Design and Development of Metabochip

The Metabochip was designed by representatives of the Body Fat Percentage [9] (link), CARDIoGRAM (coronary artery disease and myocardial infarction) [10] (link), DIAGRAM (type 2 diabetes) [11] (link), GIANT (anthropometric traits) [3] (link), [12] (link), [13] (link), Global Lipids Genetics (lipids) [4] (link), HaemGen (hematological measures) [14] (link), ICBP (blood pressure) [15] (link), MAGIC (glucose and insulin) [16] (link)–[18] (link), and QT-IGC (QT interval) [19] (link), [20] (link) GWAS meta-analysis consortia. The array is comprised of SNPs selected across two tiers of traits (Table 1). Tier 1 is comprised of eleven traits deemed to be of primary interest: type 2 diabetes (T2D), fasting glucose, coronary artery disease and myocardial infarction (CAD/MI), low density lipoprotein (LDL) cholesterol, high density lipoprotein (HDL) cholesterol, triglycerides, body mass index (BMI), systolic and diastolic blood pressure, QT interval, and waist-to-hip ratio adjusted for BMI (WHR). Tier 2 is comprised of twelve traits of secondary interest: fasting insulin, 2-hour glucose, glycated hemoglobin (HbA1c), T2D age of diagnosis, early onset T2D (diagnosis age<45 years), waist circumference adjusted for BMI, height, body fat percentage, total cholesterol, platelet count, mean platelet volume, and white blood cell count.
We included three design classes of SNPs on the Metabochip (Table 2):
In total, 217,695 SNPs were chosen for the array (Table 2). 20,970 SNPs (9.6%) failed during the assay manufacturing process, resulting in 196,725 SNPs available for genotyping. A summary file annotating each Metabochip SNP with ascertainment criteria, SNP assay, a list of unintended duplicate SNPs (Supplementary Table S4), and reference strand orientation for alleles is provided at http://www.sph.umich.edu/csg/kang/MetaboChip/.