CN105779432A - Kit and applications thereof - Google Patents
Kit and applications thereof Download PDFInfo
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- CN105779432A CN105779432A CN201410775749.3A CN201410775749A CN105779432A CN 105779432 A CN105779432 A CN 105779432A CN 201410775749 A CN201410775749 A CN 201410775749A CN 105779432 A CN105779432 A CN 105779432A
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Abstract
The invention provides a kit. The kit comprises a probe, wherein the probe is fixed to a solid-phase substrate or floats in a solution, and can specifically recognize a gene area of at least ten genes among 60 genes in the table 1. The invention further provides applications of the kit, a method for constructing a target area sequencing library, a sequencing method, a method for detecting the target area variation, a device for detecting the target area variation, as well as a method and a device for carrying out early screening on the colorectal cancer. With the adoption of the kit and/or the methods and the devices provided by the invention, the related gene sequences of the colorectal cancer can be easily and conveniently obtained in a high-specific manner at one time, and accurately detected and analyzed, and a detection and analysis result can be used for assisting the early screening judgment or monitoring on the colorectal cancer.
Description
Technical field
The present invention relates to biomedical sector, concrete, relate to test kit and application thereof, more specifically, the present invention relates to a kind of test kit, test kit purposes, a kind of build the method for target area sequencing library, a kind of sequence measurement, a kind of detect target area variation method and apparatus and a kind of method and apparatus that colorectal cancer is carried out early screening.
Background technology
Tumor is one of disease of serious threat human health, and since 20 century 70s, China's pathogenesis of cancer and mortality rate are always in rising trend, and between 20 years of the nineties, cancer mortality rises 29.42%, and ageadjusted mortality rate rises 11.56%.Pathogenesis of cancer number in 2000 is about 180-200 ten thousand, dead 140-150 ten thousand.35 years old to the 39 years old age bracket in the Cancer Mortality whole nation is 87.07/10 ten thousand, and within 40 years old to 44 years old, age bracket is almost doubled, and reaches 154.53/10 ten thousand；Crowd's morbidity in more than 50 years old accounts for more than the 80% of all morbidities, and more than 60 years old cancer morbidity, more than 1%, peaks for 80 years old.Whole nation tumor mortality rate is 180.54/10 ten thousand, every year because cancer mortality case reaches 2,700,000 examples.China resident is 13% [He Jie because of the probability of cancer mortality, Chen Wanqing. (2012) .2012 China tumor registration annual report. military medicine Science Press: 18-28.McBride, D.J.andA.K.Orpana, etal. (2010). " Useofcancer-specificgenomicrearrangementstoquantifydisea seburdeninplasmafrompatientswithsolidtumors. " GenesChromosomesCancer49 (11): 1062-1069.].Cancer not only has a strong impact on the health of working people, and becomes the key factor that medical expense goes up.China expends the substantial contribution medical expense for cancer patient every year, brings huge financial burden.
Colorectal cancer is modal malignant tumor of digestive tract, and M & M accounts for the 3rd and the 4th of China's malignant tumor respectively.According to WHO latest data, the sickness rate of China's colorectal cancer is 14.2/10 ten thousand people, mortality rate 6.9/10 ten thousand people.Colorectal cancer case 220,000 example, dead 10.9 ten thousand examples are newly sent out by China in 2008.Colorectal cancer is as a class malignant tumor occurred frequently, and one progressive process slowly during the generation of cancer, if it is accomplished early discovery, clinical effectively treatment, control to prognosis recurrence monitoring comprehensively, its incidence rate and mortality rate can be effectively reduced, to there be huge economic benefit and social benefit [JemalA, SiegelR, WardE, etal.Cancerstatistics, 2009.CACancerJClin.2009；59:225-229.].
One progressive process slowly during the generation of cancer, if it is accomplished early discovery, clinical effectively treatment, controls to relapse monitoring after operation comprehensively, can effectively reduce its incidence rate and mortality rate, will have huge economic benefit and social benefit.
Circulating DNA is present in the extracellular dissociative DNA in the body fluid such as blood, synovial fluid, and research finds that many tumor patient Circulating DNAs have very big-difference compared with normal person, due to apoptosis of tumor cells, containing certain tumor markers in cancer patient's Circulating DNA.The gene test diagnosis circulating dissociative DNA in recent years in tumor patient blood has become study hotspot, and in research display blood, Circulating tumor DNA is likely to become the mark of a kind of new early diagnosis of tumor and Index for diagnosis.Detection blood in circulation dissociative DNA in tumor-marker analyte detection have be different from tradition tissue tumor markers detection mode, there is noinvasive, the at any time advantage such as monitoring and early screening, and the sampling detection of circulation dissociative DNA is avoided the difficulty that current molecular diagnostic needs to gather cancerous tissue as Specimen origin, is the very potential tumor markers of one.Neoplastic hematologic disorder mark is combined with Clinical Laboratory, it is possible to the early diagnosis of adjuvant therapy and monitor in real time or early diagnosis or monitoring for tumor provide important clue, it is possible to early screening and the Index for diagnosis that can become tumor provide important evidence simultaneously.
The method diagnosed for colorectal cancer early screening clinically at present has a lot, China's examination colorectal cancer common approach is leading FOBT (being divided into five classes: radiometric analysis, Physical, chemical method, immuno-chemical method and haemachrome-porphyrin test), then positive is carried out colonoscopy.But major part method is still insufficient for the requirement of clinical early screening detection in specificity and accuracy.Nowadays high throughput sequencing technologies has obtained effective application in lesion detection, but owing to the plasma DNA content of Colorectal Cancer early stage is relatively low, and there is certain error rate etc. in sequencing technologies itself, adopt traditional sequence measurement to will be unable to differentiate order-checking mistake and the sudden change of tumor specimen low and medium frequency, be unfavorable for early diagnosis accuracy and the susceptiveness of colorectal cancer.Therefore exploitation easily operation, low damage, high precision technology be that colorectal cancer early screening is badly in need of.
Summary of the invention
According to an aspect of of the present present invention, the present invention provides a kind of test kit, and it comprises probe, and described probe is fixed on solid-phase matrix or is free in solution, and described probe can the gene region of at least 10 genes in 60 genes in specific recognition table 1 below.In one embodiment of the invention, described probe can cover the gene region of at least 20 genes in described 60 genes.In one embodiment of the invention, described probe can cover the gene region of at least 30 genes in described 60 genes.In one embodiment of the invention, described probe can cover the gene region of at least 40 genes in described 60 genes.In one embodiment of the invention, described probe can cover the gene region of at least 50 genes in described 60 genes.In one embodiment of the invention, described probe can cover the gene region of all described 60 genes.The test kit probe of the present invention can the gene region combination of specific recognition, be inventor through repeatedly collecting, repeatedly screening and test of many times combination obtain, the combination of these gene regions develops relevant with the generation of colorectal cancer.
The length of the probe that the test kit of the present invention comprises is 25～300nt.For obtain can in same reaction system simultaneously specificity catch described gene region combination, in one embodiment of the invention, probe is by first obtaining initial probe collection, then screens what described initial probe collection was determined.Obtain described initial probe collection and comprise determining that the reference sequences of described gene region, from one end of described reference sequences, described reference sequences obtains DNA fragmentation successively until the other end of described reference sequences, wherein, article one, DNA fragmentation is an initial probe, whole described DNA fragmentations constitute described initial probe collection, and completely overlapped between described DNA fragmentation, partly overlap or completely not overlapping, described initial probe energy collecting enough covers described gene region at least one times.The reference sequences of described gene region can obtain from reference genome, such as from people with reference to the gene region obtaining correspondence genome HG19, corresponding gene region on all of HG19 constitutes the reference sequences of described gene region, and HG19 can download from ncbi database.nullIn one embodiment of the invention，Iterative algorithm design is utilized to obtain described initial probe collection，Comprise determining that described gene region position on reference genome，Obtain the reference sequences of described gene region，Start to copy described reference sequences from the first of described reference sequences nucleotide and obtain Article 1 DNA fragmentation，Start to copy described reference sequences from the second of described reference sequences nucleotide and obtain Article 2 DNA fragmentation，Start to copy described reference sequences from the 3rd of described reference sequences the nucleotide and obtain Article 3 DNA fragmentation，Obtain follow-up DNA fragmentation so successively until one end of N article of DNA fragmentation is beyond described reference sequences，Wherein，Article one, DNA fragmentation is an initial probe，Whole described DNA fragmentations constitute described initial probe collection，N is the sum that described initial probe concentrates the initial probe comprised，So that obtain can the initial probe collection of coverage goal gene region comprehensively，And for making final probe tool high specific，In one embodiment of the invention，Further to described screening initial probe collection，Including: by described DNA fragmentation (initial probe collection) and described reference sequences comparison，Obtain each DNA fragmentation comparison number of times on reference sequences，Filter out the comparison number of times DNA fragmentation more than 1.For making final probe can catch described gene region in same reaction system, and/or make the gene region caught be eluted together under same reaction condition, further described initial probe collection is screened, including: get rid of G/C content not at the DNA fragmentation of 35-70%.
Table 1
| KRAS | SRC | TLR3 | EP300 | TMPRSS13 | EPHA5 |
| BRAF | PTEN | MC4R | CYLD | PHF2 | EPHA3 |
| APC | AXIN1 | MLH1 | FBN2 | OPRD1 | PTPRD |
| TP53 | FLG | AKT1 | NF1 | LILRB5 | NTRK3 |
| PIK3CA | LIG1 | CASD1 | ASXL1 | COL18A1 | NTRK1 |
| CTNNB1 | MAP2K1 | PTCH1 | SMAD4 | LARP4B | ALK |
| NRAS | PIK3R1 | ADAMTS18 | IRF5 | DMKN | ROS1 |
| EGFR | ERBB2 | MSH2 | DOCK3 | ROBO2 | RET |
| FBXW7 | STK11 | BAP1 | MYOM1 | KCNN3 | PDGFRA |
| ARID1A | IL7R | CTNNA1 | NEFH | INHBA | FGFR1 |
According to another aspect of the present invention, the present invention provides a kind of any of the above-described test kit purposes in obtaining colorectal cancer related gene sequence.The test kit utilizing one aspect of the present invention can the related gene sequence of acquisition colorectal cancer of disposable, simple and convenient and high specific.The description of the above-mentioned advantage to the test kit in one aspect of the present invention or arbitrary detailed description of the invention and technical characteristic, the purposes of this test kit on the one hand of the equally applicable present invention, do not repeat them here.
According to another aspect of the invention, it is provided that a kind of any of the above-described test kit purposes in colorectal cancer early screening.The test kit utilizing one aspect of the present invention can the related gene sequence of acquisition colorectal cancer of disposable, simple and convenient and high specific, these related gene sequence are analyzed in detection, detection is analyzed result and be may be used for or assist the early screening for colorectal cancer to judge, increases the probability that development occurs and the effect of artificial early intervention colorectal cancer.At present major part cancer such as colorectal cancer, pulmonary carcinoma, hepatocarcinoma, gastric cancer etc. has been late period when Hospital Pathological Department is made a definite diagnosis, and has delayed treatment time earlier and has greatly reduced the probability of healing.The description of the above-mentioned advantage to the test kit in one aspect of the present invention or arbitrary detailed description of the invention and technical characteristic, the purposes of this test kit on the one hand of the equally applicable present invention, do not repeat them here.
According to another aspect of the present invention, the present invention provides a kind of method building target area sequencing library, described method includes: (a) obtains the nucleic acid in sample to be tested, described nucleic acid is made up of multiple nucleic acid fragments, described nucleic acid fragment from fracture genomic DNA and/or free DNA；B () end repairs described nucleic acid fragment, it is thus achieved that end repairs fragment；C () adds base A and repairs the two ends of fragment to described end, it is thus achieved that sticky end fragment；D () jointing is in the two ends of described sticky end fragment, it is thus achieved that joint junction fragment；E described joint junction fragment is carried out the first amplification by (), it is thus achieved that the first amplified production；F () utilizes any of the above-described test kit that described first amplified production is caught, it is thus achieved that described target area；And described target area is carried out the second amplification by (g), it is thus achieved that the second amplified production, described second amplified production constitutes described target area sequencing library；Optionally, described connector end is T-sticky end.This sequencing library construction method on the one hand of the present invention, it is particularly well-suited to the structure of the sample sequencing library containing trace dna, in one embodiment of the invention, sample is the plasma sample containing micro free DNA fragmentation, comprise the target dissociative DNA fragment of extremely trace, first amplification makes the amount of nucleic acid can meet the demand that chip/probe hybridization is caught, and because chip hybridization catches meeting a certain amount of nucleic acid of loss, the second amplification can make the target fragment acquisition under catching again expand to meet the requirement that upper machine checks order and Quality Control detects.This library constructing method of the present invention be particularly well-suited to always to dissociate sequencing library of nucleic acid is not less than 10ng or conventional organization genomic DNA is not less than 1 μ g sample builds, utilize the library, target area that this method on the one hand of the present invention builds, the lower machine quality of data after order-checking is high, is beneficial to based on high-quality lower machine data and follow-up accurately detects analysis.
According to an aspect of of the present present invention, the present invention provides a kind of sequence measurement, and described method includes: sequencing library construction method according to an aspect of the present invention builds target area sequencing library；Described target area sequencing library being checked order, it is thus achieved that sequencing data, described sequencing data is made up of multiple reading sections.Order-checking can utilize known platform to carry out, and includes but not limited to the Hiseq2000/2500 platform of Illumina, the IonTorrent platform of LifeTechnologies and single-molecule sequencing platform.Order-checking mode can select single-ended order-checking, it is also possible to is double; two end sequencings, utilizes double; two end sequencing in one embodiment of the invention, the sequencing data of gained by multipair reading section to forming.The advantage of the above-mentioned test kit to arbitrary present invention and sequencing library construction method and the description of technical characteristic, this sequence measurement on the one hand of the equally applicable present invention, do not repeat them here.
According to an aspect of of the present present invention, the present invention provides a kind of method detecting target area variation, and described method includes: (1) utilizes arbitrary sequence measurement of the aforementioned present invention, it is thus achieved that the target area sequencing data of target sample；(2) based on described sequencing data, detect described target area variation, it is thus achieved that variant sites information, described variation include SNP (SNV), InDel, SV and CNV at least one.In one embodiment of the invention, step (2) including: described sequencing data and reference sequences is carried out the first comparison, it is thus achieved that the first comparison result；A part for described first comparison result Yu described reference sequences is carried out the second comparison, it is thus achieved that the second comparison result；Based on described first comparison result and described second comparison result, detect at least two in the SNP in described target area, InDel, SV and CNV variation simultaneously.For making variation testing result more accurately credible, in one embodiment of the invention, before described first comparison, described sequencing data is filtered, and described filtration includes getting rid of the uncertain base ratio reading section more than 10% and/or base mass value is not more than the reading section that the ratio of base number of 5 is not less than 50%.And optionally, before described second comparison, get rid of in the first comparison result one two the reading sections reading sections identical reading section centering right.A part for described reference sequences includes each known InDel site in the reference sequences of target area and the reference sequences of described each known InDel site each 1000bp of upstream and downstream.Here, the second described comparison is Local Alignment, first comparison is conventional overall comparison, may utilize but be not limited to the softwares such as SOAP or BWA and carry out according to its default setting, obtain the first comparison result, first comparison result includes reading section matched position on reference sequences and match condition information, in one embodiment of the invention, carry out the second comparison namely based on the first comparison result, all sequences information (reads) near all known INDEL in the reference sequences corresponding with the gene region caught is carried out local comparison again, the mistake in the first comparison can be eliminated, improve the accuracy of follow-up variation detection, the available GATK anharmonic ratio of second comparison to software (https://www.broadinstitute.org/gatk/) carry out.In one embodiment of the invention, detect described SNP and INDEL variation by GATKUnifiedGenotyper software simultaneously.Utilize this mutation detection method on the one hand of the present invention, it is possible to accurately detect the low frequency sudden change that mutation frequency is 1%.
In one embodiment of the invention, step (2) also includes, below at least one in detected variant sites meets, then judge that institute's test sample is originally as positive sample: the reading section in negative control sample supports that number mutation rate less than 2 and in positive control is more than 1%.In another embodiment of the present invention, step (2) also includes, below at least one in detected variant sites meets, then judge that institute's test sample is originally as positive sample: the order-checking degree of depth is not less than 10X, have at least 3 supports reading section, reading section in negative control sample supports that number is less than 2, mutation rate in positive control is more than 1%, and the reading section of the reading section support amount of variant sites and normal control sample (negative control sample) same loci is supported measurer there were significant differences.Described positive sample refers to colorectal cancer sample, decision condition in two embodiments is that inventor reports information in conjunction with presently relevant database information and lot of documents, the a large amount of positive sample of detection statistics and what a large amount of negative sample was decided, there is statistical significance, the latter is more stricter than the former, preferably, here the positive or negative control sample are more than 30, the nucleic acid of check sample can oneself be extracted by the data of check sample, sequencing obtains, can also in or public data storehouse disclosed according to other people sample sequencing data, multiple check sample data make statistical decision condition/result have statistical significance, more credible.Can assist for clinical diagnosis of colorectal carcinoma examination according to the result of the arbitrary judgement in two decision conditions, the probability for understanding surveyed individual of sample canceration and PD situation etc. can be assisted.nullIt should be noted that，The reading section of described variant sites reading section support amount in sample to be tested and normal control sample (negative control sample) same loci supports measurer, and there were significant differences，Reading section support amount therein，It can be the number of the reading section supporting this variation，Can also be that the ratio in section is read in the reading section supporting this variation this site in comparison，In one embodiment of the invention，The latter is adopted to compare，The described significant difference that has refers to have essence difference，Such as the variant sites A in sample to be tested，Reads in multiple positive sample (cancer sample) supports that ratio is all that 5/400 (make a variation 5 reads，Total 400 reads)，The i.e. average variation frequency 1.25% in this site in positive sample，And reads in multiple negative control samples supports that ratio is all that 1/200 (make a variation 1 reads，Total 200 reads)，I.e. average variation frequency 0.5% in negative control sample，If the variation frequency of this variant sites in sample to be tested is closer to 1.25%，Such as reach 0.9%，Then reach described significant difference or described essence difference.There is significant difference, the evaluation significant difference to data variance statistically can also be referred to, such as the variant sites A in sample to be tested is carried out repeated detection, obtain many groups comparison result data in this site, from often organizing, comparison result data all can obtain a reading section support ratio, described readings section support ratio=support in the reading hop count/comparison of this variant sites this site always read hop count, then the reading section comparing the variant sites A of sample to be tested supports the difference of ratio (variation frequency) and the mutation frequency in this site in negative control sample, such as can utilize z inspection or t inspection, difference has significance (p≤0.05), namely think and reach described there is significant difference.
According to an aspect of of the present present invention, the present invention also provides for a kind of device detecting target area variation, in order to realize or perform the invention described above on the one hand or the target area mutation detection method of arbitrary detailed description of the invention, described device includes: data capture unit, for realizing the invention described above sequence measurement on the one hand, obtaining the sequencing data of target area, described sequencing data is made up of multiple reading sections；Detection unit, for based on the sequencing data from data capture unit, detects the variation of described target area, it is thus achieved that variant sites information, described variation include SNP, InDel, SV and CNV at least one.It will be understood by those in the art that all or part of unit in assembly of the invention, selectable, dismountable comprise one or more subelement to perform or to realize each detailed description of the invention of aforementioned the inventive method.
nullSuch as，In one embodiment of the invention，As shown in Figure 1，Detection unit 200 in device 1000 includes the first comparer unit 13、Second comparer unit 15 and variation identify subelement 17，Described first comparer unit 13 is in order to carry out the first comparison by the sequencing data from data capture unit 100 with reference sequences，Obtain the first comparison result，Described second comparer unit 15 is in order to will carry out the second comparison from described first comparison result of the first comparer unit 13 and a part for described reference sequences，Obtain the second comparison result，Described variation identifies that subelement 17 is in order to based on the first comparison result from described first comparer unit 13 and the second comparison result from described second comparer unit 15，Detect the SNV in described target area simultaneously、InDel、At least two variation in SV and CNV variation，Obtain variant sites information，Wherein，A part for described reference sequences includes each known InDel site in the reference sequences of target area，And the reference sequences of described each known InDel site each 1000bp of upstream and downstream.In one embodiment of the invention, as shown in Figure 2, the detection unit 200 of described device 1000 also includes the first filtration subelement 12, described first filters subelement 12 is connected with described first comparer unit 13, before entering described first comparer list 13 yuan at described sequencing data, described sequencing data is filtered, and described filtration includes getting rid of the uncertain base ratio reading section more than 10% and/or base mass value is not more than the reading section that the ratio of base number of 5 is not less than 50%.Optional, as shown in Figure 3, described detection unit 200 also includes the second filtration subelement 14, described second filters subelement 14 is connected with described first comparer unit 13 and described second comparer unit 15 respectively, before entering described second comparer unit 15 at described first comparison result, get rid of two reading sections reading sections identical from a reading section centering in the first comparison result of described first comparer unit 13 right.Above-mentioned reference sequences can be HG19, and the first comparison carried out in described first comparing unit is overall comparison, and the second comparison carried out in described second comparer unit is Local Alignment.In one embodiment of the invention, as shown in Figure 4, detection unit 200 in described device 1000 also includes determining whether subelement 19, described judgement subelement 19, in order to judge from below described variation identifies whether the variant sites in subelement 17 meets, following then judges that described sample to be tested is as positive sample when at least one in described variant sites meets: the reading section support number mutation rate less than 2 and in positive control in negative control sample is more than 1%.In another embodiment of the present invention, described detection unit 200 also includes determining whether subelement 19, described judgement subelement 19 is in order to judge from below described variation identifies whether the variant sites in subelement 17 meets, below at least one in described variant sites meets, then judge that described sample to be tested is as positive sample: the order-checking degree of depth is not less than 10X, have at least 3 supports reading section, reading section in negative control sample supports that number is less than 2, mutation rate in positive control is more than 1%, and the reading section of the reading section support amount of variant sites and normal control sample same loci supports measurer there were significant differences.The description of the aforementioned technical characteristic to the target area mutation detection method in one aspect of the present invention or arbitrary detailed description of the invention and advantage, is equally applicable to this detecting device on the one hand of the present invention, does not repeat them here.
According to an aspect of of the present present invention, the present invention also provides for a kind of method of early screening colorectal cancer, and described method includes: obtain the nucleic acid in sample to be tested；Utilize one aspect of the present invention or arbitrary detailed description of the invention test kit catches described nucleic acid, it is thus achieved that target area；Described target area being carried out sequencing, it is thus achieved that sequencing data, described sequencing data is made up of multiple reading sections；Based on described sequencing data, detect the variation in described target area, it is thus achieved that variant sites information；Following (i) or (ii) is met, it is determined that described sample to be tested is positive sample: (i) reading section in negative control sample supports that number mutation rate less than 2 and in positive control is more than 1% based at least one in described variant sites；(ii) the order-checking degree of depth is not less than 10X, have at least 3 supports reading section, reading section in negative control sample supports that number is less than 2, and the mutation rate in positive control is more than 1%, and its reading section reading section support amount and normal control sample same loci is supported measurer there were significant differences.The description of the relevant art feature and advantage of the above-mentioned target area mutation detection method to one aspect of the present invention and/device, is equally applicable to this colorectal cancer methods for screening on the one hand of the present invention, does not repeat them here.It will be understood by those skilled in the art that all or part of step in this method on the one hand of the present invention, it is possible to realize by comprising the device of corresponding function unit.
The method, device of the present invention, it is a kind of high sensitivity, high specific, high-throughout method, device, it is possible to auxiliary is for the effect monitoring of the early screening of colorectal cancer, postoperative monitoring and various therapeutic modality (chemicotherapy, targeted drug treatment etc.).By using a new generation's high throughput sequencing technologies, the probe in specific gene region can be caught by specificity in conjunction with what the test kit of one aspect of the present invention comprised, many cases pattern detection can be carried out in a short period of time simultaneously, and the data mining of greater depths can be carried out based on same quantity of data, testing result specificity is high, have relatively low false positive rate, false negative rate, it can be ensured that the testing result obtained can react the real-time peripheral blood situation of person under inspection accurately.In human peripheral blood plasma DNA (cfDNA), specific molecular marker thing is monitored detection, can assistance application in the early screening of colorectal cancer, Post operation monitoring, chemotherapy/targeted therapy monitoring etc., thus being beneficial to the effect monitoring of monitoring and the kinds of tumors therapeutic modality at any time of the early prevention to Colorectal Cancer, Postoperative determination, being substantially reduced colorectal cancer incidence rate and improving survival etc..
Accompanying drawing explanation
Above-mentioned and/or the additional aspect of the present invention and advantage are from conjunction with will be apparent from easy to understand the accompanying drawings below description to embodiment, wherein:
Fig. 1 is the structural representation of the target area variation detecting device in one embodiment of the present of invention；
Fig. 2 is the structural representation of the target area variation detecting device in one embodiment of the present of invention；
Fig. 3 is the structural representation of the target area variation detecting device in one embodiment of the present of invention；
Fig. 4 is the structural representation of the target area variation detecting device in one embodiment of the present of invention.
Detailed description of the invention
" variation ", " variance " in the present invention, " genovariation " are generally applicable, " SNP " (SNV), " CNV ", " insertion and deletion " (indel) and " structure variation " (SV) in the present invention is with generally definition, but the size of various variations is not particularly limited by the present invention, what so have between these several variations has intersection, such as when insertion/deletion be large fragment even whole chromosome time, fall within generation copy number variation (CNV) or chromosomal aneuploidy, fall within SV.The size of these class form variations is intersected and is not interfered with those skilled in the art and performs realize the method for the present invention and/or device and reach described result by foregoing description.
What " reference sequences " in the present invention was known group sequence or known group sequence is at least some of, " first ", " second " that use in the present invention etc. only refer to for convenience of describing, it is not intended that instruction or hint relative importance, sequencing relation can not be interpreted as.In description of the invention, except as otherwise noted, " multiple " are meant that two or more.
Obtain the test kit of one aspect of the present invention, the method realizing one aspect of the present invention and/or device, generally comprise the target area capture probe/design of chip, trace sample builds storehouse and the upper machine order-checking of hybridization, the analysis of biological information of lower machine data and variation data are understood.
(1) chip design is caught in target area
Based on the data bases such as TCGA, ICGC, COSMIC and information that is relevant and that collect in a large amount of relevant references of extraction, adopt iterative algorithm to design and can be used in or assist the target area of colorectal cancer early sieve diagnosis to catch chip ColorectalPer.ColorectalPer chip includes important gene in the relevant driving gene (DriverGene) of colorectal cancer, high frequency mutant gene, relevant 12 signal paths of cancer, target medicine and chemotherapeutics related gene etc., amount to 60 genes, as shown in table 1,123Kb altogether.
(2) prepared by sample
1. extracting person under inspection peripheral blood 5-10mL, be stored in EDTA anticoagulant tube, in 4-6 hour, human peripheral blood is easily separated, and obtains plasma DNA (cfDNA), is likely to the DNA fragmentation (ctDNA) comprised from tumor cell in cfDNA；
2.cfDNA detection by quantitative；
(3) library preparation and the order-checking of the superelevation degree of depth
1. pair cfDNA fragment carries out end reparation；
2. pair cfDNA fragment ends adds A；
3. connect Adapter library joint: library joint (Adapter) refers to one section of base sequence through design, effect combines with primer when being in that cfDNA amplified library, DNA cloning is made to carry out, and combine with sequencing primer when upper machine checks order, be beneficial to sequencing primer be combined with tagmeme point to be measured auxiliary DNA sequencing carry out.
4. library carries out first round pcr amplification；
5. amplification after library Quality Control and with said chip hybridize；
6. Hybrid Library carries out second and takes turns pcr amplification；
7. library is quantitatively and Quality Control；
The upper machine order-checking of 8.IlluminaHiSeq2500/2000, the order-checking degree of depth reaches more than 2000X；
(4) under target area is caught and checked order, machine data carry out analysis of biological information
Need to carry out following analysis of biological information after obtaining lower machine data, obtain final variation result.
1.SOAPnukefilter: remove low quality reads；
2., with reference sequence alignment, produce bam file；
3. labelling repetitive sequence；
4. the sequence comparison again that comparison result is bad, and correction mass value；
5. remove mismatch；
6. analyze lower machine data QC；
7. find variation；
8. pair variation result annotates, and obtains final data result.
(5) variation data are understood
Variation data after analysis of biological information are carried out individuation deciphering, with reference to the tumor data base built and pertinent literature, the variation of person under inspection's detection is analyzed, with this examined samples colorectal cancer related gene state of auxiliary judgment, whether there is colorectal cancer risk, and the good malignant condition etc. of infantile tumour tissue, optimal prevention and therapeutic modality is given in order to secondary combined clinical test results.
Below in conjunction with concrete individual specimen, the testing result utilizing the test kit of the present invention, the method, device of the present invention obtains is described in detail.Example below, is only used for explaining the present invention, and is not considered as limiting the invention.Except as otherwise explaining, the reagent do not explained especially, sequence (joint, label and primer), software and the instrument related in following example, it is all conventional commercial product or increases income, such as build storehouse related kit to carry out library construction etc. purchased from the hiseq2000 of the Illumina company platform that checks order.
Embodiment
Implementation process is using the peripheral blood blood plasma of person under inspection as object of study in detail below, and sample is from Tianjin healthcare hospital for women & children, and content is as follows:
(1) this separation of peripheral blood sample
1. gather person under inspection peripheral blood 1-2 manage (5mL/ pipe) in EDTA anticoagulant tube, softly turn upside down (preventing cell rupture) 6-8 time fully mix, carry out following process taking a blood sample in the 4-6 hour same day；
2. centrifugal 10 minutes of 1600g under 4 DEG C of conditions, are dispensed in multiple 1.5mL/2mL centrifuge tube by supernatant (blood plasma) after centrifugal, can not be drawn onto intermediate layer leukocyte in suction process；
3. centrifugal 10 minutes of 16000g under 4 DEG C of conditions, remove residual cells, are transferred in new 1.5mL/2mL centrifuge tube by supernatant (blood plasma), it is impossible to be drawn onto leukocyte at the bottom of pipe, required blood plasma after namely being separated；
4., after plasma sample has processed, separate the blood plasma obtained and residue hemocyte is all saved in-80 DEG C of refrigerators, it is to avoid multigelation.
(2) plasma DNA extracts (adopting QIAampCirculatingNucleicAcidKit)
1. add 30 μ L E.C. 3.4.21.64s to 1.5mL centrifuge tube；
2. add 300 μ L blood plasma；
3. add 240 μ LBufferACL and 1.68 μ LCarrierRNA (0.2 μ g/ μ L), vortex oscillation 30s, 60 DEG C of temperature bath 30min, suitably take out vibration during temperature bath；
4. add 540 μ LBufferACB, vortex oscillation 15-30s, on ice or-20 DEG C of refrigerators place 5min；
5. taking 700 μ L plasma mixtures to add in Filter column, 7500rpm is centrifuged 30s；
6. Filter column sky gets rid of 8000rpm, 1min；
7. add 600 μ LBufferACW1,8000rpm, 1min centrifuge washings；
8. add 700 μ LBufferACW2,8000rpm, 1min centrifuge washings；
9. add 700 μ L dehydrated alcohol, 8000rpm, 1min centrifuge washing；
10. Filter column sky gets rid of 14000rpm, 3min；
11. Filter column is put in new collecting pipe, open lid, 56 DEG C of metal bath 10min；
12. pillar is put into new centrifuge tube collect, add 60 μ LBufferAVE back dissolving 3min；
13.14.000rpm centrifugal 1min, Qubit (Invitrogen, theQuant-iTTMDsDNAHSAssayKit) cfDNA that quantitatively Quality Control is extracted.
(3) library construction (adopting KAPALTPLibraryPreparationKit)
1. end reparation
Add AgencourtAMPureXPreagent120 μ L after reaction, after magnetic beads for purifying, use 42 μ LddH2O back dissolving, band magnetic bead carries out next step reaction；
2. end adds A
Add PEG/NaClSPRISolution90 μ L after reaction, be sufficiently mixed and carry out magnetic beads for purifying, Adapter and ddH in lower step Adapter coupled reaction system2O addition is calculated according to formula below: 10nM* builds initial amount of DNA (ng) * Adaper consumption (μ L)=15 μMs (Adapter concentration) the * 50 μ L in storehouse, uses ddH2O consumption (μ L)=35 μ L-Adapter consumption (μ L) back dissolving, carries out next step reaction；
3. joint connects
After reaction, add PEG/NaClSPRISolution50 μ L, carry out first time magnetic beads for purifying, use 50 μ LTris-HCl (1mM, pH8.0) back dissolvings；
Add PEG/NaClSPRISolution50 μ L, carry out second time magnetic beads for purifying, use 25 μ LTris-HCl (1mM, pH8.0) back dissolvings；
4. first round pcr amplification
Add AgencourtAMPureXPreagent90 μ L after reaction, after magnetic beads for purifying, use 31 μ LddH2O back dissolving, Quality Control carry out chip hybridization after taking supernatant.
(4) chip hybridization is caught in target area
1. adopting the above-mentioned colorectal cancer relevant range entrusting Roche synthesis to catch chip ColorectalPer-123Kb in the present embodiment, the description provided with reference to chip manufacturer carries out hybrid capture and eluting.Finally use 21 μ LddH2O back dissolving hybridization elution magnetic bead.
2. second take turns pcr amplification
Adding AgencourtAMPureXPreagent108 μ L after reaction, after magnetic beads for purifying, use 31 μ LEB back dissolvings, after taking supernatant, Quality Control upper machine check order.
(5) upper machine order-checking
In the present embodiment, adopting IlluminaHiSeq2500PE101+8+101 program to carry out upper machine order-checking, the operating instruction (announcing cBot referring to Illumina/Solexa official) that order-checking experimental implementation provides according to manufacturer carries out upper machine sequencing procedures.
(6) machine Data Bio information analysis under
1.SOAPnukefilter: remove the reads of the base number > 50% of n >=10% and base mass value≤5；
2.Bwaaln-> sampe | samtoolsview | samtoolssort: with reference sequence alignment, generation bam file；
3.MarkDuplicates.jar: the identical reads of same pe is labeled as repetition；
4.GenomeAnalysisTK.jar-TRealignerTargetCreator, IndelRealigner: by reads bad for comparison again comparison；
5.GenomeAnalysisTK.jar-TBaseRecalibrator, PrintReads: correction mass value；
6.Filt_bam: remove the reads of mismatch >=3；
7.QC: the information such as the statistics capture rate of chip, effective reads number, mean depth, repetitive rate, coverage and uncovered interval；
8. identify SNV/InDel/SV/CNV and screen high frequency closedown site therein:
With MuTect (http://www.broadinstitute.org/cancer/cga/mutect)、varScan(http://massgenomics.org/varscan) flow process identify SNP variation；
With gatk (https://www.broadinstitute.org/gatk/)、varScan、ForestSV(http://sebatlab.ucsd.edu/index.php/software-data) flow process identify InDel variation；
With contra.py (http://contra-cnv.sourceforge.net/) flow process identifies CNV；
With ForestSV (http://sebatlab.ucsd.edu/index.php/software-data) flow process identifies SV；
The screening parameter used is: the order-checking degree of depth >=10X, aberration rate≤2% in negative (normally) sample, aberration rate >=1% in positive sample, these sample to be tested data are supported reads number >=3 of this variation, supports that ratio has significant difference (p≤0.05) with the reading section of normal control (such as normal somatic cell)；
9. annotation
The function of annotation variation, reads support the variation etc. in number, variation frequency, amino acid variation and data base Cosmic；
According to variation situation judge or auxiliary judgment disease be likely to source.
10. sequencing analysis
Sequencing data statistical result such as table 2, variation testing result is as shown in table 3.
Table 2
Table 3
This sample detection KRASp. [Gly12Asp] missense mutation, this variation is recorded 10303 times in COSMIC data base, about 60% all report to colorectal cancer fall ill relevant.No. 12 codon of KRAS is positioned on GTP domain, is the most common mutations of KRAS.
KRAS belongs to Ras gene family member, encodes P21 albumen, works, be oncogene, it is possible to be combined with GDP/GTP and promote GTP enzymatic activity in MAPK signal path.Enzyme hydrolysis inactivation can not be hydrolyzed when KRAS undergos mutation, be in sustained activation state, cause the rise of RAF/MAPK, transmit multiple existence path signal, so that cellular overgrowth, propagation, the effect of opposing EGFR-TKIs.Its sudden change can cause Several Kinds of Malignancy, including pulmonary carcinoma, and mucoprotein adenoma, Pancreatic neoplasms and colon cancer etc..The KRAS gene modal mode that is activated is point mutation, mostly occurs at the 12nd of N end the, 13 and 61,146 codons, wherein the most common with the 12nd codon mutation.Different mutational sites are different to the activation mechanism of P21 albumen, and the 12nd codon mutation can weaken the GTP enzymatic activity that P21 is inherent, and makes apoptosis reduce, and cell contact suppresses to weaken.
The nonsense mutation of this sample detection MSH2p. [Arg555*], this variation is recorded in COSMIC data base nothing temporarily.No. 555 codon region functional study of MSH2 is not quite clear, but the generation of this nonsense mutation can cause the termination in advance of encoding histone so that gene major function district is beyond expression, it is possible to makes gene function sustain damage or loses.
Coded albumen is one of component of DNA mismatch repair system (MMR), form heterodimer 2 kinds different: MutS α (MSH2-MSH6 heterodimer) and MutS β (MSH2-MSH3 heterodimer), can combine with DNA mismatch position and therefore start the repair function of DNA.After mispairing combines, MutS α or β and MutL α heterodimer forms a ternary complex, is responsible for instructing the MMR event in downstream, including the identification of chain, excision and resynthesis.Combination and the hydrolysis of ATP play an important role on mispairing repair function, and atpase activity is relevant to MutS α.MutS α functionally can also work at DNA homology recombination repair.This gene is relevant to hereditary nonpolyposis colorectal cancer type I and carcinoma of endometrium.
Find out that this person under inspection detection occurs to develop relevant important variation with colorectal cancer from mutant analysis results, in conjunction with clinical diagnosis situation, can determine whether risk that this person under inspection suffers from colorectal cancer and good malignant condition.
Embodiment described above is only that the preferred embodiment of the present invention is described; not the scope of the present invention is defined; under the premise designing spirit without departing from the present invention; this area ordinary skill technical staff to the made various deformation of technical solution of the present invention and improvement, all should fall in the protection domain that claims of the present invention are determined.
Claims (14)
1. a test kit, it comprises probe, and described probe is fixed on solid-phase matrix or described probe is free in solution, and described probe can the gene region of at least 10 genes in 60 genes in specific recognition table 1；
Optionally, described probe can cover the gene region of at least 20 genes in described 60 genes；
Optionally, described probe can cover the gene region of at least 30 genes in described 60 genes；
Optionally, described probe can cover the gene region of at least 40 genes in described 60 genes；
Optionally, described probe can cover the gene region of at least 50 genes in described 60 genes；
Optionally, described probe can cover the gene region of described 60 genes；
Optionally, the length of described probe is 25-300nt.
2. the test kit of claim 1, it is characterised in that the acquisition of described probe includes, it is thus achieved that initial probe collection and screen described initial probe collection.
3. the test kit of claim 2, it is characterised in that described acquisition initial probe collection includes:
Determine the reference sequences of described gene region,
From one end of described reference sequences, described reference sequences obtains DNA fragmentation successively until the other end of described reference sequences, wherein,
Article one, DNA fragmentation is an initial probe, and whole described DNA fragmentations constitute described initial probe collection, and completely overlapped between described DNA fragmentation, partly overlap or completely not overlapping, described initial probe energy collecting enough covers described gene region at least one times.
4. the test kit of claim 2, it is characterised in that described acquisition initial probe collection includes:
Determine described gene region position on reference genome, obtain the reference sequences of described gene region,
Start to copy described reference sequences from first nucleotide of described reference sequences one end and obtain Article 1 DNA fragmentation,
Start to copy described reference sequences from second nucleotide of described reference sequences one end and obtain Article 2 DNA fragmentation,
Start to copy described reference sequences from the 3rd of described reference sequences one end the nucleotide and obtain Article 3 DNA fragmentation,
Obtain follow-up DNA fragmentation so successively until one end of N article of DNA fragmentation exceeds the other end of described reference sequences, wherein,
Article one, DNA fragmentation is an initial probe, and whole described DNA fragmentations constitute described initial probe collection, and N is the sum that described initial probe concentrates the initial probe comprised.
5. the test kit of claim 3 or 4, it is characterised in that described screening initial probe collection includes:
By described DNA fragmentation and described reference sequences comparison, it is thus achieved that each DNA fragmentation comparison number of times on reference sequences, filter out the comparison number of times DNA fragmentation more than 1.
6. the test kit of claim 5, it is characterised in that described screening initial probe also includes, gets rid of G/C content not at the DNA fragmentation of 35-70%.
7. claim 1-6 arbitrary test kit purposes in obtaining colorectal cancer related gene sequence.
8. claim 1-6 arbitrary test kit purposes in colorectal cancer early screening.
9. the method building target area sequencing library, it is characterised in that including:
A () obtains the nucleic acid in sample to be tested, described nucleic acid is made up of multiple nucleic acid fragments, and described nucleic acid fragment is from the genomic DNA of fracture and/or free DNA；
B () end repairs described nucleic acid fragment, it is thus achieved that end repairs fragment；
C () adds base A and repairs the two ends of fragment to described end, it is thus achieved that sticky end fragment；
D () jointing is in the two ends of described sticky end fragment, it is thus achieved that joint junction fragment；
E described joint junction fragment is carried out the first amplification by (), it is thus achieved that the first amplified production；
F () utilizes the arbitrary test kit of claim 1-6 that described first amplified production is caught, it is thus achieved that described target area；And,
G described target area is carried out the second amplification by (), it is thus achieved that the second amplified production, and described second amplified production constitutes described target area sequencing library；
Optionally, described connector end is T-sticky end.
10. a sequence measurement, it is characterised in that including:
Method according to claim 9 builds target area sequencing library；
Described target area sequencing library being checked order, it is thus achieved that sequencing data, described sequencing data is made up of multiple reading sections；
Optionally, described order-checking is double; two end sequencings, described sequencing data by multipair reading section to forming.
11. the method detecting target area variation, it is characterised in that include,
(1) method utilizing claim 10, it is thus achieved that sequencing data；
(2) based on described sequencing data, detect described target area variation, it is thus achieved that variant sites information, described variation include SNP, InDel, SV and CNV at least one.
12. the method for claim 11, it is characterised in that step (2) includes,
Described sequencing data and reference sequences are carried out the first comparison, it is thus achieved that the first comparison result；
A part for described first comparison result Yu described reference sequences is carried out the second comparison, it is thus achieved that the second comparison result；
Based on described first comparison result and described second comparison result, detect at least two in the SNP in described target area, InDel, SV and CNV variation simultaneously；Wherein,
A part for described reference sequences includes each known InDel site in the reference sequences of target area and the reference sequences of described each known InDel site each 1000bp of upstream and downstream；
Optionally, before described first comparison, described sequencing data being filtered, described filtration includes getting rid of the uncertain base ratio reading section more than 10% and/or base mass value is not more than the reading section that the ratio of base number of 5 is not less than 50%；
Optionally, before described second comparison, get rid of in the first comparison result one two the reading sections reading sections identical reading section centering right；
Optionally, described reference sequences is HG19；
Optionally, described first comparison is overall comparison, and described second comparison is Local Alignment.
13. the method for claim 11 or 12, it is characterised in that step (2) also includes, below at least one in described variant sites meets, then judge that described sample to be tested is as positive sample:
Reading section in negative control sample supports that number mutation rate less than 2 and in positive control is more than 1%；
Optionally, step (2) also includes, and below at least one in described variant sites meets, then judges that described sample to be tested is as positive sample:
The order-checking degree of depth is not less than 10X,
Have at least 3 supports reading section,
Reading section in negative control sample supports that number is less than 2,
Mutation rate in positive control more than 1%, and
The reading section of the reading section support amount of variant sites and normal control sample same loci supports measurer, and there were significant differences.
14. the device detecting target area variation, it is characterised in that include,
Data capture unit, for the method realizing claim 10, obtains the sequencing data of described target area, and described sequencing data is made up of multiple reading sections；
Detection unit, for based on the sequencing data from data capture unit, detects the variation of described target area, it is thus achieved that variant sites information, described variation include SNV, InDel, SV and CNV at least one；
Optionally, described detection unit includes the first comparer unit, the second comparer unit and variation and identifies subelement,
Described first comparer unit is in order to carry out the first comparison by the sequencing data from data capture unit with reference sequences, it is thus achieved that the first comparison result,
Described second comparer unit is in order to will carry out the second comparison from described first comparison result of the first comparer unit and a part for described reference sequences, it is thus achieved that the second comparison result,
Described variation identifies that subelement is in order to based on the first comparison result from described first comparer unit and the second comparison result from described second comparer unit, detect at least two in the SNV in described target area, InDel, SV and CNV variation simultaneously, obtain variant sites information, wherein
A part for described reference sequences includes each known InDel site in the reference sequences of target area and the reference sequences of described each known InDel site each 1000bp of upstream and downstream；
Optionally, described detection unit also includes the first filtration subelement, described first filters subelement is connected with described first comparer unit, before entering described first comparer unit at described sequencing data, described sequencing data is filtered, and described filtration includes getting rid of the uncertain base ratio reading section more than 10% and/or base mass value is not more than the reading section that the ratio of base number of 5 is not less than 50%；
Optionally, described detection unit also includes the second filtration subelement, described second filters subelement is connected with described first comparer unit and described second comparer unit respectively, before entering described second comparer unit at described first comparison result, get rid of two reading sections reading sections identical from a reading section centering in the first comparison result of described first comparer unit right；
Optionally, described reference sequences is HG19；
Optionally, the first comparison in described first comparing unit is overall comparison, and the second comparison in described second comparer unit is Local Alignment；
Optionally, described detection unit also includes determining whether subelement, described judgement subelement is in order to judge from below described variation identifies whether the variant sites in subelement meets, then judging that described sample to be tested is as positive sample below at least one in described variant sites meets:
Reading section in negative control sample supports that number mutation rate less than 2 and in positive control is more than 1%；
Optionally, described detection unit also includes determining whether subelement, described judgement subelement is in order to judge from below described variation identifies whether the variant sites in subelement meets, then judging that described sample to be tested is as positive sample below at least one in described variant sites meets:
The order-checking degree of depth is not less than 10X,
Have at least 3 supports reading section,
Reading section in negative control sample supports that number is less than 2,
Mutation rate in positive control more than 1%, and
The reading section of the reading section support amount of variant sites and normal control sample same loci supports measurer, and there were significant differences.
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