Method and system for detecting HLA heterozygosity deficiency
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A technology for loss of heterozygosity and balance detection, applied in the field of bioinformatics, can solve problems such as HLA gene deletion
Active Publication Date: 2021-06-01
深圳裕策生物科技有限公司
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[0005] The main technical problem to be solved by the present invention is how to determine whether it is amplification or deletion after accurately obtaining the unbalanced mutation of HLA gene
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Embodiment 1
[0128] In this example, the samples used were taken from patients with nasopharyngeal and throat cancer, the tumor samples were taken from cancer tissues, and the control samples were taken from the blood leukocytes of the same patient, specifically the samples from patients with high TMB (tumor mutation burden) who were ineffective in immunotherapy T17121390189- KY438-VS-B17120989463-KY438 (denoted as sample_1_1) and patient sample F17120989201-KY438-VS-B17120989370-KY438 (denoted as sample_1_2) from patients with effective immunotherapy and high TMB.
[0129] The specific steps for the detection of sample T17121390189-VS-B17120989463-KY438 in this example are as follows:
[0130] 1. The Agilent WES SureSelect Human All Exon V6 method was used for sequencing, and the sequencing platform was Illumina NextSeq 2000.
[0131] The Agilent WES SureSelect Human All Exon V6 method refers to the following website:
[0149] The method involved in this embodiment and the software version used are the same as those in Embodiment 1.
[0150] The sample number of this embodiment is DN1902862AZZAA02-VS-DN1902862XYZAA02 (denoted as sample_2_1), which was taken from a patient with nasopharyngeal and throat cancer, the tumor sample was taken from cancer tissue, and the control sample was taken from blood leukocytes of the same patient.
[0151] The sample test results of this embodiment are as follows:
[0152] 1. Obtain the copy number variation result of the sample, and there is no copy number deletion in the HLA region.
[0153] 2. Here, the p-value of the HLA-A gene is equal to 2.27E-04, which is less than the threshold value of 0.001, indicating that there is an imbalance between the two genotypes of the HLA-A gene.
[0154] 3. Combine the above two results to judge the HLA allele amplification / deletion status, and judge it as non-HLA-LOH.
[0155] Table 2 below is the information of the sa...
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Abstract
The invention provides a method and a system for detecting HLA (human leukocyte antigen) heterozygosity deficiency. The method comprises the following steps: data acquisition: acquiring sequencing data of a tumor sample and a control sample; hLA typing detection: detecting HLA molecular types of the tumor sample and the contrast sample; HLA allele imbalance detection: comparing the sequencing data with an HLA typing result to obtain an HLA allele imbalance detection result; copy number variation detection: performing copy number variation detection on all the target areas to obtain a copy number variation detection result of the HLA gene loci; and HLA heterozygosity deletion judgment: judging whether HLA heterozygosity deletion exists or not according to an HLA allele imbalance detection result and a copy number variation detection result. According to the invention, the sequence information on the HLA gene is used independently, and the sequence information near the HLA gene is also combined, so that an accurate HLA LOH result is obtained.
Description
technical field [0001] The invention relates to the field of bioinformatics, in particular to a method and system for detecting HLA heterozygosity loss. Background technique [0002] The full name of HLA is Human Leukocyte Antigen, that is, human leukocyte antigen, which is the expression product of human major histocompatibility complex (MHC), which is the most complex polymorphic system known in the human body. HLA is a highly polymorphic alloantigen, and its chemical essence is a kind of glycoprotein, which is composed of an α heavy chain (glycosylated) and a β light chain non-covalently combined. The amino terminal of the peptide chain is outward (accounting for about 3 / 4 of the whole molecule), the carboxyl terminal penetrates into the cytoplasm, and the middle hydrophobic part is in the cell membrane. HLA is located on the short arm of chromosome 6, and the specific position can be represented by 6p21.31. HLA contains a series of closely linked loci, which are highly...
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