Assessment of DNA quality for whole genome library preparation
(2024) In Analytical Biochemistry 695.- Abstract
In recent years, more sophisticated DNA technologies for genotyping have enabled considerable progress in various fields such as clinical genetics, archaeogenetics and forensic genetics. DNA samples previously rejected as too challenging to analyze due to low amounts of degraded DNA can now provide useful information. To increase the chances of success with the new methodologies, it is crucial to know the fragment size of the template DNA molecules, and whether the DNA in a sample is mostly single or double stranded. With this knowledge, an appropriate library preparation method can be chosen, and the DNA shearing parameters of the protocol can be adjusted to the DNA fragment size in the sample. In this study, we first developed and... (More)
In recent years, more sophisticated DNA technologies for genotyping have enabled considerable progress in various fields such as clinical genetics, archaeogenetics and forensic genetics. DNA samples previously rejected as too challenging to analyze due to low amounts of degraded DNA can now provide useful information. To increase the chances of success with the new methodologies, it is crucial to know the fragment size of the template DNA molecules, and whether the DNA in a sample is mostly single or double stranded. With this knowledge, an appropriate library preparation method can be chosen, and the DNA shearing parameters of the protocol can be adjusted to the DNA fragment size in the sample. In this study, we first developed and evaluated a user-friendly fluorometry-based protocol for estimation of DNA strandedness. We also evaluated different capillary electrophoresis methods for estimation of DNA fragmentation levels. Next, we applied the developed methodologies to a broad variety of DNA samples processed with different DNA extraction protocols. Our findings show that both the applied DNA extraction method and the sample type affect the DNA strandedness and fragmentation. The established protocols and the gained knowledge will be applicable for future sequencing-based high-density SNP genotyping in various fields.
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- author
- Jansson, Linda LU ; Aili Fagerholm, Siri ; Börkén, Emelie ; Hedén Gynnå, Arvid ; Sidstedt, Maja LU ; Forsberg, Christina ; Ansell, Ricky ; Hedman, Johannes LU and Tillmar, Andreas
- organization
- publishing date
- 2024-12
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- DNA degradation, DNA extraction, Double stranded DNA, Genome sequencing, Single stranded DNA
- in
- Analytical Biochemistry
- volume
- 695
- article number
- 115636
- publisher
- Elsevier
- external identifiers
-
- pmid:39111682
- scopus:85201474112
- ISSN
- 0003-2697
- DOI
- 10.1016/j.ab.2024.115636
- language
- English
- LU publication?
- yes
- id
- 749ae152-0980-45fb-91ef-22beea14598d
- date added to LUP
- 2024-10-28 13:00:26
- date last changed
- 2024-11-11 15:37:40
@article{749ae152-0980-45fb-91ef-22beea14598d,
abstract = {{<p>In recent years, more sophisticated DNA technologies for genotyping have enabled considerable progress in various fields such as clinical genetics, archaeogenetics and forensic genetics. DNA samples previously rejected as too challenging to analyze due to low amounts of degraded DNA can now provide useful information. To increase the chances of success with the new methodologies, it is crucial to know the fragment size of the template DNA molecules, and whether the DNA in a sample is mostly single or double stranded. With this knowledge, an appropriate library preparation method can be chosen, and the DNA shearing parameters of the protocol can be adjusted to the DNA fragment size in the sample. In this study, we first developed and evaluated a user-friendly fluorometry-based protocol for estimation of DNA strandedness. We also evaluated different capillary electrophoresis methods for estimation of DNA fragmentation levels. Next, we applied the developed methodologies to a broad variety of DNA samples processed with different DNA extraction protocols. Our findings show that both the applied DNA extraction method and the sample type affect the DNA strandedness and fragmentation. The established protocols and the gained knowledge will be applicable for future sequencing-based high-density SNP genotyping in various fields.</p>}},
author = {{Jansson, Linda and Aili Fagerholm, Siri and Börkén, Emelie and Hedén Gynnå, Arvid and Sidstedt, Maja and Forsberg, Christina and Ansell, Ricky and Hedman, Johannes and Tillmar, Andreas}},
issn = {{0003-2697}},
keywords = {{DNA degradation; DNA extraction; Double stranded DNA; Genome sequencing; Single stranded DNA}},
language = {{eng}},
publisher = {{Elsevier}},
series = {{Analytical Biochemistry}},
title = {{Assessment of DNA quality for whole genome library preparation}},
url = {{http://dx.doi.org/10.1016/j.ab.2024.115636}},
doi = {{10.1016/j.ab.2024.115636}},
volume = {{695}},
year = {{2024}},
}