Method and apparatus for detecting mutation of somatic cells
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A technology for detecting bodies and cells, applied in the field of bioinformatics, to achieve the effects of low cost, convenient transplant operation, and easy operation
Active Publication Date: 2017-01-04
BGI GUANGZHOU MEDICAL LAB CO LTD +1
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[0002] At present, in clinical tumor diagnosis, histocytological examination is used as the gold standard, and biochemical examination methods and physical examination (X-ray, B-ultrasound, CT, MRI, PET-CT, etc.) are used as auxiliary means. Limitation, that is, only lumps larger than 0.5 cm can be found
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Embodiment 1
[0039] After obtaining the off-machine data of BGISEQ-100 sequencing, such as image 3 As shown, generally include the following steps:
[0040] 1. Alignment with the reference genome
[0041] Use the tmap tool to align the sequencing data to the reference genome to obtain accurate alignment results. The tmap tool comes from: https: / / github.com / iontorrent / TS / tree / master / Analysis / TMAP
[0042] 2. Remove PCR duplicates in the comparison results
[0043] The BamDuplicates tool was used to remove PCR duplicates from the results (bam format) compared with the tmap tool. Among them, the BamDuplicates tool comes from Ion Torrent Systems, Inc.
[0044] 3. Statistics and quality control
[0045] Count the ratio of the data volume of the target area to the total data volume, the average sequencing depth of the target area, the coverage rate of the target area, etc., and generate a series of quality control indicators to judge the quality of the sequencing data.
[0046] 4. Somatic...
Embodiment 2
[0075] The cancer tissue sample and blood cell sample (sample name: TJ0002) of a female patient with colorectal cancer were obtained from the hospital for target region capture and sequencing on the BGISEQ-100 platform. BamDuplicates deduplication, quality control (QC), Somatic mutation detection, mutation annotation, report generation steps, and finally obtain the patient's individualized tumor detection report.
[0076] The process method included in the first embodiment is integrated into the software Oseq-T, and the operating environment of the software is a Unix / Linux operating system, which runs through the Unix / Linux command line.
[0077] The specific operation steps are as follows:
[0078] Enter the following command in the LINUX operating system computer terminal to invoke the software:
[0080] Oseq-T command line parameters are shown in Table 1 parameter description.
[0081] Table 1
[0082] ...
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Abstract
The present invention discloses a method for detecting the mutation of somatic cells. The method comprises: obtaining first sequencing data, wherein the first sequencing data is the determined data of the nucleic acid sequence of a sample to be detected; comparing the first sequencing data with a reference sequence to obtain a first comparing result; based on the first comparing result, recognizing a mutation site, wherein the mutation site comprises at least one of SNP and INDEL; and comparing the difference of the support read fragment number of the mutation site to the corresponding mutation site of a normal control sample to obtain the mutation site having significant difference, wherein the mutation site having significant difference comprises the mutation site having the statistically significant difference. The invention further discloses an apparatus for detecting the mutation of somatic cells. With the method and/or apparatus of the present invention, the accuracy and the sensitivity of the somatic cell mutation detection are high.
Description
technical field [0001] The invention relates to the field of biological information, specifically, the invention relates to a method for detecting somatic cell mutation and a device for detecting somatic cell mutation. Background technique [0002] At present, in clinical tumor diagnosis, histocytological examination is used as the gold standard, and biochemical examination methods and physical examination (X-ray, B-ultrasound, CT, MRI, PET-CT, etc.) are used as auxiliary means. Limitations, that is, only tumors larger than 0.5 cm can be found. When the tumor grows asymptomatic and gradually grows to the size perceived by itself, some tumors are already in the middle and advanced stages, and some tumors have already metastasized, and many patients have lost the best treatment period. Since the variation of the gene coding region is the main cause of disease, some specific gene coding regions of the individual genome, that is, the specific exon region, can be extracted and s...
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