CN105044108A - Microarray chip sample application quality automatic judgment system and judgment method - Google Patents

Microarray chip sample application quality automatic judgment system and judgment method Download PDF

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CN105044108A
CN105044108A CN201510404855.5A CN201510404855A CN105044108A CN 105044108 A CN105044108 A CN 105044108A CN 201510404855 A CN201510404855 A CN 201510404855A CN 105044108 A CN105044108 A CN 105044108A
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array chip
point
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rake
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CN105044108B (en
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李勐
赵雷
黄明辉
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GENETEL PHARMACEUTICALS (SHENZHEN) CO Ltd
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GENETEL PHARMACEUTICALS (SHENZHEN) CO Ltd
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Abstract

The invention provides a microarray chip sample application quality automatic judgment system and a judgment method. The judgment system includes a microarray chip, a scanner, a computer software digitalizer, and a software comparing device. According to different probes involved in sample application, and the relative position information of different probes on a basement membrane, biological information detection of a sample can be realized. The judgment system has high detection efficiency, and can issue 936 microarray detection reports within 15min; the system has objective results, and multiple judgment results of a same microarray are consistent; the system is low in cost, the work traditionally completed by 8-16 people can be achieved by one job post; and the system also has other significant advantages.

Description

Micro-array chip arraying quality automatization judgement system and determination methods
Technical field
The invention belongs to field of biological technology detection, particularly micro-array chip arraying quality automatization judgement system and determination methods.
Background technology
Micro-array chip refers to that to be set on substrate with array way can the microdevice of biological or chemical information in parallel processing and analyzing samples.Note: dot matrix arrangement point footpath is within 500 μm, and adjacent two dot center's spacing minor increments are as the criterion (GB/T27990-2011 " biochip basic terms ") not produce signal cross.
Because micro-array chip volume is little, some footpath is micron level, and in order to realize high density point sample, dot spacing is often less than a footpath, and naked eyes are difficult to the micro-array chip quality judging to produce.
Current enterprise carries out arraying quality and judges mostly to be artificial judgment, by scanning or camera installation, microarray images is amplified on a display screen several times display, by manually recognizing or using measurer manual measurement on a display screen.The method detection efficiency is low, and subjective factor is large, and undetected false retrieval happens occasionally.
Prior art CN101839688A is based on the biochip point sample process real-time detection system of machine vision and analytical approach, comprise: an image picking-up apparatus, the sampling head that this image picking-up apparatus follows point sample equipment carries out synchronous three-dimensional motion and takes to obtain point sample area image to spotted area; One image capture device, this image capture device is connected with described image picking-up apparatus signal, gathers the image of image picking-up apparatus shooting and completes the digital-to-analog conversion of image; One image processing equipment, this image processing equipment is connected with described image capture device signal, processes the spotted area image that image capture device gathers, analyzes, and output processing result.But in actual implementation process, because this technology needs Real-time Collection and analysis chart picture, extend biochip point sample process, reduce the service efficiency of biochip point sample instrument.Meanwhile, in order to coordinate the requirement of real-time analysis data, needing the every platform biochip point sample instrument for applying this technology to be equipped with image capture device, image processing equipment, causing the increase of production cost.And biochip point sample and biochip test and analyzing merges by this technology, constitute a more complicated new system, reduce the stability of system, in actual implementation process, point sample stability receives impact.
Summary of the invention
The efficiency existed in view of prior art is low, cost is high and the problem of poor stability, the invention provides micro-array chip arraying quality automatization judgement system and determination methods.The present invention can robotization batch detection biochip quality, and can multitask perform simultaneously, and execution efficiency is high.Due to the present invention by scanner and computer digit gasifying device and point sample instrument independent, its actual execution stability is high.
Described micro-array chip arraying quality automatization judgement system comprises: micro-array chip, scanner, computer software digitalizer, and software compare device.
The composition of described micro-array chip comprises substrate, position, set-point on substrate, and DNA probe, surface chemistry Quality Control point probe and blank probe, and each probe is corresponding with some position, and blank spot.
Described micro-array chip arranges the DNA probe of detection 26 kinds of HPV virus different genotype, and reserved 8 easily extensible point positions.
4 " summit " mark of described substrate draws 1 isolated area, and this region is a micro-array chip, is divided into a-f capable, and g-l row.
Described easily extensible point position is positioned at c capable l row point position, e capable k row point position, f capable h row point position.
Described internal reference probe is positioned at f capable i point position, f capable j row point position; Described surface chemistry Quality Control point probe is positioned at the capable g of a and arranges some position, an a capable l row point position, f capable l row point position; Described blank probe is positioned at f capable k row point position; Blank spot is positioned at f capable g row point position, and DNA probe is positioned at all the other some positions.
Wherein, micro-array chip is made up of substrate, probe.Substrate, for carrying probe, possesses certain physical strength, can realize the effect of acquisition target target by supporting probe.Be connected by chemical bond between probe with substrate, in acquisition target target process, realize stable connection.Substrate makes mainly with the material possessing certain physical strength for glass, nylon membrane, silicon chip, plastics or pottery etc., and possess profile pattern and chemical modification, two probes are main mainly with biomacromolecule, possesses specific biologically active, specificity target be can catch, conversion and the identification of target organisms information realized according to the positional information of probe in micro-array chip.Premised on the ordered microarray that micro-array chip practical function must be formed by probe particular arrangement, namely the order of micro-array chip is the prerequisite necessary condition realizing micro-array chip.
Scanner is made up of sheet glass, light source, photo-sensitive cell, driver, mainboard, USB port, micro-array chip is placed on sheet glass, be combined with the surface of probe towards light source and photo-sensitive cell, driver drives light source and photo-sensitive cell move to bottom by the top of micro-array chip, period, light source sent visible ray, throwing glass is radiated on micro-array chip, the reflected light of micro-array chip enters photo-sensitive cell, realize the collection of image, photosensitive information carries out digital conversion through mainboard, and is sent to computer software digitalizer through USB port.Scanner can realize the one-off scanning that 36 × 26 amount to 936 micro-array chips.
Computer software digitalizer consist of USB port, display, processor, internal memory, USB port receives the digitized video that scanner sends, and be temporarily stored in internal memory, software transfer digitized video, and according to choice box logarithm value Image Segmentation Using, binary picture that user delimit, and the dimension information of the position of each target spot, major axis, minor axis is temporarily stored in internal memory.
And the standard size information that in software compare device invoke memory, the dimension information of each target spot of 936 chips and user set contrasts, it is qualified that the target spot meeting standard setting is judged as, otherwise be defective, and by judged result with Excel formatted output on display.
Described determination methods comprises: adopt aforementioned micro-array chip arraying quality automatization judgement system, (1) color analyzing each pixel in picture is formed, when red pixel during the color of pixel is formed is greater than 200 and red pixel is greater than blue pixel+40, then this pixel will be construed to target spot, otherwise will background be considered for, rake pixel is transferred to white, and background pixel transfers black to; (2) according to binary picture, find out position corresponding to each rake point and size by Contour extraction, minimum dimension is less than for rake point, directly ignores; (3) if the height of rake point or width are greater than rake point full-size, then judge that this rake point is that two rake points are bonded together really, the rake point be bonded together is carried out to splitting; (4) according to the rake point position detected, size, the information such as length breadth ratio carry out comparing with the standard value of setting, generate examining report.
Present case achieves micro-array chip arraying quality automatization judgement system, this system possesses the function to micro-array chip automatic decision quality, can according to the dot matrix arrangement feature of chip, by setting array line number, array row spacing, array columns, array column spacing, target spot line number, target spot line space, target spot columns, target spot column pitch, target spot diameter, target spot maximum gauge, target spot minimum diameter, target spot aspect ratio maximal value, the parameters such as target spot maximum displacement, and software compare device carries out the quality condition that contrasts to determine every chips voluntarily and provides report with setup parameter.
Term in the present invention: HB-described internal reference probe; + VE-surface chemistry Quality Control point probe;-VE-blank probe.
Human infectious warts virus (HPV), HPV virus has more than 130 gene type, chip of the present invention can detect wherein 26 kinds of HPV Virus type (be respectively HPV16,18,31,33,35,39,45,51,52,56,58,59,68,6,11,40,42,43,44,53,54,55,57,66,67,73 types).
Compared to prior art Traditional Man, automatization judgement system of the present invention judges that system has significant advantage, details are as follows:
1. detection efficiency is high
Coordinate high-performance computer, automatization judgement system can provide the examining report of 936 parts of microarraies in 15 minutes, and can realize multi-core parallel parsing, and multi-core CPU computing machine can realize 4 ~ 8 detections and walk abreast simultaneously, Turnaround Time is constant.And Traditional Man judges that system judges that 936 parts of microarraies need 30 ~ 60 minutes (array complexity is different, judges that time difference is very large).
2. result is objective
Automatization judgement system is judged chip image by image digitizing system, obtained by high-resolution scanner during image, be identical with material object, image forms numerical value according to color composition and Color Range, logarithm value compares, and therefore with a microarray, repeatedly judged result is consistent.And Traditional Man judges that system judges according to personal experience, under the different conditions of different people and people, judged result is difficult to be consistent.
3. with low cost
A set of micro-array chip arraying quality automatization judgement system comprises scanner, computing machine and software kit and can set up enforcement.Personnel are through simple training and can realize the Quality estimation of micro-array chip according to working specification manipulation software.A work position just can realize traditional 8-16 the operation that manually can complete.Reduce the employment cost of enterprise greatly.
Accompanying drawing explanation
Fig. 1 micro-array chip arraying quality of the present invention automatization judgement working-flow figure.
A kind of micro-array chip structural drawing of Fig. 2 the present invention
A kind of microarray chip analysis figure of Fig. 3 the present invention, wherein, pictorial diagram before Fig. 3 (A) chip binaryzation to be checked, Fig. 3 (B) chip binaryzation to be checked post analysis figure.
A kind of binaryzation micro-array chip of Fig. 4 the present invention dot matrix edge junction composition, is transformed by Contour extraction and obtains.
Fig. 5 the present invention one judges Argument List chart.
A kind of single-point chip of Fig. 6 the present invention 26 × 36 chip row matrix column distribution schematic diagram
A kind of single-point chip chamber of Fig. 7 the present invention Quality Control parameter schematic diagram
Quality Control parameter schematic diagram in a kind of single-point chip of Fig. 8 the present invention.
The list of a kind of parameter judged result of Fig. 9 the present invention.
Embodiment
In order to explain the present invention, below in conjunction with Figure of description and embodiment, the invention will be further described, but the present invention is not limited thereto.
Embodiment one:
As shown in Figure 1, described micro-array chip arraying quality automatization judgement system comprises: micro-array chip, scanner, computer software digitalizer, and software compare device.
Wherein, micro-array chip is made up of following assembly:
Nylon membrane substrate: nylon membrane, has certain physical strength and DNA in conjunction with biologic activity, can be combined with DNA probe under given conditions and carry DNA probe to complete Biological Detection.Wherein in Fig. 2, nylon membrane is drawn 1 isolated area by 4 " summit " mark, and this region is a micro-array chip, is divided into a-f capable, and g-l row.
Human infectious warts virus (HPV) different genotype viral DNA probe: in Fig. 2, different digital represents different HPV gene types, amount to detection 26 kinds of HPV virus different genotype, and (in Fig. 2, " undetermined " puts position to reserve 3 easily extensible point positions, c capable l row point position, e capable k row point position, f capable h row point position).
Internal reference probe: " HB " point (f capable i point position, f capable j row point position) in Fig. 2, the point of sample of synthetic gene sequence on genetic chip, there is the ability of specific binding with related gene in human genome, in process of the test, judge whether that whether the extraction efficiency successfully obtaining cell and cell DNA is up to standard.
Surface chemistry Quality Control point: "+VE " point (the capable g of a arranges some position, the capable l of a arranges some position, the capable l of f arranges some position) in Fig. 2, containing the point of sample of synthetic gene sequence on genetic chip of specific chromogenic material, PCR primer can not be relied on to carry out Quality Control to process color.
Blank: whether "-VE " point (f capable k row point position) in Fig. 2, not containing the sampling liquid of bioactive molecule, for proofing chip deposition process, point sample mistake occurs.
Blank spot: " without point " point (f capable h row point position) in Fig. 2, this point does not carry out point sample, owing to developing the color, according to the relative position necessarily developed the color a little with+VE three in this position, realizes confirming the sense of rotation in chip process color.
Above probe specificity catches biologically active target, realizes the judgement of other differentiation of HPV different genotype and detection experiment validity according to the difference of the position of probe in micro-array chip.
Scanner: Canoscan9000FMarkII, 36 × 26 one-off scannings amounting to 936 micro-array chips.
Computer software digitalizer: desktop computer, Windows7 (64) system, can mounting software program, and provides arraying quality automatization judgement system program to run.
Embodiment two:
As Fig. 3,4,5,6,7, shown in 8 and 9, described determination methods comprises: the micro-array chip, scanner, the computer software digitalizer that adopt previous embodiment one, point sample quality automatic is installed in computer software digitalizer and judges system program, chip scanning figure service routine is opened, to its fixed point position, program completes following comparative analysis automatically:
(1) color analyzing each pixel in picture is formed, when red pixel during the color of pixel is formed is greater than 200 and red pixel is greater than blue pixel+40, then this pixel will be construed to target spot, otherwise will background be considered for, rake pixel is transferred to white, and background pixel transfers black (shown in Fig. 3) to;
(2) according to binary picture, find out position corresponding to each rake point and size by Contour extraction, minimum dimension is less than for rake point, directly ignores;
(3) if the height of rake point or width are greater than rake point full-size, then judge that this rake point is that two rake points are bonded together in fact, the rake point be bonded together is carried out to splitting (fractionation of the crosslinking points of first row shown in Fig. 4 position);
(4) according to the rake point position detected, size, the information such as length breadth ratio carry out comparing with the standard value (parameter shown in Fig. 9 is standard value range) of setting, generate examining report.
Judge that Selecting parameter as shown in Figure 8,9.
In Fig. 8, K and L parameter is less than " target spot maximum displacement " 30 in Fig. 9, for qualified.
In Fig. 8, N parameter has maximal value and minimum value two, and wherein maximal value should be less than " target spot maximum gauge " 40 in Fig. 9 is qualified, otherwise is that target spot is excessive, defective; And minimum value should be less than " target spot minimum diameter " 23 for qualified, otherwise be target spot disappearance, defective; The ratio of maxima and minima should be less than " target spot aspect ratio maximal value " 1.5 for qualified simultaneously, otherwise is target spot out-of-shape, defective.
Performance summary:
1, detection efficiency is high
Coordinate high-performance computer, automatization judgement system can provide the examining report of 936 parts of microarraies in 15 minutes, and can realize multi-core parallel parsing, and multi-core CPU computing machine can realize 4 ~ 8 detections and walk abreast simultaneously, Turnaround Time is constant.And Traditional Man judges that system judges that 936 parts of microarraies need 30 ~ 60 minutes (array complexity is different, judges that time difference is very large).
2, result is objective
Automatization judgement system is judged chip image by image digitizing system, obtained by high-resolution scanner during image, be identical with material object, image forms numerical value according to color composition and Color Range, logarithm value compares, and therefore with a microarray, repeatedly judged result is consistent.And Traditional Man judges that system judges according to personal experience, under the different conditions of different people and people, judged result is difficult to be consistent.
3, with low cost
A set of micro-array chip arraying quality automatization judgement system comprises scanner, computing machine and software kit and can set up enforcement.Personnel are through simple training and can realize the Quality estimation of micro-array chip according to working specification manipulation software.A work position just can realize traditional 8-16 the operation that manually can complete.Reduce the employment cost of enterprise greatly.
Above content is in conjunction with concrete preferred implementation further description made for the present invention, can not assert that specific embodiment of the invention is confined to these explanations.For general technical staff of the technical field of the invention, without departing from the inventive concept of the premise, some simple deduction or replace can also be made, all should be considered as belonging to protection scope of the present invention.

Claims (10)

1. micro-array chip arraying quality automatization judgement system, it is characterized in that, comprise: micro-array chip, scanner, computer software digitalizer, and software compare device, the composition of described micro-array chip comprises substrate, position, set-point on substrate, and DNA probe, surface chemistry Quality Control point probe and blank probe, each probe is corresponding with some position, and blank spot.
2. micro-array chip arraying quality automatization judgement system according to claim 1, is characterized in that, described micro-array chip arranges the DNA probe of detection 26 kinds of HPV virus different genotype, and reserved 8 easily extensible point positions.
3. micro-array chip arraying quality automatization judgement system according to claim 2, is characterized in that, 4 " summit " mark of described substrate draws 1 isolated area, and this region is a micro-array chip, is divided into a-f capable, and g-l row.
4. micro-array chip arraying quality automatization judgement system according to claim 2, is characterized in that, described easily extensible point position is positioned at c capable l row point position, e capable k row point position, f capable h row point position.
5. micro-array chip arraying quality automatization judgement system according to claim 2, is characterized in that, described internal reference probe is positioned at f capable i point position, f capable j row point position; Described surface chemistry Quality Control point probe is positioned at the capable g of a and arranges some position, an a capable l row point position, f capable l row point position; Described blank probe is positioned at f capable k row point position; Blank spot is positioned at f capable g row point position, and DNA probe is positioned at all the other some positions.
6. micro-array chip arraying quality automatization judgement system according to claim 2, it is characterized in that, each DNA probe is different, be followed successively by HPV16,18,31,33,35,39,45,51,52,56,58,59,68,6,11,40,42,43,44,53,54,55,57,66,67,73 type DNA probes.
7. micro-array chip arraying quality automatization judgement system according to claim 1, it is characterized in that, described software compare device, can analyze 936 chips simultaneously, and carries out the quality condition that contrasts to determine every chips voluntarily with setup parameter and provide report.
8. micro-array chip arraying quality automatization judgement system according to claim 1, it is characterized in that, described substrate is glass, nylon membrane, silicon chip, plastics or pottery.
9. a micro-array chip arraying quality automatization judgement method, it is characterized in that, comprise: adopt the micro-array chip arraying quality automatization judgement system described in the arbitrary claim of aforementioned claim 1-8, according to the difference of institute's point probe, and different probe relative position information on substrate realizes the detection of sample biological information.
10. a kind of micro-array chip arraying quality automatization judgement method according to claim 9, is characterized in that, comprising: concrete steps are as follows:
(1) color analyzing each pixel in picture is formed, when red pixel during the color of pixel is formed is greater than 200 and red pixel is greater than blue pixel+40, then this pixel will be construed to target spot, otherwise will background be considered for, rake pixel is transferred to white, and background pixel transfers black to;
(2) according to binary picture, find out position corresponding to each rake point and size by Contour extraction, minimum dimension is less than for rake point, directly ignores;
(3) if the height of rake point or width are greater than rake point full-size, then judge that this rake point is that two rake points are bonded together in fact, the rake point be bonded together is carried out to splitting;
(4) according to the rake point position detected, size, the information such as length breadth ratio carry out comparing with the standard value of setting, generate examining report.
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CN113658209A (en) * 2021-08-12 2021-11-16 山东省计算中心(国家超级计算济南中心) Morphology-based method for judging excellent mounting position of sliced tissue
CN113658209B (en) * 2021-08-12 2023-06-16 山东省计算中心(国家超级计算济南中心) Morphology-based excellent discriminating method for mounting position of slice tissue

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