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Coextraction and PCR Based Analysis of Nucleic Acids From Formalin-Fixed Paraffin-Embedded Specimens

Ghatak, Souvik LU ; Sanga, Zothan ; Pautu, Jeremy L and Senthil Kumar, Nachimuthu (2014) In Journal of Clinical Laboratory Analysis 29(6). p.482-485
Abstract
Background
Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffin embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. Our optimized co-extraction approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies because of the high importance and less availability of clinical FFPE specimen.

Methods
Coextraction of DNA and RNA from a single gastric cancer FFPE specimen was... (More)
Background
Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffin embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. Our optimized co-extraction approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies because of the high importance and less availability of clinical FFPE specimen.

Methods
Coextraction of DNA and RNA from a single gastric cancer FFPE specimen was optimized by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. The protocol involves modification of incubation period for 30 min with proteinase K in glycin-tris-ethylenediamine tetra acetic acid buffer before adding TRIzol.

Results
All samples tested successfully performed semiquantitative gene expression by reverse transcriptase PCR. The quantity and quality of DNA from FFPE samples was high which resulted in successful PCR amplification. The isolated DNA also aided in detection of Helicobacter pylori by amplifying the ribosomal 16S gene in a multiplex PCR reaction along with cagA.

Conclusion
These results show that the RNA/DNA isolated by this method can be used for easy clinical diagnosis of disease-related gene expression as well as mutation and pathogen detection from a homogenous population of tumor cells. (Less)
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author
; ; and
publishing date
type
Contribution to journal
publication status
published
in
Journal of Clinical Laboratory Analysis
volume
29
issue
6
pages
482 - 485
publisher
John Wiley & Sons Inc.
external identifiers
  • scopus:85000027902
ISSN
1098-2825
DOI
10.1002/jcla.21798
language
English
LU publication?
no
id
e3a273b8-0e68-49b4-a889-d5e514ead29e
date added to LUP
2021-11-09 16:23:10
date last changed
2022-03-11 21:22:16
@article{e3a273b8-0e68-49b4-a889-d5e514ead29e,
  abstract     = {{Background<br/>Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffin embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. Our optimized co-extraction approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies because of the high importance and less availability of clinical FFPE specimen.<br/><br/>Methods<br/>Coextraction of DNA and RNA from a single gastric cancer FFPE specimen was optimized by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. The protocol involves modification of incubation period for 30 min with proteinase K in glycin-tris-ethylenediamine tetra acetic acid buffer before adding TRIzol.<br/><br/>Results<br/>All samples tested successfully performed semiquantitative gene expression by reverse transcriptase PCR. The quantity and quality of DNA from FFPE samples was high which resulted in successful PCR amplification. The isolated DNA also aided in detection of Helicobacter pylori by amplifying the ribosomal 16S gene in a multiplex PCR reaction along with cagA.<br/><br/>Conclusion<br/>These results show that the RNA/DNA isolated by this method can be used for easy clinical diagnosis of disease-related gene expression as well as mutation and pathogen detection from a homogenous population of tumor cells.}},
  author       = {{Ghatak, Souvik and Sanga, Zothan and Pautu, Jeremy L and Senthil Kumar, Nachimuthu}},
  issn         = {{1098-2825}},
  language     = {{eng}},
  number       = {{6}},
  pages        = {{482--485}},
  publisher    = {{John Wiley & Sons Inc.}},
  series       = {{Journal of Clinical Laboratory Analysis}},
  title        = {{Coextraction and PCR Based Analysis of Nucleic Acids From Formalin-Fixed Paraffin-Embedded Specimens}},
  url          = {{http://dx.doi.org/10.1002/jcla.21798}},
  doi          = {{10.1002/jcla.21798}},
  volume       = {{29}},
  year         = {{2014}},
}