Device for detecting copy number variation of FFPE (formalin-fixed and paraffin-embedded) samples

A copy number variation and sample technology, applied in the direction of electronic digital data processing, special data processing applications, instruments, etc., can solve the problems of low-depth sequencing data availability and other issues

Active Publication Date: 2017-06-13
ANNOROAD GENE TECH BEIJING +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Therefore, the availability of low-depth sequencing data generated from low-quality FFPE samples has become a major technical challenge

Method used

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  • Device for detecting copy number variation of FFPE (formalin-fixed and paraffin-embedded) samples
  • Device for detecting copy number variation of FFPE (formalin-fixed and paraffin-embedded) samples
  • Device for detecting copy number variation of FFPE (formalin-fixed and paraffin-embedded) samples

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Experimental program
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Embodiment 1

[0081] The device for detecting copy number variation in FFPE samples of the present invention is used to detect CNV in tissue FFPE samples of a female breast cancer patient.

[0082] 1.1 DNA extraction from FFPE samples

[0083] Using the GeneRead DNA FFPE Kit (QIAGEN Company), the extraction operation was performed according to the instructions in the manual to obtain FFPE sample DNA.

[0084] 1.2 Sample interruption

[0085] Use the Biorupter interruption instrument to interrupt, set the interruption condition for 30 cycles, 30s ON / 30s OFF, and break the FFPE sample DNA into fragments of about 200bp, and obtain the fragmented DNA fragments.

[0086] 1.3 End Repair

[0087] (1) Take out the required reagents from the kit stored at -20°C in advance, and see Table 1 for the preparation amount of a single sample.

[0088] Table 1

[0089]

[0090](2) End repair reaction: After adding the DNA sample, place the 1.5mL centrifuge tube in a Thermomixer for 30 minutes at 20°C....

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Abstract

The invention relates to a device for detecting copy number variation of FFPE (formalin-fixed and paraffin-embedded) samples. The device for detecting the copy number variation of the FFPE samples comprises a sequencing data acquisition module, a sequence comparison module, an earlier-stage data processing module, a normalization module, a background library screening module, a data fluctuation elimination module, a GC (guanine and cytosine) correction module and an output module. The device has the advantage of high detection sensitivity.

Description

technical field [0001] The invention belongs to the field of molecular biology detection, and in particular relates to a detection device and a detection method for FFPE sample copy number variation. Background technique [0002] Tissue samples prepared by the formalin-fixed and paraffin-embedded (FFPE) method are called formalin-fixed paraffin-embedded tissue samples, FFPE samples for short. FFPE samples can be preserved for a long time, especially, a large number of tumor tissue sections are preserved in the form of FFPE samples. FFPE samples are commonly used in clinicopathological examinations, tumor gene detection, and medical science research, providing valuable resources for elucidating disease mechanisms, discovering therapeutic targets, and indicating prognosis. [0003] Gene copy number variation (Copy Number Variation, CNV) is a very important structural variation in clinical practice, which is related to the prognosis of various tumors and the sensitivity of tar...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/22
CPCG16B30/00
Inventor 荆瑞琳张萌萌董永芳王旺李雪峰玄兆伶李大为梁峻彬陈重建
Owner ANNOROAD GENE TECH BEIJING
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