title: Expression profiling of archival tumors for long-term health studies.
abstract: OBJECTIVE
  More than 20 million archival tissue samples are stored annually in the United States as formalin-fixed, paraffin-embedded (FFPE) blocks, but RNA degradation during fixation and storage has prevented their use for transcriptional profiling. New and highly sensitive assays for whole-transcriptome microarray analysis of FFPE tissues are now available, but resulting data include noise and variability for which previous expression array methods are inadequate.
  
  
  METHODS
  We present the two largest whole-genome expression studies from FFPE tissues to date, comprising 1,003 colorectal cancer (CRC) and 168 breast cancer samples, combined with a meta-analysis of 14 new and published FFPE microarray datasets. We develop and validate quality control (QC) methods through technical replication, independent samples, comparison to results from fresh-frozen tissue, and recovery of expected associations between gene expression and protein abundance.
  
  
  RESULTS
  Archival tissues from large, multicenter studies showed a much wider range of transcriptional data quality relative to smaller or frozen tissue studies and required stringent QC for subsequent analysis. We developed novel methods for such QC of archival tissue expression profiles based on sample dynamic range and per-study median profile. This enabled validated identification of gene signatures of microsatellite instability and additional features of CRC, and improved recovery of associations between gene expression and protein abundance of MLH1, FASN, CDX2, MGMT, and SIRT1 in CRC tumors.
  
  
  CONCLUSIONS
  These methods for large-scale QC of FFPE expression profiles enable study of the cancer transcriptome in relation to extensive clinicopathological information, tumor molecular biomarkers, and long-term lifestyle and outcome data.
authors.affiliation: Department of Biostatistics and Computational Biology and Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Levi
authors.initials: L
authors.lastname: Waldron
authors.forename: Shuji
authors.initials: S
authors.lastname: Ogino
authors.forename: Yujin
authors.initials: Y
authors.lastname: Hoshida
authors.forename: Kaori
authors.initials: K
authors.lastname: Shima
authors.forename: Amy E
authors.initials: AE
authors.lastname: McCart Reed
authors.forename: Peter T
authors.initials: PT
authors.lastname: Simpson
authors.forename: Yoshifumi
authors.initials: Y
authors.lastname: Baba
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Nosho
authors.forename: Nicola
authors.initials: N
authors.lastname: Segata
authors.forename: Ana Cristina
authors.initials: AC
authors.lastname: Vargas
authors.forename: Margaret C
authors.initials: MC
authors.lastname: Cummings
authors.forename: Sunil R
authors.initials: SR
authors.lastname: Lakhani
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Kirkner
authors.forename: Edward
authors.initials: E
authors.lastname: Giovannucci
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: Todd R
authors.initials: TR
authors.lastname: Golub
authors.forename: Charles S
authors.initials: CS
authors.lastname: Fuchs
authors.forename: Giovanni
authors.initials: G
authors.lastname: Parmigiani
authors.forename: Curtis
authors.initials: C
authors.lastname: Huttenhower
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism*; D015179:Colorectal Neoplasms / Q000235:genetics / Q000378:metabolism*; D005260:Female; D005404:Fixatives / Q000737:chemistry; D005500:Follow-Up Studies; D005557:Formaldehyde / Q000737:chemistry; D020869:Gene Expression Profiling / Q000592:standards*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding; D011786:Quality Control; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012016:Reference Values; D015203:Reproducibility of Results; D016707:Tissue Fixation; D059467:Transcriptome
chemical_list: D005404:Fixatives; D012333:RNA, Messenger; D005557:Formaldehyde