Robustness of genome-wide scanning using archived dried blood spot samples as a DNA source.

Author(s): Hollegaard MV, Grove J, Grauholm J, Kreiner-Møller E, Bønnelykke K, Nørgaard M, Benfield TL, Nørgaard-Pedersen B, Mortensen PB, Mors O, Sørensen HT, Harboe ZB, Børglum AD, Demontis D, Ørntoft TF, Bisgaard H, Hougaard DM

Publication: BMC Genet, 2011, Vol. 12, Page 58

PubMed ID: 21726430 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the effects of storage duration, temperature and type of filter paper on DNA yield and genotyping success from DBS using three different array platforms. The 4,641 DBS included in this study were comprised of case-controls from three different studies, each of which was genotyped using a different platform. DBS collected between 1981 and 1987 were stored at 4 degrees C, but specimens collected 1988-2006 were stored at -20 degrees C. DNA was extracted from two 3.2 mm punches using the Extract-N-Amp kit and amplified in triplicate using the REPLI-g mini kit.

   Summary of Findings:

   WGA DNA yield decreased by an average of 10.4 ng/ul with each additional year of storage, but the average decrease in yield was only 2.67 ng/ul/year in specimens stored at -20 degrees C. There was no effect of filter paper type on WGA DNA yield. The average call rates for the cohorts using the 610k, Omni1, and Axiom chip arrays were 99.38%, 99.722% and 99.206%, respectively. Despite normalization of input DNA amount, the concentration of the amplified DNA had a positive effect on the call rates for the cohorts genotyped using Omni1 and Axiom chip arrays (p<0.001 and p=0.013, respectively), but not for the cohort genotyped with the 610k chip array. Using the Omni1 chip array, specimens collected on S&S2992 filter paper had a higher genotype call rate than those collected on S&S903 filter paper (p=0.005), but this was not true for specimens genotyped using the Axiom array and was not studied using the 610k array. In the Omni1-genotyped cohort, there was an association between filter paper and duration of storage, with specimens collected on S&S903 showing a decreasing call rate with increasing storage duration, but this relationship was not seen for specimens collected on S&S902 filter paper. Generally storage duration and temperature had no effects on call rates in the cohorts genotyped using the Omni1 or 610k platforms, but storage duration and temperature significantly affected call rates for specimens genotyped using the Axiom platform (p<0.001, both). In the cohort genotyped with the Axiom chip array, storage at -20 degrees C partially attenuated the effects of increasing storage duration.

   Biospecimens

   • Bodily Fluid - Blood

   Preservative Types

   • Other Preservative

   Diagnoses:

   • Not specified

   Platform:

   Analyte	Technology Platform
   DNA	Fluorometry
   DNA	DNA microarray
   DNA	SNP assay

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Storage	Storage duration	4-28 years
   Storage	Storage temperature	4 degrees C -20 degrees C
   Storage	Storage conditions	On S&S2992 filter paper On S&S903 filter paper
   SNP assay Specific	Technology platform	Illumina Infinium HD HumanOmni1-Quad chip array Infinium Human610-Quad chip array Axiom Genome-Wide CEU Array chip

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