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Method and device for detecting instability of microsatellite locus

A technology of microsatellite sites and instability, applied in the field of bioinformatics, can solve the problems of false positives and false negatives, and achieve the effect of increasing the number of detected sites and reducing the probability of false positives and false negatives.

Active Publication Date: 2017-08-18
天津诺禾致源生物信息科技有限公司
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  • Abstract
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  • Claims
  • Application Information

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Problems solved by technology

However, this method often has false positives and false negatives due to the limitation of the number of loci.

Method used

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  • Method and device for detecting instability of microsatellite locus
  • Method and device for detecting instability of microsatellite locus
  • Method and device for detecting instability of microsatellite locus

Examples

Experimental program
Comparison scheme
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Embodiment approach

[0025] According to a typical embodiment of the present invention, the method is used to detect the instability of microsatellite sites in colorectal cancer.

[0026] The inventors of the present invention have screened out 43 microsatellite loci that are highly correlated with colorectal cancer, using these loci to judge the difference between pathological samples and control samples, and add statistical tests to determine the microsatellite instability of the samples , with high sensitivity and high specificity.

[0027] Regions of 43 microsatellite loci highly associated with colorectal cancer include:

[0028]

[0029]

[0030]

[0031] Preferably, the sample DNA includes pathological tissue sample DNA and control sample blood white blood cell DNA.

[0032] According to a typical implementation of the present invention, combined with the target region capture technology, high-throughput sequencing technology, combined with the determined information of 43 microsa...

Embodiment 1

[0043] In the first part of this embodiment, colorectal cancer pathological samples with known stable microsatellite sites and corresponding control samples are to be tested.

[0044] In the embodiment of the invention, the main reagent supplies are commercially available, and the information is as follows:

[0045]

[0046]

[0047] In this embodiment, the operation steps are as follows:

[0048] 1. Extract DNA (pathological tissue sample DNA and control sample blood leukocyte DNA), and use a fluorescence quantitator (Qubit) to quantify, the concentration is 3.8ng / ul, and the volume is 130ul; Make the DNA fragment size between 200-400bp, and then use agarose gel electrophoresis to detect whether the fragment size meets the requirements.

[0049] 2. Purify the fragmented DNA sample with magnetic beads first, and then perform end repair and 3' end adenylation. The system configuration is shown in Table 1. The basic steps are as follows: first incubate at 20°C for 30 minu...

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Abstract

The invention discloses a method and device for detecting instability of a microsatellite locus, wherein the method comprises the steps of S1, treating a sample; S2, processing data, to be specific, using comparison software to compare determined sequences to a reference genome to obtain a comparison file, allowing non-matched sequences to form soft cut-off, ranking according to comparison positions, and using the software samtools to establish an index; S3, detecting the instability of the microsatellite locus, to be specific, using locus coverage rates having significant differences to determine the microsatellite instability of the sample. By using the method and device in connection with high-throughput sequencing techniques for capturing a target area, the quantity of loci for detection can be increased greatly; differences between a pathological sample and a control sample are judged, the microsatellite stability of the sample is determined through the differences in connection with statistical testing, and chances for false positives and false negatives to occur in the detection of microsatellite locus stability in the prior art are slimmed.

Description

technical field [0001] The invention relates to the technical field of bioinformatics, in particular to a method and device for detecting instability of microsatellite sites. Background technique [0002] There are simple repeat sequences composed of uniformly distributed tandem repeats of 2 to 6 nucleotides in the human genome, that is, microsatellite sites, and some colorectal cancer patients will have insertions or deletions in specific base repeat sequences. The phenomenon is related to the occurrence and development of tumors, but this phenomenon cannot be used as the basis for disease diagnosis and disease risk judgment. In the prior art, the detection usually includes: extracting DNA from the sample, capturing tumor-related genes, performing high-throughput sequencing, and combining the sequence information of microsatellite sites to detect the stability of microsatellite sites in colorectal cancer samples . [0003] At present, the commonly used microsatellite site...

Claims

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Application Information

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IPC IPC(8): C12Q1/68G06F19/22
CPCC12Q1/6869G16B30/00C12Q2535/122C12Q2525/151
Inventor 单光宇冉霞臧晚春王棪成岗蒋智
Owner 天津诺禾致源生物信息科技有限公司
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