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A multitrait fine-mapping method, mvSuSiE, improves power and resolution over single-trait methods for identifying putative causal variants from genetic association data.
REMETA is a method for meta-analyzing gene-based associations using summary statistics, integrating with REGENIE and improving computational efficiency for large studies with many phenotypes.
Locityper is a general-purpose genotyper that can efficiently genotype and analyze a diverse set of genes, such as hyperpolymorphic HLA genes, using both short-read and long-read whole-genome sequencing data.
Ctyper is a genotyping method for copy number variation and complex genes that produces sequence-resolved genotypes by directly comparing sequencing reads to pangenome haplotypes, achieving increased robustness and copy number sensitivity with efficiency scalable to biobank analysis.
This study presents a splice-based selection method that enriches actively editing cells in base editing screening at target loci, reducing the number of unedited cells from over 40% to less than 10%.
CRISPR activation of 1,836 human transcription factors recapitulates fibroblast transcriptional states observed in vivo and identifies regulators that can revert inflammatory states.
ESCAPE-seq (enhanced single-chain antigen presentation sequencing) is a massively parallel platform for screening of class I HLA–peptide combinations for antigen presentation. The authors assess more than 75,000 peptide–HLA combinations, revealing presented epitopes from oncogenic driver mutations and fusions across diverse HLA-A, HLA-B and HLA-C alleles.
scMicro-C is a new method that provides high-resolution maps of the 3D genome. scMicro-C identifies structures called ‘promoter stripes’, which link a gene promoter to multiple downstream enhancers.
Cluster hierarchy optimization by iterative random forests (CHOIR) offers a robust and accurate method to identify cell clusters across a variety of single-cell resolution data with statistical support.
HDL-L is an extension of the high-definition likelihood method that enables local heritability and genetic correlation analysis with higher accuracy and computational efficiency than LAVA.
This study develops family-based genome-wide association study methods that maximize power in homogeneous samples through inclusion of singletons and in diverse samples by using all available parental genotypes.
Simultaneous profiling of the genome, methylome, epigenome and transcriptome using single-molecule chromatin fiber sequencing and multiplexed arrays isoform sequencing identifies the genetic and molecular basis of an undiagnosed Mendelian disease case with an X;13-balanced translocation.
Quickdraws is a mixed-model association tool with a noninfinitesimal prior for analyzing binary and quantitative traits, using a scalable variational inference that allows analysis of biobank-scale cohorts.
Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability to a broad variety of samples and cell types.
Generalized binary covariance decomposition (GBCD) applies empirical Bayes matrix factorization to identify shared and sample-specific gene expression signatures in single-cell RNA sequencing data, and can more accurately capture inter- and intrasample heterogeneity than existing methods.
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offering a refined view of the cis-regulatory code.
Deep rare variant association testing (DeepRVAT) is a deep set neural network model that flexibly integrates rare variant annotations into a trait-agnostic gene impairment score. These scores improve association testing and polygenic risk prediction.
Microfluidics-assisted grid chips for spatial transcriptome sequencing (MAGIC-seq) is a spatial transcriptomics method combining multiple-grid microfluidic design and prefabricated DNA arrays for increased throughput and reduced cost, with applications for large fields of view and 3D spatial mapping.
This study presents a synthetic surrogate (SynSurr) method for imputing missing phenotypes in biobank datasets. Joint analysis of the partially observed and imputed surrogate phenotype improves power in genome-wide association studies while being robust to imputation errors.
