Publication focus: high quality genome-wide genotyping from archived dried blood spots without DNA amplification

High Quality Genome-Wide Genotyping from Archived Dried Blood Spots without DNA Amplification
Krystal R. St. Julien et al. PLoS ONE, May 2013, 8(5): e64710. doi:10.1371/journal.pone.0064710

Abstract

Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping.

Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA.

• Genome-wide SNP genotyping was done by Illumina using their Infinium single nucleotide

extension SNP genotyping assay and a cytoSNP or Omni bead microarray.

• Successful genotyping was obtained with ~20 ng (4 ml of 5 ng/ml gDNA) or more of unamplified

gDNA.

• Krystal et al. obtained 170 ng or more of gDNA from 37% of all archived DBS using ~17% (five 2

mm punches) of each DBS. Further iterations of using sets of five 2 mm punches enabled  This

contrasts with requests from illumina who regularly ask for 1 mg DNA, provided as 20 ml of 50

ng/ml DNA, for Infinium SNP genotyping.

• A modified proteinase K digestion and isopropanol DNA precipitation protocol for extraction of

genomic DNA from DBS was used. A 96 well plate format was used together with a 1 hr

proteolysis step to provide a 48-fold increase in throughput.

• The increased throughput allowed one individual to isolate gDNA from over 1,700 archived

DBS in less than 2 months for use in genome-wide SNP genotyping for an association study.

• For any application in which only a small fraction of a DBS is available, or DNA isolation time is

critical, preparation of whole genome amplified DNA is preferred.

• The procedure described should enable large-scale, high accuracy genomic studies of

archived DBS, while helping to preserve these precious resources.

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