Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions
Urinary cell-free DNA (cfDNA) is an attractive body fluid for liquid biopsy. In this study, we compared the efficiencies of four commercial kits for urinary cell-free DNA (cfDNA) isolation and of various sample storage conditions. Urinary cfDNA was isolated from 10 healthy individuals using four com...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-04-01
|
| Series: | Diagnostics |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2075-4418/10/4/234 |
| _version_ | 1827718367777128448 |
|---|---|
| author | Eun Young Lee Eun-Ju Lee Hana Yoon Dong Hyeon Lee Kwang Hyun Kim |
| author_facet | Eun Young Lee Eun-Ju Lee Hana Yoon Dong Hyeon Lee Kwang Hyun Kim |
| author_sort | Eun Young Lee |
| collection | DOAJ |
| description | Urinary cell-free DNA (cfDNA) is an attractive body fluid for liquid biopsy. In this study, we compared the efficiencies of four commercial kits for urinary cell-free DNA (cfDNA) isolation and of various sample storage conditions. Urinary cfDNA was isolated from 10 healthy individuals using four commercial kits: QIAamp Circulating Nucleic Acid Kit (QC; Qiagen), MagMAX™ Cell-Free DNA Isolation Kit (MM; Applied Biosystems), Urine Cell-Free Circulating DNA Purification Midi Kit (NU; Norgen Biotek), and Quick-DNA™ Urine Kit (ZQ; Zymo Research). To assess the isolation efficiency, an Agilent 2100 Bioanalyzer with High Sensitivity DNA chips was used, and cfDNA yield was defined as the amount of cfDNA obtained from 1 mL of urine. MM and QC provided the highest cfDNA yield in the 50–300 bp range, and MM and NU gave the highest cfDNA yield in the 50–100 bp range. In particular, the NU kit was efficient for isolation of more fragmented cfDNA in the range of 50–100 bp with the lowest cellular genomic DNA contamination. ZQ had the best cost-efficiency for isolating the same amount of urinary cfDNA. Samples stored at −70 °C with the addition of 10 mM EDTA resulted in the highest cfDNA yield 3 months after sample collection. |
| first_indexed | 2024-03-10T20:23:07Z |
| format | Article |
| id | doaj.art-5557a5b4ee5b41a0b790c0b56569daf4 |
| institution | Directory Open Access Journal |
| issn | 2075-4418 |
| language | English |
| last_indexed | 2024-03-10T20:23:07Z |
| publishDate | 2020-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diagnostics |
| spelling | doaj.art-5557a5b4ee5b41a0b790c0b56569daf42023-11-19T22:01:51ZengMDPI AGDiagnostics2075-44182020-04-0110423410.3390/diagnostics10040234Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage ConditionsEun Young Lee0Eun-Ju Lee1Hana Yoon2Dong Hyeon Lee3Kwang Hyun Kim4Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, KoreaDepartment of Urology, College of Medicine, Ewha Womans University, Seoul 07804, KoreaDepartment of Urology, College of Medicine, Ewha Womans University, Seoul 07804, KoreaDepartment of Urology, College of Medicine, Ewha Womans University, Seoul 07804, KoreaDepartment of Urology, College of Medicine, Ewha Womans University, Seoul 07804, KoreaUrinary cell-free DNA (cfDNA) is an attractive body fluid for liquid biopsy. In this study, we compared the efficiencies of four commercial kits for urinary cell-free DNA (cfDNA) isolation and of various sample storage conditions. Urinary cfDNA was isolated from 10 healthy individuals using four commercial kits: QIAamp Circulating Nucleic Acid Kit (QC; Qiagen), MagMAX™ Cell-Free DNA Isolation Kit (MM; Applied Biosystems), Urine Cell-Free Circulating DNA Purification Midi Kit (NU; Norgen Biotek), and Quick-DNA™ Urine Kit (ZQ; Zymo Research). To assess the isolation efficiency, an Agilent 2100 Bioanalyzer with High Sensitivity DNA chips was used, and cfDNA yield was defined as the amount of cfDNA obtained from 1 mL of urine. MM and QC provided the highest cfDNA yield in the 50–300 bp range, and MM and NU gave the highest cfDNA yield in the 50–100 bp range. In particular, the NU kit was efficient for isolation of more fragmented cfDNA in the range of 50–100 bp with the lowest cellular genomic DNA contamination. ZQ had the best cost-efficiency for isolating the same amount of urinary cfDNA. Samples stored at −70 °C with the addition of 10 mM EDTA resulted in the highest cfDNA yield 3 months after sample collection.https://www.mdpi.com/2075-4418/10/4/234urinary cell DNAliquid biopsycommercial kit |
| spellingShingle | Eun Young Lee Eun-Ju Lee Hana Yoon Dong Hyeon Lee Kwang Hyun Kim Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions Diagnostics urinary cell DNA liquid biopsy commercial kit |
| title | Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions |
| title_full | Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions |
| title_fullStr | Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions |
| title_full_unstemmed | Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions |
| title_short | Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions |
| title_sort | comparison of four commercial kits for isolation of urinary cell free dna and sample storage conditions |
| topic | urinary cell DNA liquid biopsy commercial kit |
| url | https://www.mdpi.com/2075-4418/10/4/234 |
| work_keys_str_mv | AT eunyounglee comparisonoffourcommercialkitsforisolationofurinarycellfreednaandsamplestorageconditions AT eunjulee comparisonoffourcommercialkitsforisolationofurinarycellfreednaandsamplestorageconditions AT hanayoon comparisonoffourcommercialkitsforisolationofurinarycellfreednaandsamplestorageconditions AT donghyeonlee comparisonoffourcommercialkitsforisolationofurinarycellfreednaandsamplestorageconditions AT kwanghyunkim comparisonoffourcommercialkitsforisolationofurinarycellfreednaandsamplestorageconditions |