Germline SNPs were genotyped in whole blood (fourteen TFPI SNPs and six TF SNPs) or tumor tissue (four TFPI SNPs) using the iPLEX Gold massarray platform (Sequenom) at the Centre for Integrative Genetics, Norwegian University of Life Sciences, Ås, Norway, or the Affymetrix ® Genome -Wide Human SNP Array 6.0 at AROS Applied Biotechnology AS, Aarhus, Denmark, respectively.
Stage 2 genotyping (KORA S4 cohort, n = 1830) of 74 SNPs was performed using the iPLEX assay (Sequenom; primers are given in Supplementary Material, Table S5).
In validation stage, SNPs were genotyped using the iPLEX system (Sequenom, Inc., San Diego, CA, USA), in which all genotyping reactions were performed in 384-well plates according to the manufacturer's iPLEX Application Guide (Sequenom, Inc).
The candidate gene single nucleotide polymorphism (SNP) analyses were performed using the iPLEX assay in conjunction with the Sequenom MassARRAY platform.
SNP markers were genotyped using the iPlex chemistry on the Sequenom platform according to the manufacturer's instructions (Sequenom, San Diego, California, USA) [ 9].
10ng of genomic DNA from NA12878 was genotyped for 36 SNP, indel and copy number variants for CYP2D6 using the iPLEX ® ADME CYP2D6 Panel v1.0, developed by Assays by Agena (formerly Sequenom) on the MassARRAY4 System.
The SNPs were genotyped across the appropriate resources using the iPLEX system (Sequenom) according to the manufacturer's instructions.
FKBP5, NR3C1, and CRHR1 SNPs were analysed on a Sequenom platform using the iPlex technology (Sequenom, San Diego, CA, USA) in a multiplex assay using 10 ng of DNA.
Replication genotyping of seven SNPs in KORA S4 samples (n = 1,830) was performed using the iPLEX assay (Sequenom).
DNA samples (in almost all cases, obtained from blood) were genotyped using the iPLEX Mass Array platform at four genotyping centres (Additional file 1 Table S2); the iPLEX included 26 SNPs as part of a larger study.
