title: Gene expression profiling of archived dried blood spot samples from the Danish Neonatal Screening Biobank.
abstract: A large part of the human genome is transcribed into various forms of RNA, and the global gene expression profile (GEP) has been studied for several years using technology such as RNA-microarrays. In this study, we evaluate whether neonatal dried blood spot (DBS) samples stored in the Danish Neonatal Screening Biobank (DNSB) can be used for GEP. This paper is divided into sub-studies examining the effects of: 1) different whole transcriptome amplification kits (WTA); 2) years of storage and storage in room temperature (RT) versus freezers (-20°C) on DNSB DBS samples; 3) effects of RT storage vs freezer storage on DBS samples from the USA and DNSB, and 4) using smaller disc sizes, thereby decreasing DBS use. We present evidence that reliable and reproducible GEPs can be obtained using neonatal DBS samples. The main source of variation is the storage condition. When samples are stored at -20°C, the dynamic range is increased, and Pearson correlations are higher. Differential analysis reveals no statistically significant differences between samples collected a decade apart and stored at -20°C. However, samples stored at RT show differential expression for a third of the gene-specific probes. Our data also suggests that using alternate WTA kits significantly changes the GEP. Finally, the amount of input material, i.e., the size and number of DBS discs used, can be reduced to preserve this valuable and limited material. We conclude that DNSB DBS samples provide a reproducible resource for GEP. Results are improved if the cards are stored at -20°C. Furthermore, it is important to use a single type of kit for analysis because using alternate kits introduces differential expression.
authors.affiliation: Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark. Electronic address: jogr@ssi.dk.
authors.forename: Jonas
authors.initials: J
authors.lastname: Grauholm
authors.affiliation: Department of Cell and Molecular Biology, Grand Valley State University, Grand Rapids, MI 49503, USA. Electronic address: khoos@gvsu.edu.
authors.forename: Sok Kean
authors.initials: SK
authors.lastname: Khoo
authors.affiliation: Department of Mathematics & Computer Science, Fayetteville State University, Fayetteville, NC 28301, USA. Electronic address: rnickolov@uncfsu.edu.
authors.forename: Radoslav Z
authors.initials: RZ
authors.lastname: Nickolov
authors.affiliation: Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark. Electronic address: jesp@ssi.dk.
authors.forename: Jesper B
authors.initials: JB
authors.lastname: Poulsen
authors.affiliation: Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark. Electronic address: mabh@ssi.dk.
authors.forename: Marie
authors.initials: M
authors.lastname: Bækvad-Hansen
authors.affiliation: Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark. Electronic address: chsh@ssi.dk.
authors.forename: Christine S
authors.initials: CS
authors.lastname: Hansen
authors.affiliation: Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark. Electronic address: dh@ssi.dk.
authors.forename: David M
authors.initials: DM
authors.lastname: Hougaard
authors.affiliation: Section of Neonatal Genetics, Danish Centre for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark. Electronic address: mvh@ssi.dk.
authors.forename: Mads V
authors.initials: MV
authors.lastname: Hollegaard
mesh_terms: D018070:Biological Specimen Banks; D001793:Blood Preservation; D001800:Blood Specimen Collection; D015925:Cryopreservation; D003718:Denmark; D059788:Dried Blood Spot Testing; D020869:Gene Expression Profiling; D015894:Genome, Human; D006801:Humans; D007231:Infant, Newborn; D046228:Microarray Analysis; D015997:Neonatal Screening; D020871:RNA Stability; D015203:Reproducibility of Results; D013696:Temperature
keywords: Biobank; Dried blood spots; Gene expression profile; Neonatal screening; RNA storage; Whole transcriptome amplification