IFCs help hospital validate disease loci

Researchers applied the properties of the Fluidigm 96.96 Dynamic Array IFC and the EP1 System to re-genotype selected SNPs for the replication study.

In a paper entitled 'A genome-wide association study identifies two new risk loci for Graves' disease, published in the 14 August 2011 issue of Nature Genetics Magazine, researchers confirmed four previously reported loci and identified two new susceptibility loci for Graves' disease.

Graves' disease is a common autoimmune disorder characterised by thyroid-stimulating, hormone-receptor autoantibodies and hyperthyroidism.

To investigate the genetic architecture of Graves' disease, Rujin Hospital researchers conducted a genome-wide association study in 1,536 individuals with Graves' disease (cases) and 1,516 controls.

They further evaluated a group of associated SNPs in a second set of 3,994 cases and 3,510 controls.

All samples were recruited from the Chinese Han population through collaboration with hospitals in China.

'The Fluidigm EP1 microfluidic genetic analysis system proved to be a powerful tool for SNP genotyping validation research in our GWAS project,' noted Dr Chun-Ming Pan of the State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine.

'The EP1 enabled us to set up 9,216 PCR experiments at a time without using a robot.

'Within four hours we acquired almost 10,000 data points with outstanding reproducibility and accuracy.

'The nanolitre-level reaction chambers of Fluidigm chips resulted in cost savings, as we needed to only use minute amounts of the expensive SNP genotyping reagents,' he added.

GWAS was performed on a microarray system at the Chinese National Human Genome Center in Shanghai, China.

In stage 2, 100 SNPs were selected for the replication study.

Among them, 96 SNPs were genotyped using Taqman SNP Genotyping Assays using the Fluidigm 96.96 Dynamic Array IFC and EP1 platform.