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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.