Genome-wide scans using archived neonatal dried blood spot samples.

Author(s): Hollegaard MV, Grauholm J, Børglum A, Nyegaard M, Nørgaard-Pedersen B, Ørntoft T, Mortensen PB, Wiuf C, Mors O, Didriksen M, Thorsen P, Hougaard DM

Publication: BMC Genomics, 2009, Vol. 10, Page 297

PubMed ID: 19575812 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 of DBS, DNA extraction method, and WGA method on genome-wide analysis of archival DBS from volunteers and neonates enrolled in a genetic schizophrenia study. DBS from 24 neonates were stored for 15-25 years at -24 degrees C. DNA was extracted from 1 or 3 3.2 mm disks with ENA or QIAamp DNA blood micro kit (QIAamp), amplified using one of 3 different WGA kits, and hybridized to Illumina Infinium HD Human610-Quad BeadChips. Results were compared to those obtained using DNA extracted from venous blood with the Maxwell 16 DNA purification system.

   Summary of Findings:

   Extraction of DNA from DBS with ENA followed by amplification with Repli-g resulted in the highest average call rate (>99%) and the lowest call conflict with fresh reference DNA from venous blood specimens (0.02-0.03%). When DNA was extracted with QIAamp, amplification with REPLI-g led to high variability in call and conflict rates, but amplification with GenomePlex Single Cell whole genome amplification kit led to >97% call rates and less than 0.038% conflict with the reference DNA. Using 3 disks for DNA extraction instead of 1 did not improve call rates or decrease conflict rates. Further, the storage duration of DBS had no significant effects on genotyping performance.

   Biospecimens

   • Bodily Fluid - Blood

   Preservative Types

   • Other Preservative
   • None (Fresh)

   Diagnoses:

   • Not specified
   • Schizophrenia

   Platform:

   Analyte	Technology Platform
   DNA	DNA microarray
   DNA	Fluorometry
   DNA	Whole genome amplification

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Air-dried None (fresh)
   Storage	Storage duration	15-25 years
   Analyte Extraction and Purification	Analyte isolation method	Maxwell 16 DNA purification system Extract-N-Amp blood PCR kit QIAamp DNA blood micro kit
   Whole genome amplification Specific	Nucleic acid amplification	Qiagen REPLI-g kit GenomePlex Complete WGA kit (GPlex2)) GenomePlex Single Cell whole genome amplification kit (GPLex4)
   Biospecimen Aliquots and Components	Aliquot size/volume	1 x 3.2 mm disk 3 x 3.2 mm disk

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