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Two low-input tagmentation-based long-read sequencing methods, single-molecule real-time sequencing by tagmentation (SMRT-Tag), which identifies genetic variation and CpG methylation, and single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which detects chromatin accessibility, are presented. Application of SAMOSA-Tag to prostate cancer patient-derived xenograft samples identifies metastasis-associated epigenomic alterations.
MuSiCal is a mutational signature analysis tool combining minimum-volume nonnegative matrix factorization with other algorithmic innovations. Applied to PCAWG data, MuSiCal gives more accurate results, including resolving ambiguous flat signatures.
Causal-TWAS (cTWAS) is a statistical framework that adjusts for genetic confounders in transcriptome-wide association studies. Application of cTWAS on common traits leads to reliable detection of candidate causal genes.
GIFT fine-maps candidate causal genes in a transcription-wide association study by conditioning on predicted expression of nearby genes, leading to improved statistical power and enhanced mapping resolution when applied to complex traits.
A new method allows selection of matched controls from an external pool of samples without genotype sharing. This method has been implemented in an online repository containing 39,472 exome sequencing controls that can be used for association analyses.
MESuSiE extends fine-mapping approaches to multi-ancestry analysis using LD-aware bivariate normal mixture models with a variational algorithm to identify shared and ancestry-specific causal variants.