Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues.
Archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens represent a readily available but largely untapped resource for gene expression profiling-based biomarker discovery. Several technologies have been proposed to cope with the bias from RNA cross-linking and degradation associated with archival specimens to generate data comparable with RNA from fresh-frozen materials. Direct comparison studies of these RNA expression platforms remain rare. We compared two commercially available platforms for RNA expression profiling of archival FFPE specimens from clinical studies of prostate and ovarian cancer: the Affymetrix Human Gene 1.0ST Array following whole-transcriptome amplification using the NuGen WT-Ovation FFPE System V2, and the NanoString nCounter without amplification. For each assay, we profiled 7 prostate and 11 ovarian cancer specimens, with a block age of 4 to 21 years. Both platforms produced gene expression profiles with high sensitivity and reproducibility through technical repeats from FFPE materials. Sensitivity and reproducibility remained high across block age within each cohort. A strong concordance was shown for the transcript expression values for genes detected by both platforms. We showed the biological validity of specific gene signatures generated by both platforms for both cohorts. Our study supports the feasibility of gene expression profiling and large-scale signature validation on archival prostate and ovarian tumor specimens using commercial platforms. These approaches have the potential to aid precision medicine with biomarker discovery and validation.
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts. Electronic address: svitlana@jimmy.harvard.edu.
Svitlana
S
Tyekucheva
Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
Neil E
NE
Martin
Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts.
Edward C
EC
Stack
Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts.
Wei
W
Wei
Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts.
Vinod
V
Vathipadiekal
City University of New York School of Public Health, Hunter College, New York, New York.
Levi
L
Waldron
Pathology Unit, Addarii Institute, S. Orsola-Malpighi Hospital, Bologna, Italy.
Michelangelo
M
Fiorentino
Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts.
Rosina T
RT
Lis
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts; Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts.
Meir J
MJ
Stampfer
Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute, Cambridge, Massachusetts; Division of Cancer Studies, King's College London, London, United Kingdom.
Massimo
M
Loda
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts.
Giovanni
G
Parmigiani
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts.
Lorelei A
LA
Mucci
Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts.
Michael
M
Birrer
D017326:Clinical Trials, Phase III as Topic; D005260:Female; D005557:Formaldehyde / Q000737:chemistry*; D020869:Gene Expression Profiling; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D010051:Ovarian Neoplasms / Q000235:genetics* / Q000473:pathology; D016612:Paraffin Embedding / Q000379:methods*; D011446:Prospective Studies; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000473:pathology; D012333:RNA, Messenger / Q000235:genetics*; D012334:RNA, Neoplasm / Q000235:genetics; D016032:Randomized Controlled Trials as Topic; D016707:Tissue Fixation
D012333:RNA, Messenger; D012334:RNA, Neoplasm; D005557:Formaldehyde