A method for repairing DNA damage in FFPE samples

By employing methods of thermal denaturation, slow cooling renaturation, and mixed enzyme repair, the problem of short and poor-quality DNA fragments in FFPE samples is addressed, achieving efficient DNA repair, improving gene chip detection results, and reducing costs.

CN122128397APending Publication Date: 2026-06-02SHANGHAI CINOPATH MEDICAL TESTING CO LTD
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Patent Information

Authority / Receiving Office
CN · China
Patent Type
Applications(China)
Current Assignee / Owner
SHANGHAI CINOPATH MEDICAL TESTING CO LTD
Filing Date
2026-03-12
Publication Date
2026-06-02

AI Technical Summary

Technical Problem

During the preparation and preservation of FFPE sample DNA, formalin fixation causes severe DNA degradation, resulting in a large number of short fragments that cannot meet the quality requirements of gene chip detection, leading to inaccurate detection results.

Method used

The method employs heat denaturation, slow cooling annealing, and the use of mixed repair enzymes and random primers to repair DNA damage through enzymes such as uracil DNA glycosylase and formamidopyrimidine-DNA glycosidase, forming large DNA fragments, which are then purified with magnetic beads to obtain the repaired DNA.

Benefits of technology

It significantly improves the DNA quality of FFPE samples, increases the detection pass rate of Infinium CytoSNP-850K whole genome chip detection, reduces costs, and is simple to operate without the need for additional equipment.

✦ Generated by Eureka AI based on patent content.

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Abstract

This invention discloses a method for repairing DNA damage in FFPE samples, comprising: S1. subjecting FFPE sample DNA to heat denaturation; S2. allowing the DNA to fully renature by slow cooling or ice bath; S3. using random primers to bind to large nicked regions of the DNA fragment; S4. adding a mixed repair enzyme to repair the DNA damage; S5. ligating the DNA repaired in step S4 to obtain large DNA fragments, which are then purified with magnetic beads to obtain the repaired DNA. By using random primer single-strand extension to assist the enzyme reaction system, the efficiency of DNA damage / deletion repair is improved; by using random ligation to assemble fragmented DNA into large DNA fragments, the problem of ineffective amplification caused by excessive DNA fragmentation is solved, without affecting the microarray detection results. The entire DNA repair reaction is performed continuously, without the need for multiple purification operations. Compared with other DNA repair methods, it is simple to operate and low in cost, significantly improving the quality of FFPE sample DNA and increasing its detection pass rate in Infinium CytoSNP-850K whole genome microarray detection.
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