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The HDL method improves the precision in genetic correlation estimation over LD score regression when applied to GWAS summary statistics of complex traits from the UK Biobank.
SAIGE-GENE is a scalable generalized mixed-model region-based association test that can analyze large datasets while accounting for sample relatedness and unbalanced case–control ratios for binary traits.
A new association method using both case–control status and family history (LT-FH) greatly increases association power in analyses of 12 diseases from the UK Biobank.
fastGWA is a mixed linear model–based approach for performing genome-wide association analyses at biobank scale, while controlling for population stratification and relatedness.
The authors present a high-throughput single-cell ChIP-seq method with coverage of up to 10,000 loci per cell. They identify diverse chromatin landscapes in breast cancer cells characterized by dynamic H3K27me3 levels.
Signature Multivariate Analysis is a new computational tool that detects the mutational signature of homologous-recombination deficiency in clinical samples sequenced with targeted panels, enabling the identification of patients who are responsive to poly (ADP-ribose) polymerase inhibition therapy.
Linked-read analysis is a method for analyzing single-cell DNA-sequencing data that accurately identifies somatic single-nucleotide variants by using read-level phasing with nearby germline variants, enabling the characterization of mutational signatures and estimation of somatic mutation rates in single cells.
UTMOST (unified test for molecular signatures) is a method for cross-tissue gene expression imputation for transcriptome-wide association analyses. Cross-tissue TWAS using UTMOST identifies new candidate genes for late-onset Alzheimer’s disease.
GARFIELD is a new approach that classifies genomic features related to phenotypes on the basis of integrating GWAS signals with functional annotations. GARFIELD is used to characterize enrichment patterns for 29 traits integrated with ENCODE and Roadmap Epigenomics annotations.
Graph Genome Pipeline is a read-alignment and variant-calling pipeline based on graph genomes that offers improved read-mapping and variant-calling accuracy while achieving speed comparable to those of linear reference genome pipelines.
FitCons2 is a new framework that simultaneously clusters genomic sites by epigenomic features and evaluates the strength of natural selection on these sites. FitCons2 scores are used to generate fitness–consequence maps for 115 human cell types.
Multivariate adaptive shrinkage (mash) is a method for estimating and testing multiple effects in multiple conditions. When applied to GTEx data, mash can be used to analyze sharing of eQTL effects by examining variation in effect sizes.
StructLMM is a new method to identify genotype–environment interactions (G×E) that involve multiple exposures or environments. When applied to UK Biobank and eQTL data, StructLMM discovers new G×E signals.
Tri-C is a new 3C approach to identify concurrent chromatin interactions at individual alleles. The authors observe specific higher-order structures involving simultaneous interactions between multiple enhancers and promoters, called regulatory hubs.
This study presents a new latent causal variable (LCV) model that distinguishes between genetic correlation and causation. Applying LCV to genome-wide association summary statistics for 52 traits identified genetically causal effects for 59 pairs of traits.
The heteroskedastic linear mixed model is a new framework for testing both mean and variance effects on quantitative traits. Applying the heteroskedastic linear mixed model to body mass index in the UK Biobank shows that the approach increases the power to detect associated loci.
BayesTyper is a new probabilistic genotyping algorithm that offers superior sensitivity and accuracy relative to existing methods by using exact alignment of read k-mers to a graph representation of the reference and candidate variants.
DLO Hi-C is a new method to investigate the 3D genome. It requires only two rounds of digestion and ligation and removes non-ligated DNA in a cost-effective step by purifying specific linker-ligated DNA fragments.