Rarity: discovering rare cell populations from single-cell imaging data.

MOTIVATION: Cell type identification plays an important role in the analysis and interpretation of single-cell data and can be carried out via supervised or unsupervised clustering approaches. Supervised methods are best suited where we can list all cell types and their respective marker genes a priori, while unsupervised clustering algorithms look for groups of cells with similar expression properties. This property permits the identification of both known and unknown cell populations, making unsupervised methods suitable for discovery. Success is dependent on the relative strength of the expression signature of each group as well as the number of cells. Rare cell types therefore present a particular challenge that is magnified when they are defined by differentially expressing a small number of genes. RESULTS: Typical unsupervised approaches fail to identify such rare subpopulations, and these cells tend to be absorbed into more prevalent cell types. In order to balance these competing demands, we have developed a novel statistical framework for unsupervised clustering, named Rarity, that enables the discovery process for rare cell types to be more robust, consistent, and interpretable. We achieve this by devising a novel clustering method based on a Bayesian latent variable model in which we assign cells to inferred latent binary on/off expression profiles. This lets us achieve increased sensitivity to rare cell populations while also allowing us to control and interpret potential false positive discoveries. We systematically study the challenges associated with rare cell type identification and demonstrate the utility of Rarity on various IMC datasets. AVAILABILITY AND IMPLEMENTATION: Implementation of Rarity together with examples is available from the Github repository (https://github.com/kasparmartens/rarity).

Associations between baseline opioid use disorder severity, mental health and biopsychosocial functioning, with clinical responses to computer-assisted therapy treatment.

Background: Increasing rates of opioid-related overdose have been identified globally. Treatment for opioid use disorders (OUD) includes medications for opioid use disorder (MOUD) alongside behavioral support. Novel approaches to behavioral support should be explored, including computer-assisted therapy (CAT) programs.Objectives: Examine differences between baseline and post-treatment measures of opioid use and biopsychosocial functioning for individuals with OUD engaging with the CAT program 'Breaking Free Online,' and the extent to which participant characteristics may be associated with post-treatment measures.Methods: 1107 individuals engaged with CAT and provided baseline and post-treatment data - 724 (65.4%) were male, 383 (34.6%) were female.Results: Significant differences between baseline and post-treatment measures were identified (all p <.0001, effect sizes range:15 -.50). Participant characteristics were associated with post-treatment measures of opioid use, opioid dependence, mental health issues, quality of life, and biopsychosocial impairment (all p <.0001). An aggregated consensus measure of clinical impairment was found to be associated with changes in opioid use and post-treatment biopsychosocial functioning measures, with those participants with greater baseline clinical impairment demonstrating a greater magnitude of improvement from baseline to post-treatment than those with lower clinical impairment.Conclusion: CAT may reduce opioid use and improve biopsychosocial functioning in individuals with OUD. CAT could therefore provide a solution to the global opioid crisis if delivered as combination behavioral support alongside MOUD. Findings also indicate that it may be important for treatment systems to identify individuals with psychosocial complexity who might require behavioral support and MOUD.

Powerful decomposition of complex traits in a diploid model.

Explaining trait differences between individuals is a core and challenging aim of life sciences. Here, we introduce a powerful framework for complete decomposition of trait variation into its underlying genetic causes in diploid model organisms. We sequence and systematically pair the recombinant gametes of two intercrossed natural genomes into an array of diploid hybrids with fully assembled and phased genomes, termed Phased Outbred Lines (POLs). We demonstrate the capacity of this approach by partitioning fitness traits of 6,642 Saccharomyces cerevisiae POLs across many environments, achieving near complete trait heritability and precisely estimating additive (73%), dominance (10%), second (7%) and third (1.7%) order epistasis components. We map quantitative trait loci (QTLs) and find nonadditive QTLs to outnumber (3:1) additive loci, dominant contributions to heterosis to outnumber overdominant, and extensive pleiotropy. The POL framework offers the most complete decomposition of diploid traits to date and can be adapted to most model organisms.

seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data.

MOTIVATION: One of the main goals of large scale methylation studies is to detect differentially methylated loci. One way is to approach this problem sitewise, i.e. to find differentially methylated positions (DMPs). However, it has been shown that methylation is regulated in longer genomic regions. So it is more desirable to identify differentially methylated regions (DMRs) instead of DMPs. The new high coverage arrays, like Illuminas 450k platform, make it possible at a reasonable cost. Few tools exist for DMR identification from this type of data, but there is no standard approach. RESULTS: We propose a novel method for DMR identification that detects the region boundaries according to the minimum description length (MDL) principle, essentially solving the problem of model selection. The significance of the regions is established using linear mixed models. Using both simulated and large publicly available methylation datasets, we compare seqlm performance to alternative approaches. We demonstrate that it is both more sensitive and specific than competing methods. This is achieved with minimal parameter tuning and, surprisingly, quickest running time of all the tried methods. Finally, we show that the regional differential methylation patterns identified on sparse array data are confirmed by higher resolution sequencing approaches. AVAILABILITY AND IMPLEMENTATION: The methods have been implemented in R package seqlm that is available through Github: https://github.com/raivokolde/seqlm CONTACT: rkolde@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Predicting quantitative traits from genome and phenome with near perfect accuracy.

In spite of decades of linkage and association studies and its potential impact on human health, reliable prediction of an individual's risk for heritable disease remains difficult. Large numbers of mapped loci do not explain substantial fractions of heritable variation, leaving an open question of whether accurate complex trait predictions can be achieved in practice. Here, we use a genome sequenced population of ∼7,000 yeast strains of high but varying relatedness, and predict growth traits from family information, effects of segregating genetic variants and growth in other environments with an average coefficient of determination R(2) of 0.91. This accuracy exceeds narrow-sense heritability, approaches limits imposed by measurement repeatability and is higher than achieved with a single assay in the laboratory. Our results prove that very accurate prediction of complex traits is possible, and suggest that additional data from families rather than reference cohorts may be more useful for this purpose.

DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns.

BACKGROUND: DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites. RESULTS: Only 2% of the CpGs analyzed are hypermethylated in all 17 tissue specimens; these permanently methylated CpG sites are located predominantly in gene-body regions. In contrast, 15% of the CpGs are hypomethylated in all specimens and are primarily located in regions proximal to transcription start sites. A vast number of tissue-specific differentially methylated regions are identified and considered likely mediators of tissue-specific gene regulatory mechanisms since the hypomethylated regions are closely related to known functions of the corresponding tissue. Finally, a clear inverse correlation is observed between promoter methylation within CpG islands and gene expression data obtained from publicly available databases. CONCLUSIONS: This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues. Many of the genes corresponding to these differentially methylated regions contribute to tissue-specific functions. Future studies may use these data as a reference to identify markers of perturbed differentiation and disease-related pathogenic mechanisms.