ASSIMILATOR: A new tool to inform selection of associated genetic variants for functional studies

Motivation: Fine-mapping experiments from genome-wide association studies (GWAS) are underway for many complex diseases. These are likely to identify a number of putative causal variants, which cannot be separated further in terms of strength of genetic association due to linkage disequilibrium. The challenge will be selecting which variant to prioritize for subsequent expensive functional studies. A wealth of functional information generated from wet lab experiments now exists but cannot be easily interrogated by the user. Here, we describe a program designed to quickly assimilate this data called ASSIMILATOR and validate the method by interrogating two regions to show its effectiveness. Availability: http://www.medicine.manchester.ac.uk/musculoskeletal/research/arc/genetics/bioinformatics/assimilator/. Contact: [email protected]

Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition

BACKGROUND: The selection of markers in association studies can be informed through the use of haplotype blocks. Recent reports have determined the genomic architecture of chromosomal segments through different haplotype block definitions based on linkage disequilibrium (LD) measures or haplotype diversity criteria. The relative applicability of distinct block definitions to association studies, however, remains unclear. We compared different block definitions in 6.1 Mb of chromosome 17q in 189 unrelated healthy individuals. Using 137 single nucleotide polymorphisms (SNPs), at a median spacing of 15.5 kb, we constructed haplotype block maps using published methods and additional methods we have developed. Haplotype tagging SNPs (htSNPs) were identified for each map. RESULTS: Blocks were found to be shorter and coverage of the region limited with methods based on LD measures, compared to the method based on haplotype diversity. Although the distribution of blocks was highly variable, the number of SNPs that needed to be typed in order to capture the maximum number of haplotypes was consistent. CONCLUSION: For the marker spacing used in this study, choice of block definition is not important when used as an initial screen of the region to identify htSNPs. However, choice of block definition has consequences for the downstream interpretation of association study results

Music, Sound, Space and Time: A practice-based spectromorphological and space-form investigation in composition and performance

This commentary is a record of my research into the spatial characteristics in my composition and its relationship with the concepts of spectromorphology and space-fonn as proposed by Denis Smalley. My research is also info1med by the ideas of oneiric phenomenological experience of place (the home) in Gaston Bachelard's The Poetics of Space and the way Brandon Labelle extends those ideas in parts of Acoustic Territories: Sound Culture and Everyday Life. I contextualise my research with reference to composers who use space as a primary concept in their work. Phil Niblock, Steve Roden, Theodo1is Lotis and John Luther Adams have all informed my work with their differing expositions of spatial detail. My works manipulate sound to create spaces in compositions that reference ideas of human experience by Bachelard and Labelle using the tool-kit that Smalley provides. In my original contribution to knowledge I identify Smalley' s concept of transcontextuality in its ambiguous and acousmatic setting (to create imagined extrinsic connections in the listener) as a conceptual bridge between spectromorphology and the poetic image that is the genesis of oneiric reve1ie in The Poetics of Spa,ce and extended into the realm of acoustic ten-itory by Brandon Labelle. I also use Smalley' s concept of behavioural spaces and extend this to include transcontextual behaviour of oneiric reverie in a domestic setting that references my own research pieces. In summary I revisit my research questions in light of the pieces I have researched and reflect on how they have been engaged with. I also survey the research pieces and draw out examples of where oneiric experiences are invited and possible in the music. I draw conclusions that the oneiric transcontextual possibilities are linked directly to spatial properties in composition and define some basic parameters where the research shows they can exist

Association of the FCRL3 gene with rheumatoid arthritis: a further example of population specificity?

Association of a functional promoter polymorphism mapping to the Fc receptor-like 3 (FCRL3) gene has recently been reported and replicated with rheumatoid arthritis (RA) in Japanese populations. The aim of this study was to investigate association of the FCRL3 gene with RA in UK subjects. DNA was available from 1065 patients with RA and 2073 population controls from the UK. Four single nucleotide polymorphism (SNP) markers (FCRL3-169*C/T (fclr3_3, rs7528684), fclr3_4 (rs11264799), fclr3_5 (rs945635), fclr3_6 (rs3761959)) all previously associated with RA in a Japanese population were genotyped in 761 RA samples and 484 controls. In the remaining samples, only the putative disease causal polymorphism, FCRL3-169*C/T, was tested. Genotyping was performed using either the Sequenom MassArray iPlex platform or a 5' Allelic discrimination assay (Taqman, ABI). Extensive linkage disequilibrium was present across the promoter SNPs genotyped (r(2) values = 0.60-0.98). Allele frequencies did not differ between RA cases and controls either for the putative disease causal polymorphism (odds ratio FCRL3-169*C allele = 0.97 (0.87-1.07), p = 0.51) or for the other SNPs tested. Similarly, no association was detected with RA using haplotype analysis or when stratification by shared epitope carriage or by presence of rheumatoid factor was undertaken. This study was powered to detect an effect size of 1.24 or greater for the FCRL3-169*C/T functional promoter polymorphism but no evidence for association was detected, suggesting that this gene will not have a substantial effect in determining susceptibility to RA in populations of Northern European descent

The outstanding scientist, R.A. Fisher:His views on eugenics and race

R.A. Fisher was one of the greatest scientists of the 20th century (Fig. 1). He was a man of extraordinary ability and originality whose scientific contributions ranged over a very wide area of science, from biology through statistics to ideas on continental drift, and whose work has had a huge positive impact on human welfare. Not surprisingly, some of his large volume of work is not widely used or accepted at the current time, but his scientific brilliance has never been challenged. He was from an early age a supporter of certain eugenic ideas, and it is for this reason that he has been accused of being a racist and an advocate of forced sterilisation (Evans 2020). His promotion of eugenics has recently caused various organisations to remove his name from awards and dedications of buildings (Tarran 2020; Rothamsted Research 2020; Society for the Study of Evolution 2020; Gonville and Caius College 2020). A primary aim of this paper is to conduct a careful analysis of his own writings in these areas. Our purpose is neither to defend nor attack Fisher’s work in eugenics and views on race, but to present a careful account of their substance and nature.Publisher PDFPeer reviewe

Affective Computing for Late-Life Mood and Cognitive Disorders

Affective computing (also referred to as artificial emotion intelligence or emotion AI) is the study and development of systems and devices that can recognize, interpret, process, and simulate emotion or other affective phenomena. With the rapid growth in the aging population around the world, affective computing has immense potential to benefit the treatment and care of late-life mood and cognitive disorders. For late-life depression, affective computing ranging from vocal biomarkers to facial expressions to social media behavioral analysis can be used to address inadequacies of current screening and diagnostic approaches, mitigate loneliness and isolation, provide more personalized treatment approaches, and detect risk of suicide. Similarly, for Alzheimer\u27s disease, eye movement analysis, vocal biomarkers, and driving and behavior can provide objective biomarkers for early identification and monitoring, allow more comprehensive understanding of daily life and disease fluctuations, and facilitate an understanding of behavioral and psychological symptoms such as agitation. To optimize the utility of affective computing while mitigating potential risks and ensure responsible development, ethical development of affective computing applications for late-life mood and cognitive disorders is needed

Breath-based non-invasive diagnosis of Alzheimer’s disease:A pilot study

Early detection of Alzheimer's disease (AD) will help researchers to better understand the disease and develop improved treatments. Recent developments have thus focused on identifying biomarkers for mild cognitive impairment due to AD (MCI) and AD during the preclinical phase. The aim of this pilot study is to determine whether exhaled volatile organic compounds (VOCs) can be used as a non-invasive method to distinguish controls from MCI, controls from AD and to determine whether there are differences between MCI and AD. The study used gas chromatography – ion mobility spectrometry (GC-IMS) techniques. Confounding factors, such as age, smoking habits, gender and alcohol consumption are investigated to demonstrate the efficacy of results. One hundred subjects were recruited including 50 controls, 25 AD and 25 MCI patients. The subject cohort was age- and gender-matched to minimise bias. Breath samples were analysed using a commercial GC-IMS instrument (G.A.S. BreathSpec, Dortmund, Germany). Data analysis indicates that the GC-IMS signal was consistently able to separate between diagnostic groups [AUC±95%, sensitivity, specificity], controls vs MCI: [0.77 (0.64 – 0.90), 0.68, 0.80], controls vs AD: [0.83 (0.72 – 0.94), 0.60, 0.96], and MCI vs AD: [0.70 (0.55 – 0.85), 0.60, 0.84]. VOC analysis indicates that six compounds play a crucial role in distinguishing between diagnostic groups. Analysis of possible confounding factors indicate that gender, age, smoking habits and alcohol consumption have insignificant influence on breath content. This pilot study confirms the utility of exhaled breath analysis to distinguish between AD, MCI and control subjects. Thus, GC-IMS offers great potential as a non-invasive, high-throughput, diagnostic technique for diagnosing and potentially monitoring AD in a clinical setting

Identifying Causal Genes at the Multiple Sclerosis Associated Region 6q23 Using Capture Hi-C.

BACKGROUND: The chromosomal region 6q23 has been found to be associated with multiple sclerosis (MS) predisposition through genome wide association studies (GWAS). There are four independent single nucleotide polymorphisms (SNPs) associated with MS in this region, which spans around 2.5 Mb. Most GWAS variants associated with complex traits, including these four MS associated SNPs, are non-coding and their function is currently unknown. However, GWAS variants have been found to be enriched in enhancers and there is evidence that they may be involved in transcriptional regulation of their distant target genes through long range chromatin looping. AIM: The aim of this work is to identify causal disease genes in the 6q23 locus by studying long range chromatin interactions, using the recently developed Capture Hi-C method in human T and B-cell lines. Interactions involving four independent associations unique to MS, tagged by rs11154801, rs17066096, rs7769192 and rs67297943 were analysed using Capture Hi-C Analysis of Genomic Organisation (CHiCAGO). RESULTS: We found that the pattern of chromatin looping interactions in the MS 6q23 associated region is complex. Interactions cluster in two regions, the first involving the rs11154801 region and a second containing the rs17066096, rs7769192 and rs67297943 SNPs. Firstly, SNPs located within the AHI1 gene, tagged by rs11154801, are correlated with expression of AHI1 and interact with its promoter. These SNPs also interact with other potential candidate genes such as SGK1 and BCLAF1. Secondly, the rs17066096, rs7769192 and rs67297943 SNPs interact with each other and with immune-related genes such as IL20RA, IL22RA2, IFNGR1 and TNFAIP3. Finally, the above-mentioned regions interact with each other and therefore, may co-regulate these target genes. CONCLUSION: These results suggest that the four 6q23 variants, independently associated with MS, are involved in the regulation of several genes, including immune genes. These findings could help understand mechanisms of disease and suggest potential novel therapeutic targets

Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines

Background: Accurately identifying SNPs from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained. This study evaluates the performance of 209 SNP calling pipelines using a combination of simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally-sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia and Klebsiella. Results: We evaluated the performance of 209 SNP calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic, bacteria such as Escherichia coli, but less dominant for clonal species such as Mycobacterium tuberculosis. Conclusions: The accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest performing pipelines was Novoalign/GATK. By contrast, when reads were aligned to particularly divergent genomes, the highest-performing pipelines often employed the aligners NextGenMap or SMALT, and/or the variant callers LoFreq, mpileup or Strelka