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Method and device for detecting nucleotide variation based on single molecule sequencing
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A technology for single nucleotide variation and ordering of single nucleotides, applied in the field of nucleotide variation detection based on single molecule sequencing, can solve the problems of discomfort, screening SNV/SNP correlation, and high cost
Pending Publication Date: 2021-07-30
深圳思勤医疗科技有限公司
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Problems solved by technology
At present, the detection of SNP / SNV is based on high-depth sequencing platforms and complex nucleic acid sequencing data algorithmmutation detection, but the cost is generally too high, it is not suitable for large sample screening, and it is not suitable for large sample screening SNV / SNP and disease association sexual issues
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Embodiment 1
[0083] Sample processing and library sequencing. The sample can be any biological sample such as tissue, plasma, saliva, etc., using conventional kits for DNA extraction, library building, and sequencing. The following is only an example of extraction, library building, and sequencing based on blood samples.
[0085] a) Prepare the instruments, reagents, and consumables required for the experiment, and the high-speed refrigerated centrifuge should be pre-cooled to 4°C in advance.
[0086] b) If the peripheral blood sample is collected with an EDTA anticoagulant tube, put it in a 4°C refrigerator immediately after drawing the blood, and conduct plasma separation within 2 hours. If the peripheral blood sample is collected with free nucleic acid preservation tubes such as Streck tubes, it can be placed at room temperature, and plasma separation should be performed within the time specified in the blood collection tube instructions.
[0087] c) Rec...
Embodiment 2
[0197] (1) After filtering out low-quality reads, use the alignment software (bwa) to align these sequencing reads to the human reference genome (hg19).
[0198] (2) Filter the comparison results, first select the normal pairing, and then filter out the reads on the comparison:
[0199] a) Any reads comparison quality value <30,
[0200] b) Duplicate reads, and supplementary alignment reads;
[0201] c) The alignment results include insertions and deletions (InDel), the reads are aligned after 5' or 3' end splicing (softclipping / hard clipping), and the middle of the reads contains a gap (skipped region from thereference), the alignment results include The number of base mismatches is >2.
[0202] (3) Take out the comparison results of paired reads at the same time; for the overlapping region of paired reads, such as figure 1 : For the overlapping region of readsA_1 and readsA_2, perform statistics according to the following method to find single nucleotide variation;
[02...
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Abstract
The invention provides a method for determining single nucleotide variation in a nucleic acid sample. The method comprises the following steps: performing bidirectional low-depth sequencing on the nucleic acid sample to obtain sequencing data of the nucleic acid sample, wherein the sequencing data comprises a forward sequencing read segment and a reverse sequencing read segment of the nucleic acid sample; on the basis of the sequencing data, comparing the forward sequencing read section and the reverse sequencing read section to obtain an overlapping region of the sequencing read section; and obtaining the mononucleotide variation based on the overlapping region. The method can be used for detecting and screening the single nucleotide variation in the population based on large sample data, and has the advantages of low cost and high efficiency.
Description
technical field [0001] The invention relates to the field of gene sequencing, in particular to a method and device for detecting nucleotide variation based on single-molecule sequencing. Background technique [0002] SNP generally refers to single nucleotide polymorphism. Single nucleotide polymorphism mainly refers to the DNA sequence polymorphism caused by the variation of a single nucleotide at the genome level. It is the most common type of heritable variation in humans, accounting for more than 90% of all known polymorphisms. SNPs are widespread in the human genome, with an average of 1 in every 300 base pairs, and it is estimated that the total number can reach 3 million. These SNPs are closely related to human life. For example, different genotypes of some sites of alcoholdehydrogenase and acetaldehydedehydrogenase determine whether the person can drink alcohol and produce alcoholic liver; different genotypes also affect the basic probability of occurrence, For e...
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