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Usefulness of archival biobank samples for genetic epidemiologic studies

Sjöholm, Malin LU (2008) In Lund University, Faculty of Medicine Doctoral Dissertation Series 2008:26.
Abstract
Sweden has a long history of maintaining population-based registries and biobanks. This has resulted in large sample collections with long follow-up and large numbers of prospectively occurring disease endpoints providing an extensive resource for genetic research. However, the largest biobanks contain sample materials that have previously been considered suboptimal for genetic research.

We have evaluated the usefulness of archival formalin-fixed, paraffin-embedded (FFPE) tissue, plasma, maternity serum and dried blood spots (DBS) for genetic research. We also evaluated the usefulness of archival samples of various biological materials for herpesvirus detection and developed a multiplex matrix-assisted laser desorption/ionisation... (More)
Sweden has a long history of maintaining population-based registries and biobanks. This has resulted in large sample collections with long follow-up and large numbers of prospectively occurring disease endpoints providing an extensive resource for genetic research. However, the largest biobanks contain sample materials that have previously been considered suboptimal for genetic research.

We have evaluated the usefulness of archival formalin-fixed, paraffin-embedded (FFPE) tissue, plasma, maternity serum and dried blood spots (DBS) for genetic research. We also evaluated the usefulness of archival samples of various biological materials for herpesvirus detection and developed a multiplex matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) method for detection of herpesviruses.

Extraction of DNA from archival FFPE tissue was difficult and time consuming. The DNA was largely degraded and repeat extractions were often necessary. Nonetheless 94% of the FFPE tissue samples could be successfully genotyped.

Archival plasma and maternity serum samples contained small and variable amounts of DNA but 98% of the plasma and over 99% of the serum samples were successful in genetic analyses even after over 20 years of storage. The presence of realistic amounts of foetal DNA of a discordant genotype in the maternity serum will not cause false maternal genotyping results.

DBS samples contained small amounts of extractable DNA but over 97% of these samples were successful in genetic analysis even after 18 years of storage if they had been stored at -20°C to prevent DNA degradation.

DNA from plasma and DBS samples was of sufficient quality for successful multiple displacement amplification (MDA) with maintained bi-allelic representation as long as sufficient amounts of DNA was used as MDA template. DNA from FFPE tissue failed consistently and DNA from serum performed poorly in MDA.

The multiplex MALDI-TOF MS method we developed reliably detected HHVs in a wide variety of archival biological specimens. The concordance rate with reference methods was over 95%. (Less)
Please use this url to cite or link to this publication:
author
supervisor
opponent
  • Vaught, Jimmie, National Cancer Institute, USA
organization
publishing date
type
Thesis
publication status
published
subject
keywords
formailn-fixed paraffin-embedded tissue, biobank, serum, dried blood spots, plasma, archival samples
in
Lund University, Faculty of Medicine Doctoral Dissertation Series
volume
2008:26
pages
103 pages
publisher
Avd för klinisk kemi och mikrobiologi, Inst för Laboratoriemedicin, Malmö
defense location
Patologiska institutionens föreläsningssal, UMAS, Malmö
defense date
2008-03-19 09:00
ISBN
978-91-85897-79-7
language
English
LU publication?
yes
id
98fd13b8-ec37-4cd5-a36b-0982eb8d4ef9 (old id 1037994)
date added to LUP
2008-02-26 11:44:52
date last changed
2016-09-19 08:45:07
@misc{98fd13b8-ec37-4cd5-a36b-0982eb8d4ef9,
  abstract     = {Sweden has a long history of maintaining population-based registries and biobanks. This has resulted in large sample collections with long follow-up and large numbers of prospectively occurring disease endpoints providing an extensive resource for genetic research. However, the largest biobanks contain sample materials that have previously been considered suboptimal for genetic research. <br/><br>
We have evaluated the usefulness of archival formalin-fixed, paraffin-embedded (FFPE) tissue, plasma, maternity serum and dried blood spots (DBS) for genetic research. We also evaluated the usefulness of archival samples of various biological materials for herpesvirus detection and developed a multiplex matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) method for detection of herpesviruses.<br/><br>
Extraction of DNA from archival FFPE tissue was difficult and time consuming. The DNA was largely degraded and repeat extractions were often necessary. Nonetheless 94% of the FFPE tissue samples could be successfully genotyped. <br/><br>
Archival plasma and maternity serum samples contained small and variable amounts of DNA but 98% of the plasma and over 99% of the serum samples were successful in genetic analyses even after over 20 years of storage. The presence of realistic amounts of foetal DNA of a discordant genotype in the maternity serum will not cause false maternal genotyping results. <br/><br>
DBS samples contained small amounts of extractable DNA but over 97% of these samples were successful in genetic analysis even after 18 years of storage if they had been stored at -20°C to prevent DNA degradation. <br/><br>
DNA from plasma and DBS samples was of sufficient quality for successful multiple displacement amplification (MDA) with maintained bi-allelic representation as long as sufficient amounts of DNA was used as MDA template. DNA from FFPE tissue failed consistently and DNA from serum performed poorly in MDA. <br/><br>
The multiplex MALDI-TOF MS method we developed reliably detected HHVs in a wide variety of archival biological specimens. The concordance rate with reference methods was over 95%.},
  author       = {Sjöholm, Malin},
  isbn         = {978-91-85897-79-7},
  keyword      = {formailn-fixed paraffin-embedded tissue,biobank,serum,dried blood spots,plasma,archival samples},
  language     = {eng},
  pages        = {103},
  publisher    = {ARRAY(0x9786d28)},
  series       = {Lund University, Faculty of Medicine Doctoral Dissertation Series},
  title        = {Usefulness of archival biobank samples for genetic epidemiologic studies},
  volume       = {2008:26},
  year         = {2008},
}