Optimization of DNA purification nano beads specifically for FFPE samples
10.13315/j.cnki.cjcep.2024.07.012
- VernacularTitle:围绕FFPE样本特性的DNA纯化纳米磁珠优化
- Author:
Lin XIAO
1
;
Xiaofang LÜ
;
Shiyu CAO
;
Dan JIANG
;
Linyong SUN
;
Kun LI
;
Feng YE
Author Information
1. 四川大学华西医院临床病理研究所,成都 610000
- Keywords:
paraffin-embedded tissue;
DNA extraction;
nano-magnetic beads;
PCR;
Sanger
- From:
Chinese Journal of Clinical and Experimental Pathology
2024;40(7):725-730
- CountryChina
- Language:Chinese
-
Abstract:
Purpose Focusing on the characteristics of for-malin fixed paraffin embedded(FFPE)samples,explored nano-magnetic bead nucleic acid extraction solutions with higher qual-ity/yield and continued to improve molecular pathology technolo-gy.Methods Alternative magnetic beads were synthesised in four major categories and 15 sub-categories and we screened to obtain high-quality/yield magnetic beads centred on FFPE samples.Simulated conventional tissues,simulated coarse needle punctures(liver),and simulated fiberoptic bronchoscopy sam-ples(lungs)were sectioned with the same number of serial slices in tubes.The nucleic acids of slices were extracted using the best magnetic beads screened in this study and common com-mercially available kits,and then perform comparison and purifi-cation quality parameters such as total amount and fragment size.The downstream applications of nucleic acids were validated by PCR and Sanger sequencing.Results Screening all homemade nanomagnetic beads centered on the DNA of FFPE samples,the total recoveries of the best performance nanomagnetic beads were obtained to be 58.5％±1.58％,and the total recoveries of five commercially available commercial magnetic beads and three do-mestic kit magnetic beads ranged from 18.68％to 40.71％.The total amount of DNA(ng)extracted from the same amount of tis-sue(serial slices),the nucleic acid yield of this study in simu-lated conventional tissues,simulated coarse needle punctures,and simulated fiberoptic bronchoscopy samples were increased by 39.49％-181.72％compared with those of the commercially a-vailable kits(P＜0.05).The total amount of extracted nucleic acid from simulated fiberoptic bronchoscopy tissue sections can be more than 100 ng for 1 slice(4 μm)and more than 400 ng for 5 slices.Conclusion The DNA purification nanomagnetic beads screened with DNA from FFPE samples have a significant enhancement comparing to the existing commercial bead proto-cols,and provide space for quality assurance,automated testing,and program expansion for clinical molecular pathology testing.
