Genome-wide scans using archived neonatal dried blood spot samples

doi:10.1186/1471-2164-10-297

BMC Genomics. 2009; 10: 297.

Published online 2009 July 4. doi: 10.1186/1471-2164-10-297

PMCID: PMC2713266

Genome-wide scans using archived neonatal dried blood spot samples

Mads V Hollegaard,^1,² Jonas Grauholm,³ Anders Børglum,⁴ Mette Nyegaard,⁴ Bent Nørgaard-Pedersen,¹ Torben Ørntoft,^3,⁵ Preben B Mortensen,⁶ Carsten Wiuf,⁷ Ole Mors,⁸ Michael Didriksen,⁹ Poul Thorsen,¹⁰ and David M Hougaard¹

¹Section of Neonatal Screening and Hormones, Statens Serum Institut, Copenhagen, DK-2300, Denmark

²Department of Epidemiology, University of Aarhus, Aarhus, DK-8000, Denmark

³AROS Applied Biotechnology A/S, Aarhus, DK-8000, Denmark

⁴Institute of Human Genetics, University of Aarhus, Aarhus, DK-8000, Denmark

⁵Department of Clinical Biochemistry, Skejby Sygehus, Aarhus, DK-8000, Denmark

⁶The National Centre for Register Based Research, University of Aarhus, Aarhus, DK-8000, Denmark

⁷Bioinformatics Research Center, University of Aarhus, Aarhus, DK-8000, Denmark

⁸Centre for Psychiatric Research, Aarhus University Hospital Risskov, Aarhus, DK-8000, Denmark

⁹Lundbeck A/S, Taastrup, DK-2630, Denmark

¹⁰Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA

Corresponding author.

Mads V Hollegaard: mvh/at/ssi.dk; Jonas Grauholm: jg/at/arosab.com; Anders Børglum: anders/at/humgen.au.dk; Mette Nyegaard: nyegaard/at/humgen.au.dk; Bent Nørgaard-Pedersen: bnp/at/ssi.dk; Torben Ørntoft: orntoft/at/ki.au.dk; Preben B Mortensen: pbm/at/ncrr.dk; Carsten Wiuf: wiuf/at/birc.au.dk; Ole Mors: om/at/psykiatri.aaa.dk; Michael Didriksen: mdi/at/lundbeck.com; Poul Thorsen: pt/at/soci.au.dk; David M Hougaard: dh/at/ssi.dk

Received November 21, 2008; Accepted July 4, 2009.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Abstract

Background

Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects. Archived residual dried blood spot samples from national newborn screening programs may provide DNA from entire populations and medical registries the corresponding clinical information. The amount of DNA available in these samples is however rarely sufficient for reliable genome-wide scans, and whole-genome amplification may thus be necessary. This study assess the quality of DNA obtained from different amplification protocols by evaluating fidelity and robustness of the genotyping of 610,000 single nucleotide polymorphisms, using the Illumina Infinium HD Human610-Quad BeadChip. Whole-genome amplified DNA from 24 neonatal dried blood spot samples stored between 15 to 25 years was tested, and high-quality genomic DNA from 8 of the same individuals was used as reference.

Results

Using 3.2 mm disks from dried blood spot samples the optimal DNA-extraction and amplification protocol resulted in call-rates between 99.15% – 99.73% (mean 99.56%, N = 16), and conflicts with reference DNA in only three per 10,000 genotype calls.

Conclusion

Whole-genome amplified DNA from archived neonatal dried blood spot samples can be used for reliable genome-wide scans and is a cost-efficient alternative to collecting new samples.

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