For DNA extraction, one 10 ml EDTA tube from mothers, partners and children at birth have been collected and stored directly as whole blood sample at −80°C. After completion of the blood sample collection, DNA extraction was started from white blood cells. First, DNA extraction from all children has been conducted manually using the Qiagen FlexiGene Kit (Qiagen Hilden, Germany). Currently, DNA extraction from 5 ml whole blood samples from the mothers and partners is performed by a Hamilton STAR multi-channel robot using AGOWA magnetic bead technology (at 72 samples per run) and is expected to be finished in spring 2008.
Extracted DNA is automatically collected in stock tubes (2D Matrix, Micronic) that are organized in 96-wells format, but that can be individually addressed. These stock samples are split into two tubes that are stored at different locations. One of the stocks will then be used for normalising the DNA concentrations in 96 deep well (DW) plates. This protocol, as well as other manipulations of the DNA samples are performed on a Caliper ALH3000 pipetting robot (8/96/384 channels) with a Twister module and a 96/384 wells Tecan GENios plus UV reader. In total, 90 DNA samples are normalised per 96 DW plate with 6 water blancs per plate. Additionally, a random selection of 5% of the total number of samples are put into separate 96 DW plates, again with 6 blancs per plate, for control purposes. For normalisation, sample and diluent volumes are automatically calculated and produced to obtain equal DNA concentrations for all samples (25–50 ng/μl). From these stock 96-DW plates, 384 DW plates are created, which comprise 24 blancs each. Subsequently, replica PCR plates (384 wells) with a concentration of 1 ng/μl are created for genotype studies.
Stock 96-well plates (DW and 2D Matrix, Micronic) are stored at −20°C at two different locations within the Erasmus Medical Center (Genetic Epidemiology Laboratory, Genetic Laboratory Internal Medicine). The 384 DW stock and PCR plates are stored at the Genetic Laboratory Internal Medicine, Erasmus Medical Center. All genotyping studies with Generation R DNA material are performed in-house at the high throughput genotyping facility in this Laboratory.