King's College London

About: King's College London is a education organization based out in London, United Kingdom. It is known for research contribution in the topics: Population & Mental health. The organization has 43107 authors who have published 113125 publications receiving 4498103 citations. The organization is also known as: King's & KCL.

Repeatability of published microarray gene expression analyses.

Abstract: Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005-2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered.

Genes and Behavior: Nature-Nurture Interplay Explained

Abstract: Chapter 1: Why is the topic of genes and behavior controversial? Chapter 2: Concepts of behavior and of mental disorder Chapter 3: Environmentally mediated risks Chapter 4: Patterns of inheritance Chapter 5: How much is nature and how much nurture? Chapter 6: The heritability of different mental disorders and traitsChapter 7: Finding and understanding specific susceptibility genes Chapter 8: What genes do Chapter 9: Nature-nurture interplay and causal pathways from genes to psychopathology Chapter 10: What environments do to genes Chapter 11: Conclusions

Common variants at CD40 and other loci confer risk of rheumatoid arthritis

Abstract: To identify rheumatoid arthritis risk loci in European populations, we conducted a meta-analysis of two published genome-wide association (GWA) studies totaling 3,393 cases and 12,462 controls We genotyped 31 top-ranked SNPs not previously associated with rheumatoid arthritis in an independent replication of 3,929 autoantibody-positive rheumatoid arthritis cases and 5,807 matched controls from eight separate collections We identified a common variant at the CD40 gene locus (rs4810485, P = 00032 replication, P = 82 x 10(-9) overall, OR = 087) Along with other associations near TRAF1 (refs 2,3) and TNFAIP3 (refs 4,5), this implies a central role for the CD40 signaling pathway in rheumatoid arthritis pathogenesis We also identified association at the CCL21 gene locus (rs2812378, P = 000097 replication, P = 28 x 10(-7) overall), a gene involved in lymphocyte trafficking Finally, we identified evidence of association at four additional gene loci: MMEL1-TNFRSF14 (rs3890745, P = 00035 replication, P = 11 x 10(-7) overall), CDK6 (rs42041, P = 0010 replication, P = 40 x 10(-6) overall), PRKCQ (rs4750316, P = 00078 replication, P = 44 x 10(-6) overall), and KIF5A-PIP4K2C (rs1678542, P = 00026 replication, P = 88 x 10(-8) overall)

American Gut: an Open Platform for Citizen Science Microbiome Research.

Abstract: Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.