Effects of globin mRNA reduction methods on gene expression profiles from whole blood.
Excessive globin mRNA in whole blood RNA decreases transcript detection sensitivity and increases signal variation on microarrays. Hence, methods based on peptide nucleic acid inhibitory oligos and biotinylated DNA capture oligos have been developed to reduce globin mRNA. However, there is limited information about the effects of these two methods on gene expression profiles. Thus, we systematically compared the facility and effects of the two globin reduction methods on profile measurements from Jurkat cell line RNA with or without spiked globin mRNA and human blood RNA isolated using PAXgene collection tubes. We showed that the methods were efficient at increasing the sensitivity of transcript detection without loss of specificity, but neither method could recover a profile equivalent to that of an identical RNA sample without globin mRNA excesses. The capture oligo method had slightly better transcript detection sensitivity for cell line RNA, lowered signal variation for PAXgene RNA, and more similar profiles to controls than the inhibitory method. However, the capture method required larger amounts of initial high-quality RNA to yield sufficient cRNA amounts, and its procedures were more complex and time consuming than the inhibitory method. These results inform the selection of methods suitable for multicenter surveillance of gene expression profiles.
Liu
Jinny
J
Center for Biomolecular Science and Engineering, Code 6920, Naval Research Laboratory, 4555 Overlook Ave., SW, Bldg. 30, Washington, DC 20375, USA.
Walter
Elizabeth
E
Stenger
David
D
Thach
Dzung
D
D001800:Blood Specimen Collection / Q000379:methods*; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D014644:Genetic Variation; D005914:Globins / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D019169:Jurkat Cells; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012313:RNA / Q000097:blood*; D012333:RNA, Messenger / Q000097:blood*; D014158:Transcription, Genetic
D012333:RNA, Messenger; D012313:RNA; D005914:Globins