Method for evaluating HRD score based on low-depth WGS

A technology of depth and calculation method, applied in the fields of genomics, instrumentation, sequence analysis, etc., can solve the problems of high accuracy and high cost

Active Publication Date: 2021-08-13
北京橡鑫生物科技有限公司 +3
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

The advantage is high accuracy; the dis...

Method used

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  • Method for evaluating HRD score based on low-depth WGS
  • Method for evaluating HRD score based on low-depth WGS
  • Method for evaluating HRD score based on low-depth WGS

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0088] Example 1 Preprocessing of low-depth WGS data processing

[0089] 1. Use the fastp software to remove the joints on the reads from the low-depth WGS off-machine data;

[0090] 2. Compare the processed off-machine data with the reference genome of the whole human genome through bwa software, and obtain the first comparison file in bam format;

[0091] 3. Correct the base quality value of the first comparison file through GATK software;

[0092] 4. Use picard software to remove duplicate reads from the corrected first comparison file, and obtain a second comparison file that does not contain duplicate reads. The format of the file is bam format.

[0093] 5. Divide the whole human genome into windows of 100Kbp size according to the order of arrangement.

Embodiment 2

[0094] Example 2 Construction of DR fragments

[0095] 1) Taking the reads in the second comparison file in Example 1 as the basic unit, count the number of reads falling in each window in Example 1, as the reads count of the window, and record it as RC i , i is the order of the windows divided in the whole genome according to the order of arrangement, and i is 1, 2, 3....

[0096] 2) Count the GC base content of each window, merge adjacent windows with the same GC content into one group, and record the jth group as W j , the number of windows contained in group j is denoted as M j, the kth window contained in the jth group is recorded as W kj , j, k are 1,2,3....;

[0097] 3) Calculate W j The median value RC of , denoted as RC j , and the average RC of the sample to be tested as a whole, denoted as RC p , by the following formula for RC i Make corrections:

[0098]

[0099] i=M 1 +M 2 +M 3 ...+M （j-1） +k;

[0100] 4) Process the low-depth WGS data of 30 healt...

Embodiment 3

[0103] Example 3 Calculation of copy number

[0104] Count the median value of DR in each DR segment, as the DR value of the DR segment, recorded as DR q , calculate the copy number of the DR segment, denoted as C q , the calculation formula is:

[0105] .

[0106] In this embodiment, the internal cause of the patient's cancer can be preliminarily understood through the calculation of Cq (copy number).

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Abstract

The invention belongs to the technical field of gene detection, and particularly discloses a method for evaluating an HRD score based on low-depth WGS, and the method comprises the steps: processing low-depth WGS offline data of a to-be-detected sample; executing any one or more of the following three steps: step 1, establishing a calculation method of genome heterozygosity deficiency LOH to obtain an HRD-LOH score; step 2, establishing a calculation method of telomere allele imbalance TAI, and obtaining an HRD-TAI score; step 3, establishing a calculation method of the large fragment migration LST, and obtaining an HRD-LST score. The method provides by the invention has at least one of the following beneficial effects: the method for evaluating the HRD score based on the low-depth WGS performs analysis on the basis of data formed by low-depth WGS, which reduces cost and facilitates large-scale application.

Description

technical field [0001] This application belongs to the technical field of gene detection, and more specifically, it relates to a method for evaluating HRDscore based on low-depth WGS. Background technique [0002] DNA double strand breaks (double strand breaks) is a type of DNA damage, which can lead to chromosome breakage and rearrangement in severe cases. Since there is no complementary strand to repair, the DNA sequence is difficult to recover, resulting in loss of genetic information. Strand breaks require homologous recombination repair. If the homologous recombination repair ability is lost, HRD will occur, which will lead to the loss of genome stability, and DNA damage will easily accumulate under the condition of genome instability, and this vicious circle will lead to cancer. HRD has very important guiding significance for the use of platinum or PARP inhibitors. [0003] HRD is generally caused by gene variation or epigenetic variation in the homologous recombinat...

Claims

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Application Information

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IPC IPC(8): G16B20/20G16B30/10
CPCG16B20/20G16B30/10
Inventor 楼峰刘凯张萌萌郭璟孙宏曹善柏
Owner 北京橡鑫生物科技有限公司
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