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Quality assessment of biobanked nucleic acid extracts for downstream molecular analysis

Wahlberg, Karin LU ; Huggett, Jim; Sanders, Rebecca; Whale, Alexandra S; Bushell, Claire; Elaswarapu, Ramnath; Scott, Daniel J and Foy, Carole A (2012) In Biopreservation and Biobanking 10(3). p.75-266
Abstract

Sample quality is of major importance when conducting molecular analysis of nucleic acids, and factors such as degradation, presence of impurities, and enzymatic inhibitors may have a significant impact on the quality of data. Issues of quality assessment become more important as the increased use of biobanking means that whole blood samples are being stored for longer periods. A range of commercially available kits/methods have been specifically developed for extraction of high quality nucleic acids from a variety of clinical samples, including blood, but there is limited information on how best to quality assess the extracts to determine their fitness for purpose in specific downstream applications. In this study, we have performed... (More)

Sample quality is of major importance when conducting molecular analysis of nucleic acids, and factors such as degradation, presence of impurities, and enzymatic inhibitors may have a significant impact on the quality of data. Issues of quality assessment become more important as the increased use of biobanking means that whole blood samples are being stored for longer periods. A range of commercially available kits/methods have been specifically developed for extraction of high quality nucleic acids from a variety of clinical samples, including blood, but there is limited information on how best to quality assess the extracts to determine their fitness for purpose in specific downstream applications. In this study, we have performed nucleic acid extractions from stored blood using a number of different methods. The resulting extracts were analyzed by a panel of quantity and quality metrics including UV spectrophotometry, PicoGreen fluorescence, electrophoresis, and a PCR approach. To evaluate the relevance of different metrics, DNA samples were subsequently assessed for their performance in real time PCR and microarray experiments. Our findings demonstrate that the most suitable extraction technique and quality assessment approach depends on the required downstream analytical method.

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author
publishing date
type
Contribution to journal
publication status
published
keywords
Blood Banks, Electrophoresis, Humans, Male, Nucleic Acids, Quality Control, RNA, Real-Time Polymerase Chain Reaction, Spectrophotometry, Ultraviolet, Journal Article, Research Support, Non-U.S. Gov't
in
Biopreservation and Biobanking
volume
10
issue
3
pages
10 pages
publisher
Mary Ann Liebert Inc.
external identifiers
  • scopus:84862885205
ISSN
1947-5543
DOI
10.1089/bio.2012.0004
language
English
LU publication?
no
id
c6387c0d-9dfe-4075-bed6-98df6a2f454f
date added to LUP
2017-10-25 10:59:36
date last changed
2017-10-30 16:02:05
@article{c6387c0d-9dfe-4075-bed6-98df6a2f454f,
  abstract     = {<p>Sample quality is of major importance when conducting molecular analysis of nucleic acids, and factors such as degradation, presence of impurities, and enzymatic inhibitors may have a significant impact on the quality of data. Issues of quality assessment become more important as the increased use of biobanking means that whole blood samples are being stored for longer periods. A range of commercially available kits/methods have been specifically developed for extraction of high quality nucleic acids from a variety of clinical samples, including blood, but there is limited information on how best to quality assess the extracts to determine their fitness for purpose in specific downstream applications. In this study, we have performed nucleic acid extractions from stored blood using a number of different methods. The resulting extracts were analyzed by a panel of quantity and quality metrics including UV spectrophotometry, PicoGreen fluorescence, electrophoresis, and a PCR approach. To evaluate the relevance of different metrics, DNA samples were subsequently assessed for their performance in real time PCR and microarray experiments. Our findings demonstrate that the most suitable extraction technique and quality assessment approach depends on the required downstream analytical method.</p>},
  author       = {Wahlberg, Karin and Huggett, Jim and Sanders, Rebecca and Whale, Alexandra S and Bushell, Claire and Elaswarapu, Ramnath and Scott, Daniel J and Foy, Carole A},
  issn         = {1947-5543},
  keyword      = {Blood Banks,Electrophoresis,Humans,Male,Nucleic Acids,Quality Control,RNA,Real-Time Polymerase Chain Reaction,Spectrophotometry, Ultraviolet,Journal Article,Research Support, Non-U.S. Gov't},
  language     = {eng},
  number       = {3},
  pages        = {75--266},
  publisher    = {Mary Ann Liebert Inc.},
  series       = {Biopreservation and Biobanking},
  title        = {Quality assessment of biobanked nucleic acid extracts for downstream molecular analysis},
  url          = {http://dx.doi.org/10.1089/bio.2012.0004},
  volume       = {10},
  year         = {2012},
}