title: Primary central nervous system lymphomas: a validation study of array-based comparative genomic hybridization in formalin-fixed paraffin-embedded tumor specimens.
abstract: OBJECTIVE
  Only a limited number of genetic studies have been conducted in primary central nervous system lymphomas (PCNSL), partly due to the rarity of the tumors and the very limited amount of available tissue. In this report, we present the first molecular characterization of copy number abnormalities (CNA) of newly diagnosed PCNSL by array-based comparative genomic hybridization (aCGH) in formalin-fixed paraffin-embedded (FFPE) specimens and compare the results with matched, frozen tumor specimens.
  
  
  METHODS
  We conducted aCGH in FFPE tissues from PCNSL. Results were compared with matched, paired, frozen tumors.
  
  
  RESULTS
  Our analysis confirmed the good to fair quality and reliability of the data generated from limited amounts of tumoral FFPE tissue. Overall, all PCNSL cases were characterized by highly complex karyotypes, with a median of 23 CNAs per patient (range, 17-47). Overall, 20 chromosomal regions were recurrently found in more than 40% of cases. Deletions of 6p21, 6q, and 9p21.3 and gain of 12q12-q24.33 were the commonest CNAs. Other minimal affected regions were defined, and novel recurrent CNAs affecting single genes were identified in 3q26.32 (TBL1XR1) and 8q12.1 (TOX).
  
  
  CONCLUSIONS
  The results obtained are encouraging. Larger archival tissue collections can now be analyzed to complement the still fragmented knowledge we have of the genetic basis of the PCNSL.
authors.affiliation: Department of Biochemistry, Mayo Clinic, Scottsdale, Arizona, USA.
authors.forename: Esteban
authors.initials: E
authors.lastname: Braggio
authors.forename: Ellen Remstein
authors.initials: ER
authors.lastname: McPhail
authors.forename: William
authors.initials: W
authors.lastname: Macon
authors.forename: M Beatriz
authors.initials: MB
authors.lastname: Lopes
authors.forename: David
authors.initials: D
authors.lastname: Schiff
authors.forename: Mark
authors.initials: M
authors.lastname: Law
authors.forename: Stephanie
authors.initials: S
authors.lastname: Fink
authors.forename: Debra
authors.initials: D
authors.lastname: Sprau
authors.forename: Caterina
authors.initials: C
authors.lastname: Giannini
authors.forename: Ahmet
authors.initials: A
authors.lastname: Dogan
authors.forename: Rafael
authors.initials: R
authors.lastname: Fonseca
authors.forename: Brian Patrick
authors.initials: BP
authors.lastname: O'Neill
mesh_terms: D000368:Aged; D016543:Central Nervous System Neoplasms / Q000235:genetics* / Q000473:pathology; D002869:Chromosome Aberrations; D055028:Comparative Genomic Hybridization / Q000592:standards; D056915:DNA Copy Number Variations / Q000235:genetics; D005260:Female; D005404:Fixatives; D005557:Formaldehyde; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008223:Lymphoma / Q000235:genetics* / Q000473:pathology; D008297:Male; D008875:Middle Aged; D016612:Paraffin Embedding
chemical_list: D005404:Fixatives; D005557:Formaldehyde