aided in medication guide and/or risk profile for stomach cancer.
Description
Technical field
The present invention relates to biomedical sector, specifically, it is related to kit and application thereof, more specifically, the present invention relates to one
Plant kit, the purposes of kit, a kind of method of structure target area sequencing library, a kind of sequence measurement, a kind of detection
The method and apparatus of target area variation.
Background technology
Stomach cancer is one of most common malignant tumour in world wide, be number two in global tumor lethal reason position, 2012
The new patient numbers about 950,000 of global stomach cancer, mortality of gastric carcinoma number about 700,000, incidence of disease highest of the stomach cancer in East Asia.China
It is the country occurred frequently of stomach cancer, according to the data display of National Cancer Center：Stomach cancer in 2011 is in China's Cancer Mortality and extremely
Rate of dying occupies the 3rd [.2011 such as Chen Wanqing, Zheng Rongshou, Zeng Hongmei China's Incidences and the Chinese tumour of Study on mortality
2015；24(1):2.].Due to lacking effective treatment means, stomach cancer wholistic therapy effect is unsatisfactory, 5 years survival rates of patient
In 5%-20% or so, population mean life span is less than 1 year.Stomach cancer is a multifactor coefficient complexity
Process, it is now recognized that helicobacter pylori chronic infection is most important paathogenic factor, the hair of about 90% Xin Fafei orifice of the stomach stomach cancers
Life is associated.The bacterial virulence factors (such as CagA) that helicobacter pylori produces cause inflammation generation and activation oncogenic signals to lead to
Road, in this lasting chronic inflammation environment, excessive oxidative stress causes gastric epithelial cell DNA damage to occur, and induces
Oncogene, tumor suppressor gene, Cell cycle regulatory proteins, cell adhesion molecule, the hereditary change of DNA damage revision points and
Epigenetic changes, and promotes stomach cancer to develop.
Stomach cancer is a kind of heterogeneity tumour very high, there is significant Phenotypic Diversity, including different molecular isoforms.Early in 1965
Year, stomach cancer is divided into visible peristalsis visible intestinal peristalsis and diffuses type by Lauren, and the latter's invasion is strong, patient's poor prognosis.Lei in 2013 etc. is based on 248
The genetic analysis of example stomach cancer sample, proliferous type, metabolic pattern and interstitial type are divided into by stomach cancer.Wherein proliferous type stomach cancer cell is present
The hypomethylation of the genetic instability, TP53 mutation and DNA of height；Metabolic pattern stomach cancer is sensitive to 5-FU, and patient is postoperative
Whether the existence difference for receiving 5-FU auxiliary treatments is obvious；Interstitial type stomach cancer has the characteristic of tumor stem cell, right
PI3K/AKT/mTOR inhibitor is sensitive.According to molecular classification system, stomach cancer is divided into four types：Ebv infection type stomach
Cancer, microsatellite instability sizing stomach cancer, gene stable type stomach cancer and chromosome instability sizing stomach cancer.
Oncotherapy has been enter into molecular targeted agents and individualized treatment epoch.Substantial amounts of research display, patient is to antineoplastic
Whether thing (chemotherapeutics, targeted drug) is sensitive directly related with the genome mutation of its cancer cell.In October, 2012,
First, China can substantially reduce HER2 positive late gastric cancer deaths risk, improve the targeted drug He Sai of Overall survival
Spit of fland (Herceptin) official listing, it is meant that stomach cancer target treats the arrival in epoch.Other several targeting HER2, C-MET
Stomach cancer new drug with the acceptor such as VEGF has been achieved for considerable achievement in research.
Carry out Individualized Treatment for Stomach Cancer, it is necessary first to which the target medicine gene to patients with gastric cancer is detected.With cancer cognitive domain
Development and science and technology progress, genomic sequencing technique progressed into clinical tumor application.Turn in scientific research and clinic
In the prior art, mainly there are PCR-Sanger methods, PCR-Mass in change field for the detection method that somatic cell gene is mutated
Method and ARMS-PCR methods etc..The sample that this several method is applied is tumor tissues sample.PCR-Sanger methods are accurate
Property it is good, new point mutation type and InDel can be detected, but sensitivity is very low, be only capable of detecting that high frequency of the mutation rate more than 20% is dashed forward
Become, and be difficult to many site primers of competent polygenes.PCR-Mass methods can not detect unknown mutation, cannot also detect InDel,
Sensitivity is 5% or so, and the technical limitation is larger.ARMS-PCR methods specificity is good, and sensitivity is high, can detect 1%-5%
Low frequency mutation, but unknown mutation can not be detected, and be equally difficult to be detected while competent polygenes many sites.
The content of the invention
It is contemplated that at least one at least solving the above problems or providing at least one selectable commercial means.
According to an aspect of of the present present invention, the present invention provides a kind of kit, and it includes probe, and the probe is fixed on solid phase base
In matter or it is free in solution, each gene in 17 genes that the probe can be in specific recognition table 1 is at least
A part of region.
Probe in kit of the invention is capable of the gene region combination of specific recognition, be inventor by information,
Repeatedly screening, pointedly design probe and experiment is obtained, and the combination of these gene regions is related to the generation development of knot stomach cancer.
The kit can be used in obtain Associated Genes in Gastric Carcinoma sequence, and/or detect Associated Genes in Gastric Carcinoma sequence in mutation and/
Or in the medication of auxiliary direction stomach cancer, and/or in auxiliary prediction stomach cancer risk.So as to be used to predicting individuality the risk that gets a cancer of the stomach,
Prediction patients with gastric cancer uses the curative effect of corresponding antineoplastic target medicine, and auxiliary direction clinical application aids in the individuality for stomach cancer
Change treatment.
Table 1
Embodiments in accordance with the present invention, the kit of this aspect of the invention can also have following additional technical feature at least
One of：
A preferred embodiment of the invention, the region that the probe can be in specific recognition table 2.Wrap in these regions
It is record data of the inventor with reference to databases such as COSMIC, NCBI containing 17 in table 1 the 332 of gene extrons,
The extron of 17 genes using iterative algorithm to being selected into table 1 is analyzed and determines the target area of each extron
Sequence, the region in enabling target area that documented examples are carried out with maximized covering, i.e. table 2.
Table 2
Embodiments in accordance with the present invention, the length of the probe that kit is included is 25~300nt, preferably 100nt or so.
Simultaneously specific in same reaction system described areas combine, a reality of the invention can be captured to obtain
Apply example, probe is by first obtaining initial probe collection, then to screen the initial probe collection and determine.Obtain the initial spy
Pin collection includes：The reference sequences in the region are determined, since one end of the reference sequences of the gene, in the reference sequence
DNA fragmentation is obtained on row successively up to the other end of the reference sequences, wherein, a DNA fragmentation is an initial spy
Pin, all the DNA fragmentations constitute the initial probe collection, it is completely overlapped between the DNA fragmentation, partly overlap or
Do not overlap completely, the initial probe collection can cover the gene region at least one times.The reference sequences in described region can
Obtained with from reference gene group, such as from people with reference to obtaining corresponding gene region, all of HG19 on genome HG19
On corresponding region constitute the reference sequences in described region, HG19 can be downloaded from ncbi database.
A preferred embodiment of the invention, the initial probe collection is obtained using iterative algorithm design, including：It is determined that
Position of the region in reference gene group, obtains the reference sequences of the gene region, from the first of the reference sequences
Individual nucleotides starts to copy first DNA fragmentation of the reference sequences acquisition, is opened from second nucleotides of the reference sequences
Begin the copy reference sequences acquisition Article 2 DNA fragmentation, is copied since the 3rd nucleotides of the reference sequences described
Reference sequences obtain Article 3 DNA fragmentation, and follow-up DNA fragmentation is so obtained successively until the N articles the one of DNA fragmentation
End exceeds the reference sequences, wherein, a DNA fragmentation is an initial probe, and all the DNA fragmentation constitutes institute
Initial probe collection is stated, N is the sum that the initial probe concentrates the initial probe for including, so that obtain being capable of coverage goal comprehensively
The initial probe collection of gene region.
And to make final probe have high specific, a preferred embodiment of the invention, further to described initial
Probe collection is screened, including：The DNA fragmentation (initial probe collection) is compared with the reference sequences, is obtained each
Comparison number of times of the bar DNA fragmentation on reference sequences, filters out comparison DNA fragmentation of the number of times more than 1.It is final to make
Probe can capture described gene region in same reaction system, and/or make the gene region of capture under same reaction condition
Eluted together, further the initial probe collection is screened, including：G/C content is got rid of not in 35-70%
DNA fragmentation.Finally, the region of the chip of acquisition/probe Landfill covering contains 17 the 332 of gene extrons,
Total size is 79Kb.
According to another aspect of the present invention, there is provided kit in any of the above-described embodiment obtain Associated Genes in Gastric Carcinoma sequence and/
Or detect Associated Genes in Gastric Carcinoma sequence in mutation, and/or the medication of auxiliary direction stomach cancer, and/or auxiliary prediction stomach cancer wind
Purposes in danger.Using the kit in one side face of the present invention or any embodiment, can be disposable, simple and convenient
And the related gene sequence of the acquisition stomach cancer of high specific, testing and analyzing these related gene sequences, detection and analysis result can be with
For or the risk profile and medication guide that aid in for stomach cancer.It is above-mentioned to one aspect of the present invention or in any embodiment
Kit advantage and technical characteristic description, the purposes of the kit of equally applicable this aspect of the present invention, herein no longer
Repeat.
According to another aspect of the invention, there is provided a kind of method of structure target area sequencing library, methods described includes：(a)
The nucleic acid in sample to be tested is obtained, the nucleic acid is made up of multiple nucleic acid fragments, genome of the nucleic acid fragment from fracture
DNA and/or free DNA；B the nucleic acid fragment is repaired in () end, obtain end and repair fragment；(c) plus base A
The two ends of fragment are repaired to the end, cohesive end fragment is obtained；(d) jointing in the cohesive end fragment two
End, obtains joint junction fragment；E () carries out the first amplification to the joint junction fragment, obtain the first amplified production；(f)
First amplified production is captured using kit of the invention described above on the one hand or in any embodiment, obtains institute
State target area；And (g) carries out the second amplification to the target area, the second amplified production, second amplification are obtained
Product constitutes the target area sequencing library；Optionally, the connector end is T- cohesive ends.This side of the invention
The sequencing library construction method in face, is particularly well-suited to the structure of sequencing library of the sample containing trace dna.
According to one embodiment of present invention, sample is the plasma sample containing micro free DNA fragmentation, comprising extremely micro
Target dissociative DNA fragment, the first amplification enables that the amount of nucleic acid meets the demand of chip/probe hybrid capture, and because of chip
Hybrid capture can be lost a certain amount of nucleic acid, and the second amplification can make the target fragment acquisition under capture expand to meet upper machine again
Sequencing and the requirement of Quality Control detection.This library constructing method of the invention be particularly well-suited to total free nucleic acid be not less than 10ng or
The sequencing library that person's conventional organization genomic DNA is not less than the sample of 1 μ g builds, using the method for this aspect of the invention
The target area library of structure, the lower machine quality of data after sequencing is high, based on high-quality lower machine data beneficial to follow-up accurate
Detection and analysis.
According to another aspect of the present invention, there is provided a kind of sequence measurement, methods described includes：According to an aspect of the present invention or
Sequencing library construction method in any embodiment builds target area sequencing library；The target area sequencing library is carried out
Sequencing, obtains sequencing data, and the sequencing data is made up of multiple reads.
Sequencing can be carried out using known platform, the Hiseq2000/2500 platforms of including but not limited to Illumina, Life
The Ion Torrent platforms and single-molecule sequencing platform of Technologies.Sequencing mode can select it is single-ended sequencing, or
Double end sequencings, in one embodiment of the invention using double end sequencings, the sequencing data of gained is by multipair read to group
Into.
The method of this aspect of the present invention, sequencing technologies are captured by the kit and high flux that combine in any of the above-described embodiment,
Including the banking process that foregoing invention people optimizes, chip is captured the process higher efficiency of target area, height can be given full play to
Flux captures the advantages such as sequencing technologies flux is high, sensitivity is high.It is above-mentioned in any one aspect of the present invention or any embodiment
Kit and sequencing library construction method advantage and technical characteristic description, the survey of equally applicable this aspect of the invention
Sequence method, will not be repeated here.
According to an aspect of of the present present invention, the present invention provides a kind of method of detection target area variation, and methods described includes：(1)
Using the sequence measurement in foregoing any embodiment of the present invention, the target area sequencing data of target sample is obtained；(2) it is based on
The sequencing data, detects the target area variation, obtains variant sites information, and the variation includes SNP and InDel
At least one of.
According to one embodiment of present invention, step (2) includes：The sequencing data and reference sequences are carried out into first to compare,
Obtain the first comparison result；First comparison result is carried out into second with a part for the reference sequences to compare, the is obtained
Two comparison results；Based on first comparison result and second comparison result, while detecting the SNP in the target area
And InDel.
It is according to one embodiment of present invention, right before described first compares to make variation testing result more accurate credible
The sequencing data is filtered, and the filtering includes getting rid of read of the uncertain base ratio more than 10% and/or base matter
Value is not more than the read of the ratio not less than 50% of 5 base number.And preferably, before described second compares, go
Remove the two of read centering read identical reads pair in the first comparison result.A part for alleged reference sequences
It is each including each the known InDel site in the reference sequences of target area, and described each known InDel sites upstream and downstream
The reference sequences of 1000bp.Here, the second alleged comparison is Local Alignment, and the first comparison is conventional overall comparison, can profit
With but be not limited to the softwares such as SOAP or BWA and carried out according to its default setting, obtain the first comparison result, first compares knot
Fruit includes matched position and match condition information of the read on reference sequences.
According to one embodiment of present invention, carry out the second comparison i.e. based on the first comparison result, pair with the gene regions for being captured
The all sequences information (reads) near all known INDEL in the corresponding reference sequences in domain carries out part and compares again,
The mistake in the first comparison can be eliminated, the accuracy of follow-up variation detection is improved, the second comparison can utilize GATK anharmonic ratioes pair
Software (https://www.broadinstitute.org/gatk/) carry out.
According to one embodiment of present invention, Ion Proton microarray dataset of the sequencing data from Life Technologies companies,
Detect that SNP and INDEL makes a variation simultaneously using its default parameters by TVC instruments.Using the change of this aspect of the invention
Different detection method, can accurately detect the low frequency mutation that the frequency of mutation is 1%.
The method of the bioinformatic analysis optimized by foregoing invention people, can be accurately detected more low-frequency mutation
(1%).
To sum up, the PCR sequencing PCR of the use high flux capture of foregoing offer, the method is the chip probe for utilizing above-mentioned design, right
Target gene regions interested carry out hybrid capture in sample DNA, and carry out high-flux sequence, and sequencing result is given birth to
Thing bioinformatics analysis, so as to obtain the information of variant sites.The method is not high than sensitivity that preceding method is present, flux
The shortcomings of small, detection content is limited or can only detect known mutations, there is many advantages：First, flux is high, can be with
Dozens or even hundreds of gene is detected simultaneously, testing cost has been greatly reduced while more rich information is obtained；Secondly,
Sensitivity is high, and detection sensitivity can reach 1%-5%, and can be needed to adjust detection threshold value according to research, such as needs more Gao Ling
Sensitivity can increase sequencing depth and is mutated so as to obtain less than 1% ultralow frequency, and operation is flexible；Again, specificity is high, the party
Method ensure that relatively low false positive rate, false negative rate, it is ensured that the testing result for obtaining can accurately reflect that person under inspection's is prominent
Change situation；Finally, more data can be excavated using bioinformatic analysis, known mutations site can not only be provided
Information, can also excavate unknown mutation site, InDel, CNV etc. many-side data, for scientific research provides more useful
Information.Also, compared with current several method, the method for the invention described above one side is avoided that all of known method presence
It is more not enough.The kit probe combination high flux capture sequencing that the invention is provided, will be expected to be carried for clinical Individualized Treatment for Stomach Cancer
For scientific guidance.
In order to be able to give full play to the advantages such as high flux capture sequencing technologies flux is high, sensitivity is high, inventor builds storehouse to sequencing
Flow is optimized, and makes the process efficiency of chip capture target area higher；Meanwhile, inventor also optimizes biological information
The flow of credit analysis such that it is able to be accurately detected more low-frequency mutation, including the frequency of mutation 1% mutation.
The chip capture of the invention described above one side combines high flux and captures sequencing, contributes to stomach cancer individuality medication curative effect and recurrence
The research of risk profile, and be expected to that achievement in research is converted and aided in for clinic.
According to an aspect of of the present present invention, a kind of device of detection target area variation is also provided, be used to realize or perform above-mentioned
Invention one side or any embodiment target area mutation detection method, described device includes：Data capture unit,
Sequence measurement for realizing the invention described above one side, obtains the sequencing data of target area, and the sequencing data is by multiple
Read is constituted；Detection unit, for based on the sequencing data from data capture unit, detecting the target area variation,
Variant sites information is obtained, the variation includes at least one of SNP and InDel.It will be understood by those in the art that this
All or part of unit in the device of invention, it is selectable, removably comprising one or more subelements performing or real
Each embodiment of existing foregoing the inventive method.
For example, according to one embodiment of present invention, as shown in figure 1, the detection unit 200 in device 1000 includes first
Compare subelement 13, second compare subelement 15 and variation identification subelement 17, it is described first comparison subelement 13 be used to by
Sequencing data from data capture unit 100 carries out first and compares with reference sequences, obtains the first comparison result, described the
Two comparison subelements 15 are used to the first comparison result and the one of the reference sequences by subelement 13 is compared from described first
Part carries out the second comparison, obtains the second comparison result, and the variation identification subelement 17 is used to based on from the described first ratio
First comparison result of sub-unit 13 and the second comparison result from the described second comparison subelement 15, while detecting institute
The SNV and InDel in target area are stated, variant sites information is obtained, wherein, a part for the reference sequences includes mesh
Each known InDel site in mark area reference sequence, and each 1000bp of described each known InDel sites upstream and downstream
Reference sequences.
Again for example, according to one embodiment of present invention, as shown in Fig. 2 the detection unit 200 of described device 1000 is also wrapped
The first filtering subelement 12 is included, the first filtering subelement 12 compares subelement 13 and is connected with described first, in institute
State sequencing data and enter 13 yuan of the first comparer list before, the sequencing data is filtered, the filtering includes going
The ratio for removing the base number that read of the uncertain base ratio more than 10% and/or base mass value are not more than 5 is not less than 50%
Read.Optional, as shown in figure 3, the detection unit 200 also includes the second filtering subelement 14, second mistake
Filter unit 14 compares subelement 13 and described second and compares subelement 15 and be connected with described first respectively, for described
Before one comparison result enters the described second comparison subelement 15, get rid of and the first of subelement 13 is compared from described first
The two of read centering read identical reads pair in comparison result.Above-mentioned reference sequences can be HG19, described the
The first comparison carried out in one comparing unit is overall comparison, and the second comparison carried out in the second comparison subelement is local
Compare.
The method of the present invention/device, the target area capture sequencing based on new-generation sequencing technology, can be in a short period of time
Many cases pattern detection is carried out simultaneously, and under the use of target area capture chip, same quantity of data can carry out greater depths
Data mining.So, under identical cost, bigger sample size and acquisition sequencing depth higher can be studied, so that
The information of medication and the prognosis-related gene mutation needed for more likely obtaining.And it is thin in stomach corpus carcinosus compared to current scientific research bound pair
Cytoplasmic process is become with methods, the polygenes of the chip/probe included using the kit in embodiment such as more ARMS-PCR
The advantage of detection is then rather obvious simultaneously.17 the 332 of gene extrons that chip/probe is included, represent at present
The mutant gene locus in stomach cancer medication and generation developmental research having been reported that, this just can obtain multiple in once testing
The information of gene mutation, it is advantageous on flux, it is easier to pre- to stomach cancer than single or a few mutation detection method
Comprehensive, comprehensive research is carried out afterwards.
Brief description of the drawings
Of the invention above-mentioned and/or additional aspect and advantage will become bright from description of the accompanying drawings below to implementation method is combined
Show and be readily appreciated that, wherein：
Fig. 1 is the structural representation of the target area variation detection means in one embodiment of the present of invention；
Fig. 2 is the structural representation of the target area variation detection means in one embodiment of the present of invention；
Fig. 3 is the structural representation of the target area variation detection means in one embodiment of the present of invention；
Fig. 4 is the sequencing peak figure of the Sanger sequence verifications of the variant sites in one embodiment of the present of invention.
Specific embodiment
The present invention is described in detail with reference to the accompanying drawings and detailed description.
The implementation method is shown in the drawings, wherein same or similar label represents same or similar element from start to finish
Or the element with same or like function.Embodiment below with reference to Description of Drawings is exemplary, is only used for explaining
The present invention, and be not considered as limiting the invention.
" variation ", " variance " in the present invention, " genetic mutation " are generally applicable, the present invention in " SNP " (SNV),
" insertion and deletion " (indel) and " structure variation " (SV) with generally definition, but in the present invention to the size of various variations not
It is particularly limited, what is so had between this several variation has intersection.The size of these class form variations is intersected and without prejudice to this area
Personnel realize the method for the present invention and/or device and reach described result by foregoing description execution.
" reference sequences " in the present invention are known group sequence or at least a portion of known group sequence.At this
Wen Zhong, the term for being used " first ", " second " etc. are only used for describing purpose, and it is not intended that indicating or implying relative
Importance, the implicit quantity for indicating indicated technical characteristic or with ordinal relation.Thus, " first ", " are defined
Two " one or more this feature can be expressed or be implicitly included to feature.In the description of the invention, unless otherwise
Illustrate, " multiple " is meant that two or more.
Herein, unless otherwise clearly defined and limited, the term such as term " being linked in sequence ", " connected ", " connection "
Should be interpreted broadly, for example, it may be being fixedly connected, or being detachably connected, or be integrally connected；It can be machine
Tool is connected, or electrically connected；Can be joined directly together, it is also possible to be indirectly connected to by intermediary, can be two
The connection of element internal.For the ordinary skill in the art, can as the case may be understand above-mentioned term at this
Concrete meaning in invention.
The different specific embodiment of following disclosure or embodiment are used for realizing distinct methods step of the invention or device knot
Structure.In order to simplify disclosure of the invention, hereinafter to specific examples the step of and setting be described.Certainly, they are only
It is example, and purpose does not lie in the limitation present invention.Additionally, the present invention can in different examples repeat reference numerals and/or
Reference letter, this repetition is for purposes of simplicity and clarity, discussed various implementation methods itself not to be indicated and/or is set
Relation between putting.
The method of the present invention, device and/or system are described in detail below in conjunction with the drawings and specific embodiments.Show below
Example, is only used for explaining the present invention, and is not considered as limiting the invention.Except as otherwise explaining, it is related in following examples
The reagent do not explained especially, sequence (joint, label and primer), software and instrument, be all conventional commercial product or open
Source, such as purchased from Life Technologies etc..
Embodiment one
The kit of one aspect of the present invention is obtained, realizing the method and/or device of one aspect of the present invention, target area is generally comprised
The design of capture probe/chip, trace sample build storehouse and the upper machine sequencing of hybridization, the analysis of biological information and variance of lower machine data
According to deciphering.
(1) determination of the selected gene of chip, sequences Design and production.
First, mutation rate in stomach cancer classification in COSMIC databases is investigated in the gene of first 20, filter out with
The important oncogene found in stomach cancer medication related gene, stomach cancer and tumor suppressor gene, and add the medium-high frequency mutation of stomach cancer
Gene, obtain the final list of genes of chip, 17 altogether, as shown in table 1.
The program that the target area of chip is independently write by Hua Da and optimized is calculated to be come.The algorithm combine COSMIC,
The record data of the databases such as NCBI, are analyzed and are caught using iterative algorithm to the extron for being selected in 17 genes
Obtain the sequence of target area.17 the 332 of gene extrons of chip final goal region overlay, total size is 79Kb.
Detailed target area is as shown in table 2.
The initial probe collection is obtained using iterative algorithm design, including：Determine position of the region in reference gene group,
The reference sequences of the gene region are obtained, copying the reference sequences since first nucleotides of the reference sequences obtains
First DNA fragmentation is taken, the reference sequences is copied since second nucleotides of the reference sequences and is obtained Article 2
DNA fragmentation, the reference sequences is copied since the 3rd nucleotides of the reference sequences and obtains Article 3 DNA fragmentation,
Follow-up DNA fragmentation is so obtained successively up to the N articles one end of DNA fragmentation is beyond the reference sequences, wherein, one
DNA fragmentation is an initial probe, and all the DNA fragmentation constitutes the initial probe collection, and N is the initial probe
The sum of initial probe that concentration is included, the initial probe collection of coverage goal gene region comprehensively is capable of to obtain, and to make
Final probe tool high specific, further to the screening initial probe collection, including：The DNA fragmentation is (initial to visit
Pin collection) compared with the reference sequences, comparison number of times of each DNA fragmentation on reference sequences is obtained, filter out comparison
DNA fragmentation of the number of times more than 1.Further, to enable final probe that described gene is captured in same reaction system
Region, and/or the gene region of capture is eluted together under same reaction condition, further to the initial probe
Collection is screened, including：G/C content is got rid of not in the DNA fragmentation of 35-70%.Finally, the chip/probe of acquisition is most
The region of covering contains 17 the 332 of gene extrons eventually, and total size is 79Kb.
The preparation of the chip probe for determining is by the autonomous chip production department liable of Hua Da gene.
(2) preparation of sequencing library
2.1 pairs of sample extraction DNA fragmentations, and detectable concentration；
The DNA fragmentation of 2.2 pairs of extractions carries out fragmentation treatment；
2.3 pairs of DNA fragmentations carry out end reparation；
2.4 connection Adapter libraries joints：Library joint (Adapter) refers to one section of base sequence by designing,
DNA library is combined when expanding with primer, carries out DNA cloning, and when upper machine is sequenced and Standard Anchor
It is combined, auxiliary DNA sequencing is combined with tagmeme point to be measured beneficial to probe is carried out；
2.5 libraries carry out the amplification of first round PCR；
2.6 purifying, quality control, and carry out stomach cancer chip hybridization capture purpose region；
Library after 2.7 hybridization carries out the second wheel PCR amplifications；
2.8 libraries quantify and quality control；
Machine sequencing on the Ion proton sequenators of 2.9 Life companies.
(3) lower machine Data Bio information analysis is sequenced
Need to carry out following analysis of biological information after obtaining lower machine data, and obtain final mutational site annotation result：
3.1 removal low quality reads；
3.2 with reference sequence alignments, produce bam files；
3.3 mark repetitive sequences；
The bad sequence of 3.4 comparison results is compared again, and correction mass value；
3.5 removal mismatch；
In 3.4 and 3.5, to make variation testing result more accurate credible, before comparison, the sequencing data is filtered,
The filtering includes getting rid of read of the uncertain base ratio more than 10% and/or base mass value be not more than 5 base number
Read of the ratio not less than 50%.Also, before (second compares) is compared again, knot is once compared before getting rid of
The two of read centering read identical reads pair in fruit.The second described comparison is Local Alignment, and the first comparison is
Conventional overall comparison, using but be not limited to the softwares such as SOAP or BWA and carried out according to its default setting, obtain first and compare
To result, the first comparison result includes matched position and match condition information of the read on reference sequences, carries out the second comparison
The first comparison result is based on, near all known INDEL in pair reference sequences corresponding with the gene region for being captured
All sequences information (reads) carry out it is local compare again, the mistake in the first comparison can be eliminated, improve follow-up variation
The accuracy of detection, second compare can using GATK anharmonic ratioes to software (https://www.broadinstitute.org/gatk/)
Carry out.
The lower machine data QC of 3.6 analyses；
3.7 find variation；
3.8 pairs of variation results are annotated, and obtain final data result.
(4) targeted drug database sharing and tumour variation is understood
Targeted drug has the characteristics of drug effect is notable, toxic and side effect is small in oncotherapy, but its to target spot (including albumen,
Gene etc.) there is specific dependence, it is necessary to target spot analysis is first done to patient, just can determine that patient if appropriate for medication.Integrate mesh
Preceding FDA ratify for treat stomach cancer targeted drug, the targeted drug for other treatments of cancer and in clinical II,
III phase medicines, according to NCCN clinical therapeutic guidelines, newest clinical medicine gene studies arranges drug target gene and target
To curative effect of medication relation, tumour individuation targeted drug unscrambling data storehouse is formed.And targeted drug database integration is entered into tumour
Individuation analysis of biological information flow, the database sharing and automation for completing targeted drug is understood.
Individuation deciphering is carried out to the variation data after analysis of biological information, with reference to the tumour database and pertinent literature that build,
Variation to patient's detection is analyzed, judgement the benefit targeted drug and drug resistance targeted drug that are best suitable for, and auxiliary allows clinic
Doctor is more targeted for the medication treatment of tumor patient, removes quality time and toxic and side effect that invalid medication is delayed from
To the treatment pain that patient takes.
Field is instructed in tumour personalized medicine, during target area capture high throughput sequencing technologies are current genomics research
One hot spot technology.Sequencing is captured by carrying out high flux to the lesion tissue cut off in person under inspection's therapeutic process, can be had following
Clinical practice：
(1) stomach cancer target treatment key gene variation situation analysis；
(2) the postoperative targeted therapy guiding opinion of patients with gastric cancer.
Compared to foregoing other technologies means, above-mentioned application has following advantage：
1st, high flux.Target area capture sequencing based on new-generation sequencing technology, can be carried out simultaneously in a short period of time
Many cases pattern detection, and under the use of target area capture chip, the data that same quantity of data can carry out greater depths are dug
Pick.
2nd, high sensitivity：Sequencing is captured by the target area of high depth, can detect that the low frequency that the frequency of mutation is 1% becomes
Different, the somatic variation individual for patients with gastric cancer can be detected exactly.
3rd, high specific：The application ensure that relatively low false positive rate, false negative rate, it is ensured that the testing result for obtaining can
Accurately reflect the catastrophe of person under inspection.
4th, using wide：For the patients with gastric cancer of each underwent operative removal of lesions tissue, this technology can be used.Sample collection
Process additionally will not cause burden to person under inspection.
Embodiment 2
1st, samples selection and DNA are extracted.
The 1 formalin fix paraffin with known mutations TP53 genes I195F mutation is selected in an embodiment of the present invention
The stomach organization sample of (FFPE) is embedded, specific sample information is shown in Table 3.
Table 3
| Sample number | Organization type | Source | Mutational site | Access approaches |
| SC1 | FFPE | Low differentiation patients with gastric adenocarcinoma | TP53-I195F | Clinical sample |
The TP53 genes I195F mutation of SC1 samples institute band are shown in Fig. 4 by Sanger sequence verifications, sequencing peak figure.
Using DneasyBlood＆Tissue Kit genomes extracts kits (Qiagen, article No.：69504) base therein is extracted
Because of a group DNA.Using the sepectrophotofluorometers of Qubit 2.0 (Life technologies, article No.：Q32866) Detection and Extraction
The DNA concentration for being obtained.
2nd, genomic DNA fragment
Sample is interrupted can be controlled in 100~500bp scopes sample dna fragment using the Covaris system of AB companies.
After sample interrupts end, taking a small amount of (about the 1/30 of total amount) and interrupting rear sample carries out 1*TAE on 2% Ago-Gel
Electrophoresis detection, and keep glue figure.The general library fragments size with required preparation of effect is interrupted in interrupted DNA Smea
Master tape position it is ideal.For example, if it is desired to prepare insertion 100bp Paired End libraries, then interrupt rear DNA
Smear master tapes at 100bp, if interrupt effect it is undesirable if need to be interrupted again.Sample fragment step
Other can be used to interrupt system, design parameter can be adjusted according to the requirement of instrument.Covaris system interrupt concrete operations
For：
1) daily using the preceding water that must be changed in Covaris S2 instrument lucite tanks, the water surface must reach " WATER LINE "
Boundary line.The water for using must be the water or ultra-pure water of Milli-Q, and daily instrument after finishing using needing in time to fall the water in tank
Fall, every month must clear up lucite tank at least one times with ultra-pure water.
2) the special notebook computers of Covaris are opened, checks whether it is connected with each instrument terminal.Open Covaris S2 instrument
Device and refrigeration instrument switch and check refrigeration instrument temperature setting whether be 4 DEG C.
3) double-click and open Covaris main programs " SonoLAB S-Series V2.54 " clicks " Start [Enter] " afterwards, treat that instrument is arranged
Gas 30min, and water temperature be reduced to 10 DEG C or so rears can be used.Must first determine to smash instrument before opening main program and cool down instrument
Whether power switch is opened, and otherwise main program can point out mistake and retry.
4) during sample to add the covarismicroTube of 100 stand-by μ l, the μ g of sample introduction 5, finally by final volume
Mended to 100 μ l with TE, sample solution is blown and beaten with pipettor is mixed.Click on " Configure ", according to the form below arrange parameter：
Selection mode is " Frequency Sweeping ".It is all be provided with after click on " Save " or " Save As... " keep journey
Sequence, then click on " Return to Main Panel " and return to main interface.Pipe will be interrupted to be put into Covaris devices, program will be chosen,
Start to smash.Just smashing for next sample can be carried out after the completion of being smashed by set program, if must be beaten without other samples
It is broken can close smash instrument and refrigeration instrument power supply be then shut off smashing main program and computer.
5) sample after interrupting is suctioned out from glass tube, is put into 1.5mlEP pipes.The sample for taking out 3 μ l is used for 2% fine jade
Sepharose carries out 1*TAE electrophoresis detections, and with 1.8 times of AgencourtAmpure XP of Beckman Coulter companies
Magnetic bead (A63881) is reclaimed, and product is dissolved in the Elution Buffer (EB) of 32 μ l.
3rd, end is repaired
10x Polynucleotide Kinase buffer and 10mM dNTPs are taken out from -20 DEG C of kits of preservation in advance
Mix, is placed on and melt on ice and fully mix 10x Polynucleotide Kinase buffer.In the centrifuge tube of 1.5ml
It is middle to prepare last 100 μ l ends reparation reaction system：The fragmentation recovery product of 30 μ l, 12 μ l ultra-pure waters, 5 μ l 10x
Polynucleotide Kinase Buffer (B904), 0.4 μ ldNTP Solution Set (oneself dilution be mixed into 25mM each),
1.2 μ l T4 DNA Polymerase, 0.2 μ lKlenow Fragment and 1.2 μ l T4Polynucleotide Kinase.20℃
After warm bath 30min, with DNA, product DNA in 1.8 times of AgencourtAmpure XP magnetic bead recovery purifying reaction systems
It is dissolved in the EB of 33.5 μ l.
4th, Primer Adapter connections
1) joint coupled reaction system, gentle centrifugation after fully mixing are prepared according to following system in product centrifuge tube；
| Reagent | Volume (μ l) |
| DNA | 31.5 |
| 2×Ligation buffer | 37.5 |
| P1_Adapters (10uM, from synthesis) | 1.5 |
| A_Adapters (10uM, from synthesis) | 1.5 |
| DNA Ligase | 3 |
| Total volume | 75 |
2) centrifuge tube is placed on 20 DEG C of incubation 30min in Thermomixer；
3) with 1.5 × volume AgencourtAMPURE Beads purification reaction products, finally with 52 μ l Elution Buffer back dissolvings
Product；
4) with 1.5 × volume AgencourtAMPURE Beads purify for the first time purifying back dissolving product, finally with 33 μ l Elution
Buffer back dissolving products；
5) production concentration after being connected with Qubit2.0 detection tabs.
5th, PCR amplifications before hybridizing
Pre-PCR hybridization system is as follows：
| Reagent | Volume (μ l) |
| DNA | 15 |
| Nuclease-free water | 31 |
| 2×Phusion HF PCR Master Mix | 50 |
| P1 Primer (10 μM synthesize certainly) | 2 |
| A Primer (10 μM synthesize certainly) | 2 |
| Total volume | 100 |
Reagent is transferred to completely in a new PCR pipe, enters performing PCR according to following program and react：
0.9 times of AgencourtAMPure XP magnetic bead is first added after reaction carries out large fragment selection, then shifts supernatant and adds 0.15
Times AgencourtAMPure XP magnetic beads are purified, and with 33 μ lNucleas-free water back dissolvings, Qubit2.0 are used after taking supernatant
Quality Control simultaneously carries out chip hybridization.
6th, target area capture chip hybridization
1) hybridization volume is calculated：By different PCR primer mixed in equal amounts (pooling), common 750ng after being quantified with Qubit.
2) take 750ng pooling products to be transferred in a new centrifuge tube, using vacuum concentration 60 DEG C of about 40min of instrument by product
It is evaporated.
3) required reagent is placed in thawed on ice, gentle centrifugation after fully mixing；
4) it is formulated for being enriched with the sample library system of purpose fragment according to following table in centrifuge tube；
| Reagent | Volume (μ l) |
| Pre-PCR library | 750ng |
| Nuclease-free Water | Moisturizing is to 2.8 μ l |
| BGI Block#1 | 2.5 |
| BGI Block#2 | 2.5 |
| Ion Xpress_P1 block(500μM) | 0.6 |
| Ion Xpress_A_X block(500μM) | 0.6 |
| Total volume | 9 |
5) reaction system is all transferred in a new PCR pipe, prehybridization is carried out according to following reaction condition；
| Temperature | Time |
| 95℃ | 5min |
| 65℃ | Holding |
6) according to following table preparing hybrid buffer solution reaction system in a new 1.5ml centrifuge tube；
| Reagent | Volume (μ l) |
| Hybridization Buffer 1 | 25 |
| Hybridization Buffer 2 | 1 |
| Hybridization Buffer 3 | 10 |
| Hybridization Buffer 4 | 14 |
| Total volume | 50 |
7) according to example reaction number, it is added separately in PCR pipe by the amount of 13 μ l of each reaction, covers lid, then will
It is put into 65 DEG C of incubation at least 5min in PCR instrument, does not have crystal settling to use in confirmation system；
8) Oligo Library Mix are prepared according to following table in a 96 new hole PCR pipes；
| Reagent | Volume (μ l) |
| Nuclease-free water | 1.5 |
| RNase Block | 0.5 |
| Oligo Capture Library | 5 |
| Total volume | 7 |
Points for attention：This operation is carried out on ice.
9) reaction system is put into 65 DEG C of incubation 2min in PCR instrument；
10) keep each reaction system in 65 DEG C, the lid of sample library pipe and hybridization Buffer pipes is opened, rapidly the miscellaneous of 13 μ l
Buffer is handed over to be transferred in the pipe of sample library；
11) keep each reaction system in 65 DEG C, the Oligo Library Mix lids on 96 orifice plates are opened, rapidly by sample library
All reaction systems in pipe are transferred completely into Oligo Library Mix pipes, are blown and beaten with pipettor and mixed；
12) keep PCR plate in 65 DEG C, hybridize 24h.
7th, chip wash-out and the second wheel PCR amplifications
1) each hybridization reaction takes 50 μ l DynabeadsM-280 Streptavidin Beads in a new 1.5ml centrifuge tubes；
2) by 200 μ l Binding buffer addition magnetic beads, the resuspended magnetic beads of 5s are acutely vibrated with whirlpool mixed instrument；
3) centrifuge tube is placed in 2min on magnetic frame, treats that liquid is clarified completely；It is careful to draw and supernatant discarded；
4) repeat step 2) to step 3) 2 times；
5) (resuspended magnetic bead and hybridization system rotate on vertical blending instrument together to add the 200 resuspended magnetic beads of μ l Binding buffer
Mix)；
6) directly whole hybrid mixed liquid are transferred in ready magnetic bead from PCR instrument, turn upside down centrifuge tube 3 to 5
It is secondary until mix；
7) centrifuge tube that will be equipped with hybrid mixed liquid and magnetic bead rotates mixing on vertical blending instrument, and 30min is mixed at room temperature；
8) sample is removed from evenly mixing device, brief centrifugation 5s ensures do not have liquid residue in lid；
9) transfer of 1.5ml centrifuge tubes is placed on magnetic frame, stands 3-5min and treat that liquid is clarified completely, it is careful to draw simultaneously
Supernatant discarded；
10) with the 500 μ l Wash resuspended magnetic beads of Buffer#1, and sample is mixed in 5s is vibrated on whirlpool mixed instrument, at room temperature
Samples of incubation 15min；
11) by centrifuge tube brief centrifugation 3s, it is then placed within magnetic frame, stands 3-5min and treat that liquid is clarified completely, carefully
Draw and supernatant discarded；
12) with the 500 μ l Wash resuspended magnetic beads of Buffer#2, and in 5s is vibrated on whirlpool mixed instrument to mix sample, by it
It is placed in 65 DEG C of incubation 10min in Thermomixer；
13) centrifuge tube is overturned to mix sample, then brief centrifugation 3s is placed it on magnetic frame, stand 3-5min and treat
Liquid is clarified completely, careful to draw and supernatant discarded；
14) repeat step 12) to step 13) 2 times；
15) with the 28 μ l Nuclease-free resuspended magnetic beads of water.
16) reaction system, gentle centrifugation after fully mixing are prepared according to following table in centrifuge tube：
| Reagent | Volume (μ l) |
| DNA | 30 |
| Nuclease-free water | 16 |
| 2×Phusion HF PCR Master Mix | 50 |
| P1 Primer (10 μM synthesize certainly) | 2 |
| A Primer (10 μM synthesize certainly) | 2 |
| Total volume | 100 |
17) reagent is transferred to completely in a new PCR pipe, enters performing PCR according to following program and react：
1.5 times of AgencourtAMPureXPreagent are added after reaction, after magnetic beads for purifying, 52 μ l Nuclease-free is used
Water back dissolvings, add 1.5 times of AgencourtAMPureXPreagent magnetic beads for purifying, finally with 33 μ l Nuclease-free again
Upper machine sequencing after water back dissolvings, Qubit 2.0 and the Quality Control of Agilent 2100.
8th, sequencing and interpretation of result.
High flux is carried out to the library for building with the proton sequenators (Life technologies) of Ion torrent companies
Sequencing.Sequencing experimental implementation is operated according to the operational manual that manufacturer provides.
After obtaining the data of lower machine, the sequencing result to obtaining carries out data filtering and quality control, then according to following scheme
Carry out bioinformatic analysis：
1)tmap：With reference sequence alignments, bam files are produced；
2)BamDuplicates：Repetition reads to being generated during PCR is marked；
3)QC：Count the capture rate of chip, effective reads numbers, mean depth, repetitive rate, coverage and uncovered
The information such as interval；
4)Call SNP/InDel：
Detect that SNP/InDel makes a variation with TVC instruments default parameters；
5) annotate
The function of annotation variation, reads support variation in number, variation frequency, amino acid variation and Cosmic etc.；
The lower machine data result that this example is obtained is as shown in table 4.
The lower machine data result of the example of table 4 sequencing
| Sample | Sequencing data amount (bp) | ≥Q20 | Reads quantity | Average length |
| SC1 | 465,768,497 | 391,700,861 | 3,102,543 | 132bp |
Quality of data result is as shown in table 5.
The example sequencing result Data Quality Analysis of table 5
| Sample | SC1 |
| Total valid data amount (Mb) | 69.25 |
| Target area capture rate | 26.00% |
| Target area is averagely sequenced depth | 166.55 |
| Target area coverage | 99.70% |
| Repetitive rate | 81.61% |
Meanwhile, whether the known mutation that inventor demonstrates entrained by sample in sequencing result can be detected, as a result
As shown in table 6.
The testing result of the known mutations of table 6
| Sample | Positive mutants site | Whether detection is mutated | Sequencing depth | The frequency of mutation |
| SC1 | TP53-I195F | It is | 164 | 41% |
Data results according to more than, inventor obtains drawing a conclusion：
1. according to the data of table 4, this time the index such as sequencing data amount, Q20 data volumes, reads average lengths of sequencing is just
In normal scope, this sequencing result data reliability is illustrated；
2. according to the data of table 5,26% or so, target area is averagely sequenced depth in 166X to target area capture rate
Left and right, numerical value illustrates that the capture result of the chip is normal in normal range (NR).Meanwhile, the chip is for target area
Coverage is 99.7%, can preferably cover the target area of chip design；
3. according to the result of table 6, the known mutations that this time the FFPE samples of test are included successfully are detected, and illustrate the core
Piece can correctly detect the gene mutation included in sample.
In sum, chip involved in the present invention realizes the capture to sample DNA target area and sample in instances
The detection of included gene mutation.Among research present invention could apply to stomach cancer individuality medication guide.
In the description of this specification, reference term " one embodiment ", " some embodiments ", " example ", " specific example ",
Or the description of " some examples " etc. means that the specific features, material or the feature that are described with reference to the embodiment or example are contained in this
In at least one embodiment or example of invention.In this manual, the schematic representation to above-mentioned term is not necessarily referring to
Identical embodiment or example.And, the specific features of description, structure, material or feature can at any one or
Combined in an appropriate manner in multiple embodiments or example.
Claims (10)
1. a kind of kit, it includes probe, and the probe is fixed on solid-phase matrix or is free in solution, the spy
Pin can be in specific recognition table 1 17 genes in each gene at least a portion region；
Optionally, the region that the probe can be in specific recognition table 2；
Optionally, the length of the probe is 25-300nt.
2. the kit of claim 1, it is characterised in that being included for the probe, obtains initial probe collection and sieve
Select the initial probe collection.
3. the kit of claim 2, it is characterised in that the acquisition initial probe collection includes：
Determine the reference sequences in the region,
Since one end of the reference sequences in the region, DNA fragmentation is obtained successively on the reference sequences until the ginseng
The other end of sequence is examined, wherein,
One DNA fragmentation is an initial probe, and all the DNA fragmentation constitutes the initial probe collection, the DNA
It is completely overlapped between fragment, partly overlap or do not overlap completely, the initial probe collection can cover the region at least one times.
4. the kit of claim 2, it is characterised in that the acquisition initial probe collection includes：
Determine position of the region in reference gene group, to determine the reference sequences in the region,
The reference sequences are copied since first nucleotides of described reference sequences one end and obtain first DNA fragmentation,
The reference sequences are copied since second nucleotides of described reference sequences one end and obtain Article 2 DNA fragmentation,
The reference sequences are copied since the 3rd nucleotides of described reference sequences one end and obtain Article 3 DNA fragmentation,
DNA fragmentation is so obtained successively up to the N articles one end of DNA fragmentation is beyond the other end of the reference sequences, its
In,
One DNA fragmentation is an initial probe, and all the DNA fragmentation constitutes the initial probe collection, and N is described
Initial probe concentrates the sum of the initial probe for including.
5. the kit of claim 3 or 4, it is characterised in that the screening initial probe collection includes：
The DNA fragmentation is compared with the reference sequences, the comparison on reference sequences time of each DNA fragmentation is obtained
Number, filters out comparison DNA fragmentation of the number of times more than 1.
6. the kit of claim 5, it is characterised in that the screening initial probe also includes, gets rid of G/C content not
In the DNA fragmentation of 35-70%.
7. any kits of claim 1-6 are obtaining Associated Genes in Gastric Carcinoma sequence, and/or are detecting Associated Genes in Gastric Carcinoma sequence
In mutation, and/or the medication of auxiliary direction stomach cancer, and/or auxiliary prediction stomach cancer risk in purposes.
8. the method for a kind of structure target area sequencing library, it is characterised in that including：
A () obtains the nucleic acid in sample to be tested, the nucleic acid is made up of multiple nucleic acid fragments, and the nucleic acid fragment is from fracture
Genomic DNA and/or free DNA；
B the nucleic acid fragment is repaired in () end, obtain end and repair fragment；
C () plus base A repair the two ends of fragment to the end, obtain cohesive end fragment；
D () jointing obtains joint junction fragment in the two ends of the cohesive end fragment；
E () carries out the first amplification to the joint junction fragment, obtain the first amplified production；
F () is captured using any kits of claim 1-6 to first amplified production, obtain the target area；
And,
G () carries out the second amplification to the target area, obtain the second amplified production, and second amplified production constitutes described
Target area sequencing library；
Optionally, the connector end is T- cohesive ends.
9. a kind of sequence measurement, it is characterised in that including：
Method according to claim 8 builds target area sequencing library；
The target area sequencing library is sequenced, sequencing data is obtained, the sequencing data is made up of multiple reads；
Optionally, the sequencing is double end sequencings, and the sequencing data is by multipair read to constituting.
10. a kind of method that detection target area makes a variation, it is characterised in that including,
(1) using the method for claim 9, sequencing data is obtained；
(2) based on the sequencing data, the target area variation is detected, obtains variant sites information, the variation includes
At least one of SNP and InDel, including,
The sequencing data and reference sequences are carried out into first to compare, the first comparison result is obtained,
At least a portion of first comparison result is carried out into second with a part for the reference sequences to compare, the is obtained
Two comparison results,
Based on first comparison result and second comparison result, while the target area variation is detected, wherein,
A part for the reference sequences includes each the known InDel sites, Yi Jisuo in the reference sequences of target area
State the reference sequences of each 1000bp of each known InDel sites upstream and downstream；
Optionally, before described first compares, the sequencing data is filtered, the filtering includes getting rid of
The ratio that uncertain read of the base ratio more than 10% and/or base mass value are not more than 5 base number is not less than 50%
Read；
Optionally, before described second compares, the two of read centering readings in the first comparison result are got rid of
Section identical read pair；
Optionally, the reference sequences are HG19；
Optionally, first comparison is overall comparison, and described second compares as Local Alignment.
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| CN105925663A (en) * | 2016-03-30 | 2016-09-07 | 广州精科生物技术有限公司 | Kit and application thereof, and method and system for detecting area target variation |
| CN112680794A (en) * | 2020-12-28 | 2021-04-20 | 深圳海普洛斯医学检验实验室 | Ultramicro nucleic acid sample library building method applied to NGS platform |
| CN114438206A (en) * | 2021-12-29 | 2022-05-06 | 苏州方科生物科技有限公司 | Gastric cancer molecular typing DNA probe pool, preparation method, kit and use method |
| CN114438206B (en) * | 2021-12-29 | 2023-09-22 | 苏州方科生物科技有限公司 | Stomach cancer molecular parting DNA probe pool, preparation method, kit and use method |
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