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Detection analysis method for breast cancer susceptibility gene heritable variation point

A susceptibility gene and genetic variation technology, applied in the field of biological information data processing, can solve problems such as poor readability, numerous software, and long analysis time

Inactive Publication Date: 2017-03-22
SHANGHAI PERSONAL BIOTECH
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  • Abstract
  • Description
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AI Technical Summary

Problems solved by technology

[0005] 1. The analysis steps are cumbersome: from the off-machine of sequencing data, to further quality control and subsequent analysis process, there are many software involved, and the analysis process is cumbersome
[0006] 2. The analysis cycle is long: some analysis steps in the traditional analysis process have certain deficiencies in algorithm and data structure processing, which makes the analysis time relatively long
[0007] 3. The readability of the results is not good: in the general analysis process, there are only some simple chart files in the results, and there are still many data information that are not effectively presented

Method used

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  • Detection analysis method for breast cancer susceptibility gene heritable variation point
  • Detection analysis method for breast cancer susceptibility gene heritable variation point
  • Detection analysis method for breast cancer susceptibility gene heritable variation point

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Embodiment Construction

[0057] In order to achieve the purpose of the present invention, the present invention includes five main steps, ① data quality control → ② sequence comparison → ③ variation detection → ④ variation annotation → ⑤ statistical report, as attached figure 1 As shown, the specific steps and methods are as follows:

[0058] 1. Data quality control steps

[0059] 1.1 First use FastQC to check the sequencing quality, including: base quality, GC content, sequence length distribution, sequence repetition level, etc.; to guide subsequent further quality control. In addition to the conventional program, the present invention utilizes the perl language to develop a faster and more efficient quality statistics program. The traditional program reads the sequencing data line by line, and the speed is slow. This program uses the special header file of the sequencing data to read by sequence module, and combines the double hash table to optimize the data structure, and the speed is faster than t...

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Abstract

The invention discloses a detection analysis method for a breast cancer susceptibility gene heritable variation point. The detection analysis method is characterized by comprising the following steps: (1) a data quality control step; (2) a sequence alignment step; (3) variation detection step; (4) a variation annotation step; and (5) a statistical report step. The detection analysis method has the advantages of integration, high efficiency and visualization.

Description

technical field [0001] The invention belongs to the technical field of biological information data processing, and in particular relates to a method for detecting and analyzing genetic variation sites of breast cancer susceptibility genes. Sequencing, detection and analysis of SNP and INDEL mutation sites of breast cancer susceptibility genes BRCA1 and BRCA2. Background technique [0002] As a very important group in social and family life, women are under unprecedented pressure from work and life. Coupled with changes in environmental factors, many female diseases are becoming younger, such as breast cancer. Its pathogenesis is often related to genetics, about 5-10% of breast cancers are related to gene mutations, and these mutations can be passed on from parents to the next generation. Among them, BRCA1 and BRCA2 gene mutations are the most common in breast cancer. Women with a BRCA1 gene mutation have a 55-65% lifetime chance of developing breast cancer, and women with ...

Claims

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Application Information

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IPC IPC(8): G06F19/00G06F19/20
CPCG16B25/00G16H50/30
Inventor 刘港飚朱月艳孙子奎
Owner SHANGHAI PERSONAL BIOTECH
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