Acquiring genome-wide gene expression profiles in Guthrie card blood spots using microarrays

Standard Guthrie cards have been widely used to collect blood samples from essentially all USA and Japanese neonates for newborn screening programs. Thus, archival blood spot samples are a unique and comprehensive resource for molecular pathology studies. However, the challenge in using these sample...

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Bibliographic Details
Published in:Pathology international 2011-01, Vol.61 (1), p.1-6
Main Authors: Khoo, Sok Kean, Dykema, Karl, Vadlapatla, Naga Manjari, LaHaie, David, Valle, Saul, Satterthwaite, David, Ramirez, Sara Angeline, Carruthers, Janell Alee, Haak, Peterson Todd, Resau, James Howard
Format: Article
Language:English
Subjects:
Agilent microarray
Blood Specimen Collection - methods
blood spots
gene expression profiles
Gene Expression Profiling - methods
genome-wide
Guthrie card
Humans
Indexing in process
Infant, Newborn
Neonatal Screening - methods
Oligonucleotide Array Sequence Analysis - methods
Polymerase Chain Reaction
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Summary:Standard Guthrie cards have been widely used to collect blood samples from essentially all USA and Japanese neonates for newborn screening programs. Thus, archival blood spot samples are a unique and comprehensive resource for molecular pathology studies. However, the challenge in using these samples is the presumed low quantity and degraded quality of nucleic acids that can be isolated from these samples, particularly the RNA. Here, we report a new assay using Agilent 4x44K microarrays for acquiring genome‐wide gene expression profiles from blood spots on Guthrie cards. Due to the small amount of RNA obtained from each sample, major modifications, such as concentrating and amplifying the RNA and using a different labeling procedure, were performed. Approximately 9000 expressed genes can be detected after normalization of data, an increment of 260% in detection power compared with previously reported cDNA microarrays made in‐house with standard procedures. The correlation coefficients in technical and biological replicates were 0.92 and 0.85, respectively, confirming the reproducibility of this study. This new and comprehensive assay will add value to the utility of archival Guthrie cards (e.g. neonatal blood spot cards) and open new opportunities to molecular epidemiology, pathology, genomic, and diagnostic studies of perinatal diseases.
ISSN:1320-5463
1440-1827
DOI:10.1111/j.1440-1827.2010.02611.x