title: MicroRNA profiling of patient plasma for clinical trials using bioinformatics and biostatistical approaches.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are short noncoding RNAs that function to repress translation of mRNA transcripts and contribute to the development of cancer. We hypothesized that miRNA array-based technologies work best for miRNA profiling of patient-derived plasma samples when the techniques and patient populations are precisely defined.
  
  
  METHODS
  Plasma samples were obtained from five sources: melanoma clinical trial of interferon and bortezomib (12), purchased normal donor plasma samples (four), gastrointestinal tumor bank (nine), melanoma tumor bank (ten), or aged-matched normal donors (eight) for the tumor bank samples. Plasma samples were purified for miRNAs and quantified using NanoString®arrays or by the company Exiqon. Standard biostatistical array approaches were utilized for data analysis and compared to a rank-based analytical approach.
  
  
  RESULTS
  With the prospectively collected samples, fewer plasma samples demonstrated visible hemolysis due to increased attention to eliminating factors, such as increased pressure during phlebotomy, small gauge needles, and multiple punctures. Cancer patients enrolled in a melanoma clinical study exhibited the clearest pattern of miRNA expression as compared to normal donors in both the rank-based analytical method and standard biostatistical array approaches. For the patients from the tumor banks, fewer miRNAs (<5) were found to be differentially expressed and the false positive rate was relatively high.
  
  
  CONCLUSIONS
  In order to obtain consistent results for NanoString miRNA arrays, it is imperative that patient cohorts have similar clinical characteristics with a uniform sample preparation procedure. A clinical workflow has been optimized to collect patient samples to study plasma miRNAs.
authors.affiliation: Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, FL; Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Oncologic Sciences, USF Morsani School of Medicine, Tampa, FL; Division of Medical Oncology, The Ohio State University Wexner Medical Center.
authors.forename: Joseph
authors.initials: J
authors.lastname: Markowitz
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Biomedical Informatics.
authors.forename: Zachary
authors.initials: Z
authors.lastname: Abrams
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Radiation Oncology.
authors.forename: Naduparambil K
authors.initials: NK
authors.lastname: Jacob
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Center for Biostatistics.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, FL.
authors.forename: John N
authors.initials: JN
authors.lastname: Hassani
authors.affiliation: Department of Surgery, The Ohio State University, Columbus, OH, USA.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Latchana
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Center for Biostatistics.
authors.forename: Lai
authors.initials: L
authors.lastname: Wei
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Biomedical Informatics.
authors.forename: Kelly E
authors.initials: KE
authors.lastname: Regan
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH.
authors.forename: Taylor R
authors.initials: TR
authors.lastname: Brooks
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH.
authors.forename: Sarvani R
authors.initials: SR
authors.lastname: Uppati
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH.
authors.forename: Kala M
authors.initials: KM
authors.lastname: Levine
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Division of Medical Oncology, The Ohio State University Wexner Medical Center.
authors.forename: Tanios
authors.initials: T
authors.lastname: Bekaii-Saab
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Division of Medical Oncology, The Ohio State University Wexner Medical Center.
authors.forename: Kari L
authors.initials: KL
authors.lastname: Kendra
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Division of Medical Oncology, The Ohio State University Wexner Medical Center.
authors.forename: Gregory B
authors.initials: GB
authors.lastname: Lesinski
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Surgery, The Ohio State University, Columbus, OH, USA.
authors.forename: J Harrison
authors.initials: JH
authors.lastname: Howard
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Division of Medical Oncology, The Ohio State University Wexner Medical Center.
authors.forename: Thomas
authors.initials: T
authors.lastname: Olencki
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Biomedical Informatics.
authors.forename: Philip R
authors.initials: PR
authors.lastname: Payne
authors.affiliation: Comprehensive Cancer Center, The Ohio State University, Columbus, OH; Department of Surgery, The Ohio State University, Columbus, OH, USA.
authors.forename: William E
authors.initials: WE
authors.lastname: Carson
keywords: melanoma; miRNA; profiling; rank-based statistic