Method and device for identifying and eliminating false positive in nucleic acid variation detection

A technology for mutation detection and nucleic acid mutation, applied in the fields of instrumentation, genomics, proteomics, etc., can solve problems such as affecting accuracy, increasing the workload of manual screening of false positive sites, and alignment errors in sequence comparison software, achieving The effect of improving accuracy

Active Publication Date: 2019-04-19
SHENZHEN HAPLOX BIOTECH
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Problems solved by technology

However, due to the influence of the existing sequencing library construction technology and sequencing technology, a large number of sequencing errors will be introduced during the sequencing process; at the same time, sequence comparison software may also generate alignment errors; thus

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  • Method and device for identifying and eliminating false positive in nucleic acid variation detection
  • Method and device for identifying and eliminating false positive in nucleic acid variation detection

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Embodiment

[0066] The method for identifying and eliminating false positives in nucleic acid variation detection in this example includes the following steps:

[0067] a, Step of reading mutation information: read the result file generated by the mutation detection software, the main information includes the mutation position, the base type at this position on the reference genome, and the variant base type at this position in the sample;

[0068] b, Gene fragment filtering step: Read the comparison file generated by comparing the off-machine sequence of the sample to be tested to the human reference gene, screen and obtain the read pair comparison results covered by each variant site, and then filter out the comparison results with the reference genome Compare read pairs with more than 2 mismatches, filter out read pairs with mutation base quality values ​​less than 25, and filter out read pairs with inconsistent bases at mutation positions;

[0069] c, Judgment step of mutation site: j...

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Abstract

The invention discloses a method and a device for identifying and eliminating false positive in nucleic acid variation detection. The method of the invention comprises the steps of reading a variationdetecting software result file of a to-be-detected sample; reading a comparison file of a sequence read after eliminating PCR repetitions, and obtaining a read pair comparison result which is coveredby each variation site; determining whether the variation site is in a read pair overlap area of the DNA molecule, and performing analysis and statistics on the read pair which is covered by each abrupt change; performing statistics on each molecule and the read which support the abrupt change, and marking a characteristic which can be used for filtering the abrupt change; and filtering the variation site based on the characteristic value. According to the method of the invention, nucleic acid variation detecting results are filtered according to the distribution characteristic of nucleic acid variation false positive sites and true positive sites; not only can the false positive sites be effectively eliminated, but also accuracy of a nucleic acid variation detecting result is improved.

Description

technical field [0001] The present application relates to the field of nucleic acid variation detection, in particular to a method and device for identifying and eliminating false positives in nucleic acid variation detection. Background technique [0002] Nucleic acid variation or gene mutation refers to the change of base pair composition or arrangement order in the structure of the gene, including single nucleotide site variation (abbreviated SNV), insertion-deletion variation (abbreviated INDEL), frameshift mutation, etc. Nucleic acid variation is a ubiquitous phenomenon in nature. For the human genome, nucleic acid variation usually causes physiological or pathological changes; therefore, nucleic acid variation detection and related research are the focus of human genome research. [0003] At present, nucleic acid variation detection is mainly through high-throughput sequencing, and the sequencing results are compared with the reference genome to obtain nucleic acid var...

Claims

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Application Information

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IPC IPC(8): G16B30/00G16B20/50
Inventor 周衍庆汪周阳方文张实唯
Owner SHENZHEN HAPLOX BIOTECH
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