Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance
Abstract Background Molecular and genomic surveillance is becoming increasingly used to track malaria control and elimination efforts. Blood samples can be collected as whole blood and stored at − 20 °C until DNA extraction, or as dried blood spots (DBS), circumventing the need for a cold chain. Des...
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ftdoajarticles:oai:doaj.org/article:b74b605ec3d1470d92bf5caaee102868 2023-05-15T15:16:44+02:00 Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance Aurel Holzschuh Cristian Koepfli 2022-03-01T00:00:00Z https://doi.org/10.1186/s12936-022-04122-9 https://doaj.org/article/b74b605ec3d1470d92bf5caaee102868 EN eng BMC https://doi.org/10.1186/s12936-022-04122-9 https://doaj.org/toc/1475-2875 doi:10.1186/s12936-022-04122-9 1475-2875 https://doaj.org/article/b74b605ec3d1470d92bf5caaee102868 Malaria Journal, Vol 21, Iss 1, Pp 1-9 (2022) Plasmodium falciparum Dried blood spot DBS DNA extraction Whole blood Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 article 2022 ftdoajarticles https://doi.org/10.1186/s12936-022-04122-9 2022-12-31T07:12:18Z Abstract Background Molecular and genomic surveillance is becoming increasingly used to track malaria control and elimination efforts. Blood samples can be collected as whole blood and stored at − 20 °C until DNA extraction, or as dried blood spots (DBS), circumventing the need for a cold chain. Despite the wide use of either method, systematic comparisons of how the method of blood sample preservation affects the limit of detection (LOD) of molecular diagnosis and the proportion of DNA recovered for downstream applications are lacking. Methods Extractions based on spin columns, magnetic beads, Tween-Chelex, and direct PCR without prior extraction were compared for whole blood and dried blood spots (DBS) using dilution series of Plasmodium falciparum culture samples. Extracted DNA was quantified by qPCR and droplet digital PCR (ddPCR). Results DNA recovery was 5- to 10-fold higher for whole blood compared to DBS, resulting in a 2- to 3-fold lower LOD for both extraction methods compared to DBS. For whole blood, a magnetic bead-based method resulted in a DNA recovery rate of 88–98% when extracting from whole blood compared to 17–33% for a spin-column based method. For extractions from DBS, the magnetic bead-based method resulted in 8–20% DNA recovery, while the spin-column based method resulted in only 2% DNA recovery. The Tween-Chelex method was superior to other methods with 15–21% DNA recovery, and even more sensitive than extractions from whole blood samples. The direct PCR method was found to have the lowest LOD overall for both, whole blood and DBS. Conclusions Pronounced differences in LOD and DNA yield need to be considered when comparing prevalence estimates based on molecular methods and when selecting sampling protocols for other molecular surveillance applications. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Malaria Journal 21 1 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
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English |
topic |
Plasmodium falciparum Dried blood spot DBS DNA extraction Whole blood Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
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Plasmodium falciparum Dried blood spot DBS DNA extraction Whole blood Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 Aurel Holzschuh Cristian Koepfli Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance |
topic_facet |
Plasmodium falciparum Dried blood spot DBS DNA extraction Whole blood Arctic medicine. Tropical medicine RC955-962 Infectious and parasitic diseases RC109-216 |
description |
Abstract Background Molecular and genomic surveillance is becoming increasingly used to track malaria control and elimination efforts. Blood samples can be collected as whole blood and stored at − 20 °C until DNA extraction, or as dried blood spots (DBS), circumventing the need for a cold chain. Despite the wide use of either method, systematic comparisons of how the method of blood sample preservation affects the limit of detection (LOD) of molecular diagnosis and the proportion of DNA recovered for downstream applications are lacking. Methods Extractions based on spin columns, magnetic beads, Tween-Chelex, and direct PCR without prior extraction were compared for whole blood and dried blood spots (DBS) using dilution series of Plasmodium falciparum culture samples. Extracted DNA was quantified by qPCR and droplet digital PCR (ddPCR). Results DNA recovery was 5- to 10-fold higher for whole blood compared to DBS, resulting in a 2- to 3-fold lower LOD for both extraction methods compared to DBS. For whole blood, a magnetic bead-based method resulted in a DNA recovery rate of 88–98% when extracting from whole blood compared to 17–33% for a spin-column based method. For extractions from DBS, the magnetic bead-based method resulted in 8–20% DNA recovery, while the spin-column based method resulted in only 2% DNA recovery. The Tween-Chelex method was superior to other methods with 15–21% DNA recovery, and even more sensitive than extractions from whole blood samples. The direct PCR method was found to have the lowest LOD overall for both, whole blood and DBS. Conclusions Pronounced differences in LOD and DNA yield need to be considered when comparing prevalence estimates based on molecular methods and when selecting sampling protocols for other molecular surveillance applications. |
format |
Article in Journal/Newspaper |
author |
Aurel Holzschuh Cristian Koepfli |
author_facet |
Aurel Holzschuh Cristian Koepfli |
author_sort |
Aurel Holzschuh |
title |
Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance |
title_short |
Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance |
title_full |
Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance |
title_fullStr |
Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance |
title_full_unstemmed |
Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance |
title_sort |
tenfold difference in dna recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance |
publisher |
BMC |
publishDate |
2022 |
url |
https://doi.org/10.1186/s12936-022-04122-9 https://doaj.org/article/b74b605ec3d1470d92bf5caaee102868 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Malaria Journal, Vol 21, Iss 1, Pp 1-9 (2022) |
op_relation |
https://doi.org/10.1186/s12936-022-04122-9 https://doaj.org/toc/1475-2875 doi:10.1186/s12936-022-04122-9 1475-2875 https://doaj.org/article/b74b605ec3d1470d92bf5caaee102868 |
op_doi |
https://doi.org/10.1186/s12936-022-04122-9 |
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Malaria Journal |
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21 |
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1 |
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1766347036792193024 |