Amyotrophic lateral sclerosis (ALS) is due to loss of motor neurons in several regions. This study involved genotyping 2,532 people with ALS and 5,940 controls using Illumina BeadChips. They found “a common variant in intron 21 of UNC13A.” UNC13A is a neuronal presynaptic protein involved in glutamate transmission; Unc13a-deficient mice have spinal cord motor neurons, muscle, and neuromuscular synapse defects. They also found two SNPs on chromosome 19 in areas previously linked to ALS.

MicroRNA (miRNAs) may contribute to development of prostate cancer. The authors initially used five prostate cancer cells transfected with mimics of around 200 miRNAs. MiR-16 caused a decrease in cell proliferation in four of the cell lines to varying degrees, correlated to miR-16 phenotypic response. They used Illumina mRNA arrays and BeadScan/BeadStation to investigate gene expression in miR-16 mimic transfected PC-3M-luc cells and found alterations in pathways associated with cell division and cell cycle control among others.

The authors investigated risk loci for type 2 diabetes (T2D). They initially used Illumina Hap300 and Human-1 bead arrays and data from the first study was used to create an iSelect array. Along with a further study they found four SNPs that reached significance, three associated with known T2D risk genes and one upstream of the insulin receptor substrate 1 gene (IRS1). Further investigation found a “35% increased relative risk of T2D” with the IRS1 loci rs2943541 and a subsequent study found this associated with increased fasting serum insulin.

Using 3,941 samples from people with Alzheimer’s disease (AD) and 7,848 controls, SNPs were investigated using the Human610-Quad, HumanHap550, or HumanHap300 DNA Analysis BeadChips. A genome-wide association study confirmed the association of AD with the APOE locus, and identified two new loci – CLU and PICALM (CALM). A further 2,023 AD and 2,340 control cases confirmed these. CLU encodes clusterin, a brain apolipoprotein linked to inflammation. PICALM is expressed in neurons and is involved in endocytosis.

Here, 2,034 individuals with late-onset Alzheimer’s disease (AD) and 5,328 controls were investigated with Illumina’s Human 610-Quad BeadChip and a marker within CLU (aka APO J, which codes for apolipoprotein J or clusterin) showed significance. A further 3,978 AD subjects and 3,297 controls confirmed this and also highlighted “a gene encoding complement component receptor 1 (CR1)”. Markers in these loci were significantly associated with AD, especially in those with APOE e4 status.

Primary fibroblasts, EBV-immortalized B-cells and T-cells from 75 umbilical cords were used to examine gene expression-relevant cis expressive quantitative trait loci (eQTLs). The authors used Illumina’s WG-6 v2 BeadExpression array and 550K SNP array. They found 8.5% of 1,007 genes with cis eQTLs in all three cell types, 12% in two types, and 79% that were cell-type specific. These correlated positively with transcript number per gene. They suggested that “the majority of cell type specificity is due to cell type-specific use of regulatory elements.”

Childhood acute lymphoblastic leukemia (ALL) was investigated for heritable factors. The authors carried out a genome-wide association study with 2,398 control cases compared it to 907 ALL cases, utilizing data from Illumina Hap550K BeadChip studies. They found a strong association with regions of the Ikaros family zinc finger 1 (IKZF1) at 7p12.2, which has a known role in ALL, ARID5B at 10q21.2 and CEBPE at 14q11.2, but no inter-association between these three.