title: A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood.
abstract: BACKGROUND
  Although microarray technology has become the most common method for studying global gene expression, a plethora of technical factors across the experiment contribute to the variable of genome gene expression profiling using peripheral whole blood. A practical platform needs to be established in order to obtain reliable and reproducible data to meet clinical requirements for biomarker study.
  
  
  RESULTS
  We applied peripheral whole blood samples with globin reduction and performed genome-wide transcriptome analysis using Illumina BeadChips. Real-time PCR was subsequently used to evaluate the quality of array data and elucidate the mode in which hemoglobin interferes in gene expression profiling. We demonstrated that, when applied in the context of standard microarray processing procedures, globin reduction results in a consistent and significant increase in the quality of beadarray data. When compared to their pre-globin reduction counterparts, post-globin reduction samples show improved detection statistics, lowered variance and increased sensitivity. More importantly, gender gene separation is remarkably clearer in post-globin reduction samples than in pre-globin reduction samples. Our study suggests that the poor data obtained from pre-globin reduction samples is the result of the high concentration of hemoglobin derived from red blood cells either interfering with target mRNA binding or giving the pseudo binding background signal.
  
  
  CONCLUSIONS
  We therefore recommend the combination of performing globin mRNA reduction in peripheral whole blood samples and hybridizing on Illumina BeadChips as the practical approach for biomarker study.
authors.affiliation: Informatics Program, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA.
authors.forename: Ze
authors.initials: Z
authors.lastname: Tian
authors.forename: Nathan
authors.initials: N
authors.lastname: Palmer
authors.forename: Patrick
authors.initials: P
authors.lastname: Schmid
authors.forename: Hui
authors.initials: H
authors.lastname: Yao
authors.forename: Michal
authors.initials: M
authors.lastname: Galdzicki
authors.forename: Bonnie
authors.initials: B
authors.lastname: Berger
authors.forename: Erxi
authors.initials: E
authors.lastname: Wu
authors.forename: Isaac S
authors.initials: IS
authors.lastname: Kohane
mesh_terms: D015415:Biomarkers / Q000097:blood*; D020869:Gene Expression Profiling; D005914:Globins / Q000235:genetics; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000235:genetics
chemical_list: D015415:Biomarkers; D012333:RNA, Messenger; D005914:Globins