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System for detecting cancer recurrence by using low-depth whole genome sequencing

A whole genome sequencing and cancer technology, applied in the field of systems for detecting cancer recurrence, can solve problems such as difficulty, high detection cost, and inability to detect false negative results, and achieve the effect of eliminating errors and low sequencing costs

Pending Publication Date: 2018-12-04
成都中珠健联基因科技有限责任公司
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Since the content of ctDNA in the blood is very low, half of which is about tens of nanograms, the detection of gene mutations, especially the NGS method, requires hundreds of sequencing of the same site, which brings great difficulties. In some cases, no mutations can be detected, resulting in false negative results, and the cost of testing is high

Method used

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  • System for detecting cancer recurrence by using low-depth whole genome sequencing
  • System for detecting cancer recurrence by using low-depth whole genome sequencing
  • System for detecting cancer recurrence by using low-depth whole genome sequencing

Examples

Experimental program
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Effect test

Embodiment 1

[0038] like figure 1 The system for detecting cancer recurrence using low-depth whole-genome sequencing is composed of an acquisition unit, a detection unit, an information storage unit, a discrimination unit and an output unit connected in sequence.

[0039] When in use, about 10 mL of peripheral blood from cancer patients is collected by the collection unit. The QIAGEN circulating DNA kit kit of the acquisition unit extracts 2-1000ng of ctDNA, and delivers 2-10ng to the detection unit. The WGA kit of the detection unit (such as ThruPLEX Plasma-Seq Kit, Rubicon Genomics) builds a library for ctDNA sequencing, and performs low-depth whole-genome sequencing on the DNA of the built library on a high-throughput NGS sequencer such as Illumina NextSeq, with an average sequencing depth of 1x Or 0.5x, and send the produced sequencing data to the CNV analysis unit in BAM file format for analysis. The analysis software of the CNV analysis unit can be Nexus Copy Number or CNVKit, etc.,...

Embodiment 2

[0040] Example 2 Effect of Different Sequencing Depths on ctDNA CNV Results of Breast Cancer

[0041] The other operations are exactly the same. The sequencing depth of the detection unit is set to 1x, 0.5x, 0.25x and 0.1x respectively, and the same breast cancer patient is sampled for detection. The sequencing data is as follows: figure 2 shown. The arrow is the CNV repeat of the chr17q12 fragment containing the ERBB2 gene. It can be seen from the figure that the CNV data quality of 1x or 0.5x sequencing depth is good, the data quality of 0.25x data begins to decline, and the data of 0.1x is basically unusable. Therefore, the detection unit of the system of the present invention sets the sequencing depth to 1x or 0.5x, which ensures low cost and high quality.

Embodiment 3

[0042] Embodiment 3 Accuracy Research

[0043] The system of Example 1 of the present invention was used to perform 0.5x low-depth whole-genome sequencing on the ctDNA of two breast cancer patients (patient A and patient B), and the CNV results detected by the detection unit were as follows: image 3 shown. At the same time, the ctDNA of the two patients was detected by qPCR method, and the results were as follows: Figure 4 shown. The results of the two methods were compared, and the gene duplications in the CNV results were confirmed in the qPCR results, showing a high degree of consistency.

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Abstract

The invention discloses a system for detecting cancer recurrence by using low-depth whole genome sequencing. The system comprises an acquisition unit for acquiring and processing a blood sample of a patient, a detection unit for detecting the CNV result of the blood sample of the patient, an information storage unit for storing the CNV result from the detection unit, a discrimination unit for discriminating the CNV result, and an output unit for processing a discriminating result, wherein the acquisition unit, the detection unit, the information storage unit, the discrimination unit and the output unit are sequentially connected. The system of the invention has the advantages of noninvasiveness, rapidness, accuracy, high efficiency, low detection cost and the like in detection of cancer recurrence; and the system has significant advantages and great practical significance in clinical application compared with existing surgical biopsy, needle biopsy, image detection, PCR detection, etc.

Description

technical field [0001] The invention belongs to the field of disease diagnosis equipment, and in particular relates to a system for detecting cancer recurrence by using low-depth whole-genome sequencing. Background technique [0002] Cancer is already the second leading cause of death worldwide. Whether in developed or developing countries, cancer is the disease with the highest mortality rate, and its mortality and morbidity are still increasing. According to the United States Global Cancer Disease Burden Collaborative Research, Washington University and other reports: In the past ten years, the global cancer incidence has increased by 33%. In 2015 alone, 15.2 million people were diagnosed with cancer and 8.8 million people died from it. The cancer mortality rate in developing countries is higher than that in developed countries, accounting for 57% of the global cases and 65% of the deaths. [0003] In the results of cancer screening in our country, only 20% are early st...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6886C12Q1/6869
CPCC12Q1/6869C12Q1/6886
Inventor 车志伟
Owner 成都中珠健联基因科技有限责任公司
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