CN113957131A - Method for reprocessing and reusing waste chips - Google Patents
Method for reprocessing and reusing waste chips Download PDFInfo
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- CN113957131A CN113957131A CN202111206609.0A CN202111206609A CN113957131A CN 113957131 A CN113957131 A CN 113957131A CN 202111206609 A CN202111206609 A CN 202111206609A CN 113957131 A CN113957131 A CN 113957131A
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- 239000002699 waste material Substances 0.000 title claims abstract description 60
- 238000000034 method Methods 0.000 title claims abstract description 23
- 238000012958 reprocessing Methods 0.000 title claims abstract description 16
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- 238000012163 sequencing technique Methods 0.000 claims abstract description 85
- 238000000137 annealing Methods 0.000 claims abstract description 60
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6869—Methods for sequencing
Abstract
The invention discloses a method for reprocessing and reusing waste chips, which comprises the following steps: s1: with a mixture of annealing buffer and nuclease-free water according to (0.75-1.25): 1, washing the waste chips which fail to be sequenced for 3-5 times by using the AB solution prepared according to the volume ratio; s2: 200-250uL of Tween solution and NaOH solution are divided into two parts according to the proportion of (6-8): 1, adding the eluent prepared according to the volume ratio into the chip hole, and incubating at room temperature of 25 ℃ for 3-5 min; s3: cleaning the chip with AB solution for 3-5 times; s4: uniformly mixing 35-45uL sequencing primer and 30-35uL annealing buffer solution, adding the mixture into a chip hole, and then putting the chip hole into a pcr instrument for annealing; s5: washing the chip with 80-150uL AB solution for 3-5 times, adding 60-70uL enzyme reaction solution into the chip hole, incubating at 25 deg.C for 4-8min, and sequencing; the enzyme reaction solution is composed of 55-63 μ L AB solution and 5-7 μ L sequencing polymerase. According to the invention, the waste chips which fail in sequencing are treated and utilized, so that the waste chips can be sequenced again, the cyclic regeneration of the waste chips is realized, the resources are saved, and the waste is avoided.
Description
Technical Field
The invention belongs to the field of chip recycling, and particularly relates to a method for reprocessing and recycling waste chips.
Background
Based on the high-throughput sequencing basic principle, a universal sequencing joint is added at two ends of a free DNA fragment in the plasma of a pregnant woman, and a sequencing library which can be used for sequencing is constructed. And amplifying the sequencing library by using an emulsion PCR technology to form a sequencing template, and enriching the positive template to meet the sequencing requirement.
A semiconductor sequencing system is utilized to synthesize a complementary DNA strand by fixing a DNA strand in a micropore of a semiconductor chip and using single-stranded DNA as a template by DNA polymerase according to the base complementary principle. When a DNA chain extends for one base, one proton is released to cause local pH change, the ion sensor detects the pH change and converts a chemical signal into a digital signal, so that the base can be interpreted in real time, and the base sequence of each DNA fragment is finally obtained. The sequences are mapped to a human genome reference map using bioinformatic analysis, and the specific numerical proportion of the sample's free DNA sequences assigned to each chromosome is calculated. When the number of a certain chromosome of a fetus is increased, the number of the corresponding free DNA sequence is slightly increased, and the trace change can be detected through a semiconductor sequencing technology and bioinformatics data analysis, so that the information of the number of the chromosome is obtained, and the rapid prenatal auxiliary diagnosis of trisomy 21 syndrome, trisomy 18 syndrome and trisomy 13 syndrome is realized. However, in the case of using semiconductor sequencing, sequencing failure may occur due to reagents, samples, and the like, and the specific reasons are as follows: 1) in the step of enriching the template sequence, the 1M NaOH and the eluent are wrongly prepared, so that the double-stranded DNA cannot be subjected to alkali denaturation into single-stranded DNA, the base complementary pairing cannot be carried out, and the sequencing fails; 2) when the chip is cleaned, the isopropanol is not completely dried by nitrogen, residual isopropanol exists in the chip, so that polyclonal is higher, Low Quality is increased, Usable Reads are lower, and sequencing fails; 3) a sample loading sequencing step, wherein a sequencing reagent is wrongly prepared, so that isopropanol remains, the polyclone is higher, the Low Quality is increased, the Usable Reads is lower, and the sequencing fails; 4) adding errors of the annealing buffer solution and the sequencing primer, and setting errors of an annealing reaction program, so that the sequencing primer cannot be connected to the single-stranded DNA template, and the sequencing fails; 5) the enzyme reaction solution is wrongly prepared, sequencing polymerase necessary for base complementary pairing does not exist, and sequencing fails. In the existing method, after the semiconductor sequencing fails or fails, because the DNA in the used semiconductor chip is in a double-chain structure, the DNA cannot be accurately identified and sequenced, the used semiconductor chip can only be used for secondary detection, and the waste semiconductor chip is usually treated as waste, so that the medical detection cost is increased, and the resource waste is caused.
Disclosure of Invention
Aiming at the defects in the prior art, the invention aims to provide a method for reprocessing and reusing waste chips.
The technical scheme of the invention is summarized as follows:
a method for reprocessing and reusing waste chips comprises the following steps:
s1: washing the waste chip with AB solution for 3-5 times, wherein the amount of the AB solution is 80-150uL for each washing;
the AB solution was prepared from annealing buffer and nuclease-free water according to (0.75-1.25): 1 in a volume ratio;
s2: adding 200-250uL eluent into the chip hole twice, and incubating at 25 ℃ for 3-5 min;
the eluent is prepared from tween solution and NaOH solution according to the ratio of (6-8): 1 in a volume ratio;
s3: cleaning the chip with AB solution for 3-5 times, wherein the dosage of the AB solution is 80-150 uL;
s4: uniformly mixing 35-45uL sequencing primer and 30-35uL annealing buffer solution to prepare a 65-80uL annealing system, adding the annealing system into a chip hole, and then putting the chip hole into a pcr instrument for annealing;
s5: washing the chip with 80-150uL AB solution for 3-5 times, adding 60-70uL enzyme reaction solution into the chip hole, incubating at 25 deg.C for 4-8min, and sequencing;
the enzyme reaction solution is prepared from 55-63 mul AB solution and 5-7 mul sequencing polymerase.
Preferably, the waste chips contain 9-20 samples to be sequenced, the sequencing of which has failed last time.
Preferably, the total volume of the sample to be sequenced is 50-60. mu.L.
Preferably, the AB solution is prepared from annealing buffer and nuclease-free water in a ratio of 1: 1, and mixing the components according to the volume ratio.
Preferably, the eluent is prepared from tween solution and NaOH solution according to a ratio of 7: 1, and mixing the components according to the volume ratio.
Preferably, the mass concentration of the tween solution is 1-5%.
Preferably, the concentration of the NaOH solution is 0.8-1.2M.
Preferably, the annealing reaction conditions are as follows: denaturation at 93-97 deg.C for 1.5-3min, annealing at 36-38 deg.C for 1.5-3min, and storing at 18-22 deg.C.
Preferably, the annealing reaction conditions are as follows: denaturation at 95 deg.C for 2min, annealing at 37 deg.C for 2min, and storing at 20 deg.C.
Preferably, the enzyme activity of the sequencing polymerase is 10-20U/. mu.L.
The invention has the beneficial effects that:
1. the sequencing chip is cleaned by the AB solution, so that surface impurities such as polymerase, basic groups, generated phosphate ions and the like added in the last sequencing process can be washed clean, and the other useless single-stranded DNA and eluent generated in the S2 elution process can be removed.
2. The eluent is added into a chip hole, the chip hole is incubated for 3-5min at room temperature, double-stranded DNA is uncoiled into single-stranded DNA according to the principle of alkali denaturation, and then the single-stranded DNA is used for sequencing on a computer, so that the single-stranded DNA is continuously used as a template for base complementary pairing in the subsequent steps, and the aim of precise sequencing is fulfilled.
3. The annealing system is put into a chip and put into a pcr instrument for annealing, isopropanol volatilizes by high-temperature heating, the problem of sequencing failure caused by the residue of the isopropanol in the chip is solved, and meanwhile, a sequencing primer is connected to a single-stranded DNA template for later computer sequencing, so that the problem of sequencing failure caused by the addition of errors in the annealing system (annealing buffer solution and the sequencing primer) is solved.
4. The enzyme reaction liquid is added into the chip hole, incubated for 4-8min at room temperature of 25 ℃, and then incubated again after being processed in the steps S2 and S4, so that the problem of sequencing failure caused by wrong preparation of the enzyme reaction liquid is solved.
5. According to the invention, the waste chips which fail in sequencing are treated and utilized, so that the waste chips can be sequenced again, the cyclic regeneration of the waste chips is realized, the resources are saved, and the waste is avoided.
Drawings
FIG. 1 is a flow chart of a method for reprocessing and recycling waste chips;
FIG. 2 is a quality control analysis chart of the sequencing result of the waste chip before the treatment in comparative example 1;
FIG. 3 is a diagram of the quality control analysis of the sequencing results of the waste chips treated in example 1;
FIG. 4 is a quality control analysis chart of the sequencing result of the waste chip before the treatment in comparative example 2;
FIG. 5 is a diagram of the quality control analysis of the sequencing results of the waste chips processed in example 2;
FIG. 6 is a quality control analysis chart of the sequencing result of the waste chip treated in comparative example 3;
FIG. 7 is a diagram of the quality control analysis of the sequencing result of the waste chip processed in example 3.
Detailed Description
The present invention is further described in detail below with reference to examples so that those skilled in the art can practice the invention with reference to the description.
The invention provides a method for reprocessing and reusing waste chips, which comprises the following steps:
s1: washing the waste chip with AB solution for 3-5 times, wherein the amount of the AB solution is 80-150uL for each washing; the waste chips contain 9-20 samples to be sequenced, wherein the samples to be sequenced fail in the last sequencing, and the total volume of the samples to be sequenced is 50-60 mu L;
the AB solution was prepared from annealing buffer and nuclease-free water according to (0.75-1.25): 1 in a volume ratio; further, the AB solution was prepared from annealing buffer and nuclease-free water according to 1: 1 in a volume ratio;
s2: adding 200-250uL eluent into the chip hole twice, and incubating at 25 ℃ for 3-5 min;
the eluent is composed of tween solution and NaOH solution according to the ratio of (6-8): 1 in a volume ratio; further, the eluent is prepared by mixing 1-5% of Tween solution and 0.8-1.2M of NaOH solution according to the mass ratio of 7: 1 in a volume ratio;
s3: cleaning the chip with AB solution for 3-5 times, wherein the dosage of the AB solution is 80-150 uL;
s4: uniformly mixing 35-45uL sequencing primer and 30-35uL annealing buffer solution to prepare a 65-80uL annealing system, adding the annealing system into a chip hole, and then putting the chip hole into a pcr instrument for annealing; the annealing reaction conditions are as follows: denaturation at 93-97 deg.C for 1.5-3min, annealing at 36-38 deg.C for 1.5-3min, and storing at 18-22 deg.C; further, the annealing reaction conditions are as follows: denaturation at 95 deg.C for 2min, annealing at 37 deg.C for 2min, and storing at 20 deg.C;
s5: washing the chip with 80-150uL AB solution for 3-5 times, adding 60-70uL enzyme reaction solution into the chip hole, incubating at 25 deg.C for 4-8min, and sequencing;
the enzyme reaction solution is prepared from 55-63 mu L of AB solution and 5-7 mu L of sequencing polymerase with enzyme activity of 10-20U/mu L.
The validity of the detection result of the embodiment of the invention is subjected to quality control, and the following standards are required at the same time, so that the sequencing is successful, and the detection result is valid:
(1) the Uusable Reads number of each sample in the chip is not less than 3500000;
(2)loading>85%,
Usable Reads>60%,
polyclonal is controlled in the range of 25% -35%,
Low Quality<10%;
Total Reads(M)>75%。
the waste chips used in examples 1 to 3 were chips in a "general kit for sequencing reaction (semiconductor method)" after the on-machine test failed (kit cat # S10010-4C8R, specification: 4C 8R/set, available from Dougu Bao mu Hua Gene science and technology Co., Ltd.).
The waste chip selected in the embodiment 1 contains 16 samples to be sequenced, wherein the samples to be sequenced fail in the last sequencing, and the total volume of the samples to be sequenced is 50 mu L; the unprocessed waste chips are directly subjected to computer sequencing to serve as a comparative example 1.
Example 1
A method for reprocessing and reusing waste chips comprises the following steps:
s1: washing the sequencing failure waste chips containing 16 samples to be sequenced with a total volume of 50 mu L by using an AB solution for 3-5 times, wherein the using amount of the AB solution is 80 uL;
the AB solution was prepared from 500. mu.L of annealing buffer and 500. mu.L of nuclease-free water, i.e., 1: 1 in a volume ratio;
s2: adding 200uL of the eluent into the chip holes twice, and incubating at 25 ℃ for 3 min;
the eluent is prepared from 280 mu L of tween solution with the mass concentration of 3 percent and 40 mu L of 1M NaOH solution, namely, the eluent is prepared according to the following steps of 7: 1 in a volume ratio;
s3: cleaning the chip with AB solution for 3 times, wherein the dosage of the AB solution is 80 uL;
s4: after mixing 35uL sequencing primer and 30uL annealing buffer solution uniformly, preparing a 65uL annealing system, adding the annealing system into a chip hole, and then putting the chip hole into a pcr instrument for annealing, wherein the annealing reaction conditions are as follows: denaturation at 95 deg.C for 2min, annealing at 37 deg.C for 2min, and storing at 20 deg.C;
s5: washing the chip with 80uL AB solution for 3 times, adding 60uL enzyme reaction solution into the chip hole, incubating at 25 deg.C for 5min, and directly performing sequencing;
the enzyme reaction solution is prepared from 55 mu L of AB solution and 5 mu L of sequencing polymerase with the enzyme activity of 10U/mu L.
Table 1 shows the quality control results after resequencing in example 1 and comparative example 1:
TABLE 1
loading | Usable Reads | Polyclonal | Low Quality | Total Reads(M) | |
Example 1 | 94 | 51 | 38.9 | 16 | 71.3 |
Comparative example 1 | 94 | 76 | 23.4 | 0.3 | 105.8 |
Table 2 lists the Useable Reads number for each sample after resequencing example 1 and comparative example 1:
TABLE 2
Example 1 | Comparative example 1 | |
Sample 1 | 4631797 | 2381929 |
Sample 2 | 5496969 | 2935820 |
Sample 3 | 5328212 | 2970239 |
|
5525374 | 3040149 |
Sample 5 | 5930532 | 2863247 |
|
5849822 | 3272822 |
Sample 7 | 6303293 | 3458675 |
Sample 8 | 5111298 | 2648790 |
|
5150465 | 2587411 |
Sample 10 | 4941509 | 2380938 |
Sample 11 | 4796578 | 2575243 |
|
4722414 | 2579176 |
Sample 13 | 4941740 | 2475150 |
Sample 14 | 13369047 | 6439180 |
|
13085565 | 6095477 |
|
5046944 | 2214824 |
With reference to tables 1-2 and fig. 2-3 (fig. 2 is a quality control analysis chart of sequencing results of the waste chips before being processed in comparative example 1, and fig. 3 is a quality control analysis chart of sequencing results of the waste chips processed in example 1), it is known that the waste chips which are not processed in comparative example 1 fail to be subjected to on-machine sequencing and are unqualified to be detected, and the waste chips processed in example 1 are successfully sequenced, so that the detection results are valid.
The waste chip selected in the embodiment 2 contains 16 samples to be sequenced, wherein the samples to be sequenced fail in the last sequencing, and the total volume of the samples to be sequenced is 55 mu L; the unprocessed waste chips are directly subjected to computer sequencing to serve as a comparative example 2.
Example 2
S1: washing waste chips containing 16 samples to be sequenced with a total volume of 55 mu L and failed in sequencing by using an AB solution for 4 times, wherein the using amount of the AB solution is 100uL in each washing;
the AB solution was prepared from 500. mu.L of annealing buffer and 500. mu.L of nuclease-free water, i.e., 1: 1 in a volume ratio;
s2: adding 200uL of eluent into the chip hole twice, and incubating at 25 ℃ for 4 min;
the eluent is prepared from 280 mu L of tween solution with the mass concentration of 4% and 40 mu L of 1M NaOH solution, namely, the eluent is prepared according to the following steps of 7: 1 in a volume ratio;
s3: cleaning the chip with AB solution for 4 times, wherein the dosage of the AB solution is 100 uL;
s4: after 40uL sequencing primer and 30uL annealing buffer solution are uniformly mixed, a 70uL annealing system is prepared, then the annealing system is added into a chip hole and then put into a pcr instrument for annealing, and the annealing reaction conditions are as follows: denaturation at 95 deg.C for 2min, annealing at 37 deg.C for 2min, and storing at 20 deg.C;
s5: washing the chip with 100uL AB solution for 4 times, adding 65uL enzyme reaction solution into the chip hole, incubating at 25 deg.C for 5min, and sequencing;
the enzyme reaction solution is prepared from 59 mu L of AB solution and 6 mu L of sequencing polymerase with the enzyme activity of 15U/mu L.
Table 3 shows the quality control results after resequencing in example 2 and comparative example 2:
TABLE 3
loading | Usable Reads | Polyclonal | Low Quality | Total Reads(M) | |
Example 2 | 94 | 68 | 31.7 | 0.3 | 93.7 |
Comparative example 2 | 94 | 55 | 36.8 | 13.6 | 75.5 |
Table 4 lists the Useable Reads number for each sample after resequencing example 2 and comparative example 2:
TABLE 4
By combining tables 3-4 and fig. 4-5 (fig. 4 is a quality control analysis chart of sequencing results of the waste chips before being processed in comparative example 2, and fig. 5 is a quality control analysis chart of sequencing results of the waste chips processed in example 2), it is known that the waste chips which are not processed in comparative example 2 fail to be subjected to on-machine sequencing and are unqualified to be detected, and the waste chips processed in example 2 are successfully sequenced, so that the detection results are effective.
Example 3 the waste chip selected contains 16 samples to be sequenced which have failed the sequencing last time
Example 3
S1: washing waste chips containing 16 samples to be sequenced with a total volume of 60 mu L and failed in sequencing by using an AB solution for 5 times, wherein the using amount of the AB solution is 150uL in each washing;
the AB solution was prepared from 500. mu.L of annealing buffer and 500. mu.L of nuclease-free water, i.e., 1: 1 in a volume ratio;
s2: adding 250uL of eluent into the chip holes twice, and incubating at 25 ℃ for 5 min;
the eluent is prepared from 280 mu L of Tween solution with the mass concentration of 5% and 40 mu L of 1M NaOH solution, namely, the eluent is prepared from the following components in percentage by mass according to the weight ratio of 7: 1 in a volume ratio;
s3: cleaning the chip with AB solution for 5 times, wherein the dosage of the AB solution is 150 uL;
s4: after uniformly mixing 45uL sequencing primer and 35uL annealing buffer solution, preparing an 80uL annealing system, adding the annealing system into a chip hole, and then putting the chip hole into a pcr instrument for annealing, wherein the annealing reaction conditions are as follows: denaturation at 95 deg.C for 2min, annealing at 37 deg.C for 2min, and storing at 20 deg.C;
s5: washing the chip with 150uL AB solution for 5 times, adding 70uL enzyme reaction solution into the chip hole, incubating at 25 deg.C for 8min, and sequencing;
the enzyme reaction solution is prepared from 63 mu L of AB solution and 7 mu L of sequencing polymerase with the enzyme activity of 20U/mu L.
Comparative example 3 is the same as example 3: except that comparative example 3 did not have the steps of S2 and S3, i.e., no incubation with eluent.
Table 5 shows the quality control results after resequencing in example 3 and comparative example 3:
TABLE 5
loading | Usable Reads | Polyclonal | Low Quality | Total Reads(M) | |
Example 3 | 96 | 75 | 25.2 | -0.1 | 106.1 |
Comparative example 3 | 96 | 54 | 39.3 | 11.3 | 76.2 |
Table 6 lists the Useable Reads number for each sample after resequencing example 3 and comparative example 3:
TABLE 6
With reference to tables 5 to 6 and fig. 6 to 7 (fig. 6 is a quality control analysis chart of the sequencing result of the waste chip treated in comparative example 3, and fig. 7 is a quality control analysis chart of the sequencing result of the waste chip treated in example 3), it is known that, since the eluent is not used in the DNA double strand unwinding treatment in comparative example 2, the sequencing on the machine fails, the detection result is invalid, and the sequencing of the waste chip treated in example 3 succeeds, and the detection result is valid.
While embodiments of the invention have been disclosed above, it is not limited to the applications listed in the description and the embodiments, which are fully applicable in all kinds of fields of application of the invention, and further modifications may readily be effected by those skilled in the art, so that the invention is not limited to the specific details without departing from the general concept defined by the claims and the scope of equivalents.
Claims (10)
1. A method for reprocessing and reusing waste chips is characterized by comprising the following steps:
s1: washing the waste chip with AB solution for 3-5 times, wherein the amount of the AB solution is 80-150uL for each washing;
the AB solution was prepared from annealing buffer and nuclease-free water according to (0.75-1.25): 1 in a volume ratio;
s2: adding 200-250uL eluent into the chip hole twice, and incubating at 25 ℃ for 3-5 min;
the eluent is prepared from tween solution and NaOH solution according to the ratio of (6-8): 1 in a volume ratio;
s3: cleaning the chip with AB solution for 3-5 times, wherein the dosage of the AB solution is 80-150 uL;
s4: uniformly mixing 35-45uL sequencing primer and 30-35uL annealing buffer solution to prepare a 65-80uL annealing system, adding the annealing system into a chip hole, and then putting the chip hole into a pcr instrument for annealing;
s5: washing the chip with 80-150uL AB solution for 3-5 times, adding 60-70uL enzyme reaction solution into the chip hole, incubating at 25 deg.C for 4-8min, and sequencing;
the enzyme reaction solution is prepared from 55-63 mul AB solution and 5-7 mul sequencing polymerase.
2. The method of claim 1, wherein the waste chips contain 9-20 samples to be sequenced that have failed the last sequencing.
3. The method for reprocessing and reusing waste chips according to claim 2, wherein the total volume of the sample to be sequenced is 50-60 μ L.
4. The method of claim 1, wherein the AB solution is prepared from an annealing buffer and nuclease-free water in a ratio of 1: 1, and mixing the components according to the volume ratio.
5. The method of claim 1, wherein the eluent is prepared from tween solution and NaOH solution according to a ratio of 7: 1, and mixing the components according to the volume ratio.
6. The method for reprocessing and recycling the waste chips according to any of claims 1 or 5, wherein the mass concentration of the Tween solution is 1-5%.
7. The method for reprocessing and recycling waste chips according to any of claims 1 or 5, wherein the concentration of the NaOH solution is 0.8-1.2M.
8. The method for reprocessing and reusing waste chips according to claim 7, wherein the annealing reaction conditions are as follows: denaturation at 93-97 deg.C for 1.5-3min, annealing at 36-38 deg.C for 1.5-3min, and storing at 18-22 deg.C.
9. The method for reprocessing and reusing waste chips according to claim 8, wherein the annealing reaction conditions are as follows: denaturation at 95 deg.C for 2min, annealing at 37 deg.C for 2min, and storing at 20 deg.C.
10. The method for reprocessing and reusing waste chips according to claim 1, wherein the enzyme activity of the sequencing polymerase is 10-20U/μ L.
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WO2020258037A1 (en) * | 2019-06-25 | 2020-12-30 | Ardent Biomed Guangdong Co., Ltd | Apparatus and method for high throughput parallel nucleic acid sequencing on surfaces of microbeads |
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