Whole genome microarray analysis, from neonatal blood cards

Abstract

Background: Neonatal blood, obtained from a heel stick and stored dry on paper cards, has been the standard for birth defects screening for 50 years. Such dried blood samples are used, primarily, for analysis of small-molecule analytes. More recently, the DNA complement of such dried blood cards has been used for targeted genetic testing, such as for single nucleotide polymorphism in cystic fibrosis. Expansion of such testing to include polygenic traits, and perhaps whole genome scanning, has been discussed as a formal possibility. However, until now the amount of DNA that might be obtained from such dried blood cards has been limiting, due to inefficient DNA recovery technology.

Results: A new technology is employed for efficient DNA release from a standard neonatal blood card. Using standard Guthrie cards, stored an average of ten years post-collection, about 1/40th of the air-dried neonatal blood specimen (two 3 mm punches) was processed to obtain DNA that was sufficient in mass and quality for direct use in microarray-based whole genome scanning. Using that same DNA release technology, it is also shown that approximately 1/250th of the original purified DNA (about 1 ng) could be subjected to whole genome amplification, thus yielding an additional microgram of amplified DNA product. That amplified DNA product was then used in microarray analysis and yielded statistical concordance of 99% or greater to the primary, unamplified DNA sample.

Conclusion: Together, these data suggest that DNA obtained from less than 10% of a standard neonatal blood specimen, stored dry for several years on a Guthrie card, can support a program of genome-wide neonatal genetic testing.

Figure 1

Samples to be used for Illumina 610 Microarrays, without prior WGA. Samples were applied at 100 ng per well and run on an Invitrogen 0.8% agarose E-gel for 30 minutes, and visualized by ethidium bromide staining.

Figure 2

Samples not used for Illumina 610 Microarrays, without prior WGA. Samples were applied at 100 ng per well and run on an Invitrogen 0.8% agarose E-gel for 30 minutes, and visualized by ethidium bromide staining.

Figure 3

Samples not used for Illumina 610 Microarrays, without prior WGA. Samples were applied at 100 ng per well and run on an Invitrogen 0.8% agarose E-gel for 30 minutes, and visualized by ethidium bromide staining.

Figure 4

Samples to be used for Illumina 610 Microarrays, subsequent to WGA. Samples were applied at 100 ng per well and run on an Invitrogen 1.2% agarose E-gel for 30 minutes, and visualized by ethidium bromide staining.