This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Sjöholm, M. I.L. Articles by Carlson, J. Search for Related Content PubMed PubMed Citation Articles by Sjöholm, M. I.L. Articles by Carlson, J.

Comparison of Archival Plasma and Formalin-Fixed Paraffin-Embedded Tissue for Genotyping in Hepatocellular Carcinoma

Departments of ¹ Clinical Chemistry, ² Medical Microbiology, and ³ Gastroenterology; and ⁴ the 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

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), ₁-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.

Key Words: biobank samples • archival plasma • archival tissue • formalin-fixed paraffin-embedded tissue • hepatocellular carcinoma (HCC)

This article has been cited by other articles:

				D. T. Croft Jr, R. M. Jordan, H. L. Patney, C. D. Shriver, M. N. Vernalis, T. J. Orchard, and D. L. Ellsworth Performance of Whole-Genome Amplified DNA Isolated from Serum and Plasma on High-Density Single Nucleotide Polymorphism Arrays J. Mol. Diagn., May 1, 2008; 10(3): 249 - 257. [Abstract] [Full Text] [PDF]

				M. I. L. Sjoholm, J. Dillner, and J. Carlson Assessing Quality and Functionality of DNA from Fresh and Archival Dried Blood Spots and Recommendations for Quality Control Guidelines Clin. Chem., August 1, 2007; 53(8): 1401 - 1407. [Abstract] [Full Text] [PDF]

				U. Lehmann, L. U. Wingen, K. Brakensiek, H. Wedemeyer, T. Becker, A. Heim, K. Metzig, B. Hasemeier, H. Kreipe, and P. Flemming Epigenetic defects of hepatocellular carcinoma are already found in non-neoplastic liver cells from patients with hereditary haemochromatosis Hum. Mol. Genet., June 1, 2007; 16(11): 1335 - 1342. [Abstract] [Full Text] [PDF]

				R. M. Santella Approaches to DNA/RNA Extraction and Whole Genome Amplification. Cancer Epidemiol. Biomarkers Prev., September 1, 2006; 15(9): 1585 - 1587. [Abstract] [Full Text] [PDF]

				R. M. Santella Approaches to DNA/RNA Extraction and Whole Genome Amplification Am. Assoc. Cancer Res. Educ. Book, April 1, 2006; 2006(1): 372 - 376. [Full Text] [PDF]