Introduction We identified rare coding variants associated with Alzheimer’s disease (AD) in a 3-stage case-control study of 85,133 subjects. In stage 1, 34,174 samples were genotyped using a whole-exome microarray. In stage 2, we tested associated variants (P<1×10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, an additional 14,997 samples were used to test the most significant stage 2 associations (P<5×10-8) using imputed genotypes. We observed 3 novel genome-wide significant (GWS) AD associated non-synonymous variants; a protective variant in PLCG2 (rs72824905/p.P522R, P=5.38×10-10, OR=0.68, MAFcases=0.0059, MAFcontrols=0.0093), a risk variant in ABI3 (rs616338/p.S209F, P=4.56×10-10, OR=1.43, MAFcases=0.011, MAFcontrols=0.008), and a novel GWS variant in TREM2 (rs143332484/p.R62H, P=1.55×10-14, OR=1.67, MAFcases=0.0143, MAFcontrols=0.0089), a known AD susceptibility gene. These protein-coding changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified AD risk genes. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to AD development.

Norwegian Cancer Society.

Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnostics, and prediction and monitoring of treatment response, but its amount is usually limited. Therefore, the choice of methods to extract and characterize ccfDNA is crucial. In the current study, we performed the most comprehensive comparison of methods for ccfDNA extraction (11 methods), quantification (3 methods), and estimation of the integrity index (2 methods) from small quantities of different kinds of plasma. The QIAamp® Circulating Nucleic Acid Kit and the Norgen Plasma/Serum Circulating DNA Purification Mini Kit showed the best accuracy and reproducibility, but the Norgen kit allowed to extract a higher amount of ccfDNA. This workflow provides a reliable protocol for the multiple applications of ccfDNA in biomedicine.

Mammalian SWI/SNF complexes (mSWI/SNF) are ATP-dependent chromatin remodelling factors that possess tumour suppressor properties1. Brg1 (Smarca4), the catalytic subunit of mSWI/SNF, is essential for chromatin opening at enhancers2,3, but the detailed mechanism of this activity remains unclear. Using mouse embryonic stem (ES) cells, we show that Brg1 generates subnucleosomal particles which protect genomic DNA fragments of 50-80 bp in length from micrococcal nuclease (MNase) digestion. These particles, which contain all four histones H3, H4, H2A, and H2B, sediment in sucrose gradients with an apparent molecular weight markedly inferior to that of canonical nucleosomes. Genome-wide analysis of the positioning of these particles provides strong evidence that they arise from the splitting of Brg1-targeted nucleosomes into hemisomes. In vivo, these hemisome-like particles are bound by Oct4 (Pou5f1), a transcription factor essential for the maintenance of the ES cell phenotype. Oct4 has a mode of interaction with these particles that is distinct from its binding to accessible, histone-free DNA. Whereas Oct4 binds the latter substrate at the level of its consensus DNA motif, its interaction with the subnucleosome persists even when Oct4 motifs are removed from the particle, suggesting that Oct4 binding is stabilized by contacts with histones. Our data establish that one critical activity of Brg1 at enhancers involves splitting selected nucleosomes into subnucleosomes, which are major genomic binding targets for transcription factors.