Citations

Abstract Methods that map genetic risk to cells do not directly test whether spatially organized ligand–receptor (LR) gene annotations carry conditional heritability association. Here we introduce EdgeMap, which scores each gene by the spatial activity of its LR contexts in spatial transcriptomics data, maps these scores alongside cell-intrinsic annotations to SNP-level LD scores, and tests both jointly against GWAS summary statistics. Across 17 traits and five human tissues, edge z -scores are systematically higher in biologically matched tissues: all 15 traits with both matched and unmatched tissue classes show this ordering (median Δ z = 1.51 ; sign P = 3.1 × 10 −5 ), and 11 of 13 nominal-positive associations concentrate in the biologically matched set ( P = 1 × 10 −4 ). The pattern survives broad LR-gene-class and cell-type composition controls. Donor-level cross-section summaries, independent GWAS replication for LDL and CAD, and cell-segmented Visium HD liver data provide convergent support. A secondary analysis prioritizes constituent genes within active LR contexts; sixteen of 31 prioritized genes are absent from standard gene-level methods. These results establish spatially weighted LR-gene annotations as a complementary layer for interpreting complex-trait genetic architecture.

Abstract Coarsening Visium HD resolution from 8 to 64 µ m can flip cell-type co-localization from negative to positive ( r = −0.12 → +0.80 ), yet many widely used compositional deconvolution workflows require coarsening or subsampling at million-bin scale. Here we introduce FlashDeconv, which combines leverage-score importance sampling with sparse spatial regularization to achieve competitive benchmark accuracy while processing 1.6 million bins in 153 seconds on commodity hardware. Systematic multi-resolution analysis of Visium HD mouse intestine reveals a tissue-specific resolution horizon (8–16 µ m)—the scale at which this sign inversion occurs—validated by Xenium ground truth. Below this horizon, FlashDeconv provides, to our knowledge, the first sequencing-based quantification of Tuft cell chemosensory niches (15.3-fold stem cell enrichment). In a 1.6-million-bin human colorectal cancer cohort, FlashDeconv uncovers neutrophil inflammatory microdomains co-localized with immunoregulatory dendritic cells (mRegDC) at the tumor–stroma interface—spatial niches largely missed by discrete-label summaries, with RCTD doublet mode labeling only 2.3% of hotspot bins as neutrophil singlets.

Abstract Microbiome sequencing data are inherently sparse and compositional, with excessive zeros arising from biological absence or insufficient sampling. These zeros pose significant challenges for downstream analyses, particularly those that require log-transformation. We introduce BMDD (BiModal Dirichlet Distribution), a novel probabilistic modeling framework for accurate imputation of microbiome sequencing data. Unlike existing imputation approaches that assume unimodal abundance, BMDD captures the bimodal abundance distribution of the taxa via a mixture of Dirichlet priors. It uses variational inference and a scalable expectation-maximization algorithm for efficient imputation. Through simulations and real microbiome datasets, we demonstrate that BMDD outperforms competing methods in reconstructing true abundances and improves the performance of differential abundance analysis. Through multiple posterior samples, BMDD enables robust inference by accounting for uncertainty in zero imputation. Our method offers a principled and computationally efficient solution for analyzing high-dimensional, zero-inflated microbiome sequencing data and is broadly applicable in microbial biomarker discovery and host-microbiome interaction studies. BMDD is available at: https://github.com/zhouhj1994/BMDD . Author Summary Understanding the microbes living in and on our bodies—the microbiome—relies on analyzing complex sequencing data. However, these data often contain many zeros, either because a microbe is truly absent or simply missed due to insufficient sampling. These missing values make it hard to accurately analyze microbial patterns and identify important differences between groups, especially for methods that work on a log scale. To address this, we developed a new method called BMDD that uses a more realistic model to impute the zeros. Unlike existing tools that assume each microbe follows an unimodal abundance distribution, BMDD allows for microbes to follow a bimodal distribution, so they could behave differently in different conditions. It provides not just a single guess, but a range of possible values to better reflect the uncertainty. Our testing shows that BMDD more accurately recovers the true microbial profiles and improves the ability to detect meaningful differences between groups. This method can help researchers gain clearer insights into how the microbiome affects health and disease.

It is well known that the microbiome data are ridden with outliers and have heavy distribution tails, but the impact of outliers and heavy-tailedness has yet to be examined systematically. This paper investigates the impact of outliers and heavy-tailedness on differential abundance analysis (DAA) using the linear models for the differential abundance analysis (LinDA) method and proposes effective strategies to mitigate their influence. The presence of outliers and heavy-tailedness can significantly decrease the power of LinDA. We investigate various techniques to address outliers and heavy-tailedness, including generalizing LinDA into a more flexible framework that allows for the use of robust regression and winsorizing the data before applying LinDA. Our extensive numerical experiments and real-data analyses demonstrate that robust Huber regression has overall the best performance in addressing outliers and heavy-tailedness.

AbstractMotivationGenomic data are subject to various sources of confounding, such as demographic variables, biological heterogeneity, and batch effects. To identify genomic features associated with a variable of interest in the presence of confounders, the traditional approach involves fitting a confounder-adjusted regression model to each genomic feature, followed by multiplicity correction.ResultsThis study shows that the traditional approach is suboptimal and proposes a new two-dimensional false discovery rate control framework (2DFDR+) that provides significant power improvement over the conventional method and applies to a wide range of settings. 2DFDR+ uses marginal independence test statistics as auxiliary information to filter out less promising features, and FDR control is performed based on conditional independence test statistics in the remaining features. 2DFDR+ provides (asymptotically) valid inference from samples in settings where the conditional distribution of the genomic variables given the covariate of interest and the confounders is arbitrary and completely unknown. Promising finite sample performance is demonstrated via extensive simulations and real data applications.Availability and implementationR codes and vignettes are available at https://github.com/asmita112358/tdfdr.np.

Abstract Summary Due to the sparsity and high dimensionality, microbiome data are routinely summarized into pairwise distances capturing the compositional differences. Many biological insights can be gained by analyzing the distance matrix in relation to some covariates. A microbiome sampling method that characterizes the inter-sample relationship more reproducibly is expected to yield higher statistical power. Traditionally, the intraclass correlation coefficient (ICC) has been used to quantify the degree of reproducibility for a univariate measurement using technical replicates. In this work, we extend the traditional ICC to distance measures and propose a distance-based ICC (dICC). We derive the asymptotic distribution of the sample-based dICC to facilitate statistical inference. We illustrate dICC using a real dataset from a metagenomic reproducibility study. Availability and implementation dICC is implemented in the R CRAN package GUniFrac. Supplementary information Supplementary data are available at Bioinformatics online.

Abstract Summary PERMANOVA (permutational multivariate analysis of variance based on distances) has been widely used for testing the association between the microbiome and a covariate of interest. Statistical significance is established by permutation, which is computationally intensive for large sample sizes. As large-scale microbiome studies, such as American Gut Project (AGP), become increasingly popular, a computationally efficient version of PERMANOVA is much needed. To achieve this end, we derive the asymptotic distribution of the PERMANOVA pseudo-F statistic and provide analytical P-value calculation based on chi-square approximation. We show that the asymptotic P-value is close to the PERMANOVA P-value even under a moderate sample size. Moreover, it is more accurate and an order-of-magnitude faster than the permutation-free method MDMR. We demonstrated the use of our procedure D-MANOVA on the AGP dataset. Availability and implementation D-MANOVA is implemented by the dmanova function in the CRAN package GUniFrac. Supplementary information Supplementary data are available at Bioinformatics online.

SummaryThe familywise error rate has been widely used in genome-wide association studies. With the increasing availability of functional genomics data, it is possible to increase detection power by leveraging these genomic functional annotations. Previous efforts to accommodate covariates in multiple testing focused on false discovery rate control, while covariate-adaptive procedures controlling the familywise error rate remain underdeveloped. Here, we propose a novel covariate-adaptive procedure to control the familywise error rate that incorporates external covariates which are potentially informative of either the statistical power or the prior null probability. An efficient algorithm is developed to implement the proposed method. We prove its asymptotic validity and obtain the rate of convergence through a perturbation-type argument. Our numerical studies show that the new procedure is more powerful than competing methods and maintains robustness across different settings. We apply the proposed approach to the UK Biobank data and analyse 27 traits with 9 million single-nucleotide polymorphisms tested for associations. Seventy-five genomic annotations are used as covariates. Our approach detects more genome-wide significant loci than other methods in 21 out of the 27 traits.