Chromosome structure variation identification method taking breakpoint as center

A technology of structural variation and chromosome, applied in the field of nucleic acid sequencing, can solve the problems of low specificity of detection results, low detection sensitivity and specificity, and omissions

Active Publication Date: 2021-04-20
上海思路迪医学检验所有限公司
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Problems solved by technology

The difficulty of the former is that the assembly process consumes a lot of resources and the accuracy of the assembly result is low, resulting in low detection sensitivity and specificity. The difficulty of the latter is that without the reads with secondary alignment results, it is impossible to identify the structural variation. Specific breakpoints, as well as the fact that this method misses some reads that support structural variation, and because a large number of false positive reads with secondary alignment results will inevitably be generated during...

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  • Chromosome structure variation identification method taking breakpoint as center
  • Chromosome structure variation identification method taking breakpoint as center
  • Chromosome structure variation identification method taking breakpoint as center

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Embodiment

[0066] A total of 604 FFPE samples prepared from surgically resected tissues of patients with solid tumors were collected, and DNA and RNA were extracted to build a library. The DNA library was captured and subjected to next-generation sequencing, and the RNA library was subjected to whole-transcriptome sequencing. The DNA sequence and RNA sequence of each sample were obtained by sequencing. The DNA sequence was compared to the human reference genome version hg19 by BWA, and the RNA sequence was compared to the transcript corresponding to the human reference genome version hg19 by STAR. The BAM file obtained by comparing the sample DNA sequences is used as the input file of the present invention. Any published DNA fusion detection software can be used as the DNA detection result comparison method of the present invention. A specific available DNA fusion detection software such as GeneFuse can be used as a comparison method of the present invention. As the second comparison me...

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Abstract

The invention relates to a chromosome structure variation identification method taking a breakpoint as a center. Specifically, the invention relates to a computer-implemented method for identifying chromosome structural variation by taking a breakpoint as a center. The invention also relates to a computer system or device for implementing the method, and a computer readable medium storing a computer program capable of implementing the method.

Description

technical field [0001] The invention relates to the field of nucleic acid sequencing. The invention relates to a method for identifying chromosome structure variation centered on breakpoints. In particular, the present invention relates to a computer-implementable breakpoint-centric method for identifying structural variations in chromosomes. The invention also relates to a computer system or apparatus for implementing the method, and a computer-readable medium storing a computer program capable of implementing the method. Background technique [0002] Chromosomal structural variation refers to changes in the original genome sequence and structure of chromosomes, such as insertions, deletions, inversions, translocations, etc., resulting in new chromosome structures. Chromosomal structural variation often occurs in tumor cells, such as EML4-ALK gene fusion phenomenon, EGFR kinase domain duplication, etc. Detection of chromosomal structural variation has important clinical s...

Claims

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Application Information

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IPC IPC(8): G16B30/10
Inventor 韩志军王杰张倩倩梁雷谢正华
Owner 上海思路迪医学检验所有限公司
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