Open Access Highly Accessed Methodology article

Optimized DNA extraction from neonatal dried blood spots: application in methylome profiling

Akram Ghantous1, Richard Saffery2, Marie-Pierre Cros1, Anne-Louise Ponsonby34, Steven Hirschfeld5, Carol Kasten5, Terence Dwyer346, Zdenko Herceg1 and Hector Hernandez-Vargas1*

Author Affiliations

1 Epigenetics Group, International Agency for Research on Cancer (IARC), 150 rue Albert-Thomas, 69008 Lyon, France

2 Cancer and Disease Epigenetics, Murdoch Childrens Research Institute Royal Children's Hospital, Flemington Road Parkville, Victoria 3052, Australia

3 Environmental & Genetic Epidemiology Research, Murdoch Children’s Research Institute Royal Children’s Hospital, Flemington Road Parkville, Victoria 3052, Australia

4 Menzies Research Institute, University of Tasmania, Hobart TAS 7000, Australia

5 Department of Health and Human Services, National Children’s Study, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health U.S., 6100 Executive Boulevard, Room 3A01, Bethesda, MD 20892, USA

6 Chair, Steering Committtee, International Childhood Cancer Cohort Consortium (I4C

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BMC Biotechnology 2014, 14:60  doi:10.1186/1472-6750-14-60

Published: 1 July 2014

Abstract

Background

Neonatal dried blood spots (DBS) represent an inexpensive method for long-term biobanking worldwide and are considered gold mines for research for several human diseases, including those of metabolic, infectious, genetic and epigenetic origin. However, the utility of DBS is restricted by the limited amount and quality of extractable biomolecules (including DNA), especially for genome wide profiling. Degradation of DNA in DBS often occurs during storage and extraction. Moreover, amplifying small quantities of DNA often leads to a bias in subsequent data, particularly in methylome profiles. Thus it is important to develop methodologies that maximize both the yield and quality of DNA from DBS for downstream analyses.

Results

Using combinations of in-house-derived and modified commercial extraction kits, we developed a robust and efficient protocol, compatible with methylome studies, many of which require stringent bisulfite conversion steps. Several parameters were tested in a step-wise manner, including blood extraction, cell lysis, protein digestion, and DNA precipitation, purification and elution. DNA quality was assessed based on spectrophotometric measurements, DNA detectability by PCR, and DNA integrity by gel electrophoresis and bioanalyzer analyses. Genome scale Infinium HumanMethylation450 and locus-specific pyrosequencing data generated using the refined DBS extraction protocol were of high quality, reproducible and consistent.

Conclusions

This study may prove useful to meet the increased demand for research on prenatal, particularly epigenetic, origins of human diseases and for newborn screening programs, all of which are often based on DNA extracted from DBS.

Keywords:
Blood spot; DNA extraction; Epigenetics; Methylome; HM450; Pyrosequencing; Whole bisulfitome amplification; QIAamp; GenSolve; NucleoSpin