title: Transcriptional profiling and genotyping of degraded nucleic acids from autopsy tissue samples after prolonged formalin fixation times.
abstract: BACKGROUND
  Samples used for genotyping and transcription studies are obtained and conserved in very specific conditions. The possibility to use autopsy tissue samples, which contain nucleic acids of very poor quality, would open new possibilities for genetic studies.
  
  
  METHODS
  We have used liver tissue samples from autopsy cases to (i) determine its quality; (ii) study gene expression of 13 genes involved in different cell processes, before and after cDNA pre-amplification (quantitative reverse transcriptase polymerase chain reaction); and (iii) analyze the presence of 2 common polymorphisms of relevance for illness (ACE I/D genotype by PCR amplification, and TNF-α promoter gene polymorphism, by DNA sequencing).
  
  
  RESULTS
  Samples were grouped according to different buffered formalin fixation times (group 1, <15 days; group 2, 60-90 days; group 3, 150-180 days; group 4, 240-270 days). Nucleic acids showed a time-dependent degradation. The expression of 13 genes could be studied in all cases from groups 1 and 2, only 7 from group 3 and none from group 4. cDNA preamplification allowed the study of all genes in all samples. DNA genotyping for ACE and TNF-α promoter region was possible in all cases.
  
  
  CONCLUSIONS
  We conclude that nucleic acids extracted from autopsy specimens after prolonged periods of time in formalin were of sufficient quality to study gene expression and genotyping using currently available methodology and cDNA pre-amplification.
authors.affiliation: Critical Care Department, Hospital Universitario de Getafe, Madrid, Spain
authors.forename: Antonio
authors.initials: A
authors.lastname: Ferruelo
authors.forename: Mariam
authors.initials: M
authors.lastname: El-Assar
authors.forename: José A
authors.initials: JA
authors.lastname: Lorente
authors.forename: Nicolás
authors.initials: N
authors.lastname: Nin
authors.forename: Oscar
authors.initials: O
authors.lastname: Peñuelas
authors.forename: Pilar
authors.initials: P
authors.lastname: Fernández-Segoviano
authors.forename: Constancio
authors.initials: C
authors.lastname: Gonzalez
authors.forename: Andrés
authors.initials: A
authors.lastname: Esteban
mesh_terms: D016477:Artifacts; D001344:Autopsy; D004247:DNA / Q000737:chemistry*; D005404:Fixatives / Q000737:chemistry*; D005557:Formaldehyde / Q000737:chemistry*; D020869:Gene Expression Profiling / Q000379:methods*; D005838:Genotype; D006801:Humans; D008099:Liver / Q000737:chemistry; D007703:Peptidyl-Dipeptidase A / Q000235:genetics; D011401:Promoter Regions, Genetic; D012313:RNA / Q000737:chemistry*; D020871:RNA Stability; D013997:Time Factors; D016707:Tissue Fixation / Q000379:methods; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics
chemical_list: D005404:Fixatives; D014409:Tumor Necrosis Factor-alpha; D005557:Formaldehyde; D012313:RNA; D004247:DNA; C488034:ACE protein, human; D007703:Peptidyl-Dipeptidase A