Comparison of Archival Plasma and Formalin-Fixed Paraffin-Embedded Tissue for Genotyping in Hepatocellular Carcinoma
- Malin I.L. Sjöholm1,2,4,
- Gunilla Hoffmann3,
- Stefan Lindgren3,
- Joakim Dillner2,4 and
- Joyce Carlson1,4
- Departments of 1Clinical Chemistry, 2Medical Microbiology, and 3Gastroenterology; and 4the Swedish National Biobanking Program, Lund University, Malmö University Hospital, Malmö, Sweden
- Requests for reprints:
Joyce Carlson, Clinical Chemistry, University Hospital MAS, Entrance 71, 205-02 Malmö, Sweden. Phone: 46-4033-1493; Fax: 46-4033-6296. E-mail: Joyce.Carlson{at}klkemi.mas.lu.se
Abstract
Biobanks containing formalin-fixed paraffin-embedded tissue, as well as frozen serum or plasma, are important resources for molecular epidemiologic studies. However, few studies have compared the reliability of formalin-fixed tissue samples and archival plasma samples for genotyping. We determined the genotype of four proposed genetic risk factors for hepatocellular carcinoma [hereditary hemochromatosis (HFE 63 and 282), α1-antitrypsin deficiency (AAT 342) and cystic fibrosis (CFTR 508)] on formalin-fixed tissue samples, stored for up to 25 years, from 318 patients diagnosed with hepatocellular carcinoma and on plasma or serum samples from 31 of these patients. The genotypes were analyzed by RFLP or allele-specific amplification as well as by TaqMan assays. In addition, genotyping was attempted after whole genome amplification by multiple displacement amplification (MDA). Genotyping was successful in 94% of the tissue samples and successful and identical to the tissue samples from the same subjects in 98% of the plasma/serum samples. DNA from plasma samples could be amplified >5,000-fold by MDA and genotyping after MDA gave identical results to the genotyping of the same subjects before whole genome amplification. MDA amplification of the tissue samples was not successful. In summary, archival plasma was found to be an adequate source of efficiently amplifiable DNA. MDA on plasma samples allows analysis of multiple genotypes in epidemiologic studies.
- biobank samples
- archival plasma
- archival tissue
- formalin-fixed paraffin-embedded tissue
- hepatocellular carcinoma (HCC)
Footnotes
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Grant support: Grants from the MAS Cancer Fund, the Swedish Cancer Society, the Swedish Society of Medicine and the Lundstro¨m Foundation. The Swedish National Biobanking Program is funded by the Knut and Alice Wallenberg Foundation via SWEGENE and the Wallenberg Consortium North.
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The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
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- Accepted August 18, 1904.
- Received June 17, 1904.
- Revision received July 30, 1904.
