MESC: Mediated Expression Score Regression

Method for quantifying the fraction of disease heritability mediated by all QTL effects.

REF:Quantifying genetic effects on disease mediated by assayed gene expression levels. pre-print

PLASMA: PopuLation Allele-Specific MApping

Method for fine-mapping functional data using eQTL and allelic-imbalance signal.

REF:Wang et al. Allele-Specific QTL Fine Mapping with PLASMA. AJHG. 2020


Method for identifying allelic imbalance in functional features and testing for context-specific imbalance.

REF: Allelic imbalance reveals widespread germline-somatic regulatory differences and prioritizes risk loci in Renal Cell Carcinoma. pre-print

Interactive browser for TWAS results from hundreds of complex traits.

Chromatin TWAS

Data and analysis of chromatin/expression/splicing and schizophrenia (see below for TWAS methods). Includes genome-wide results from TWAS of expression/splicing in three tissues (four studies) and schizophrenia. Additionally, genome-wide results from TWAS of expression/splicing TWAS and chromatin activity measured in ~100 individuals (two studies) by ChIP-Seq.

REF: Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights. Nature Genetics. 2018


Methods and data for performing a transcriptome-wide (or any other *ome-wide) association study. Includes a streamlined pipeline for quantifying genetic components of functional features (such as gene expression), building predictive models, predicting functional features into GWAS data, and joint/conditional analyses of associated features. Also includes a resource of trained predictive models from multiple large cohorts, tissues, and functional assays.

REF: Integrative approaches for large-scale transcriptome-wide association studies. Nature Genetics. 2016


Methods for performing a Transcriptome-wide Association Study. Identify associations between genetic component of gene expression and trait using eQTL and GWAS data only. This has now been superseded by the FUSION software above. Legacy implementation archived here.

REF: Integrative approaches for large-scale transcriptome-wide association studies. Nature Genetics. 2016

Functional Annotations

Atlas of functional annotations used Gusev et al 2014 AJHG and Gusev et al 2016 Nat Comms. Includes tissue-specific and cross-tissue measures of open chromatin, tissue-specific histone modifications, and prostate-cancer specific epigenetic activity. Epigenetic experiments performed by ENCODE and M Freedman lab; peak calling performed by XS Liu lab.

REF: Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. The American Journal of Human Genetics. 2014

REF: Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Nature communications. 2016


Method for detection of IBD shared haplotypes and association to trait. Infers haplotype clusters from IBD segments (for example, detected by the GREMLIN algorithm below), generating pseudo-SNP data for association testing.

REF: DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation. The American Journal of Human Genetics. 2011


Method for fast, pairwise detection of segments identical by descent. Uses hashing techniques to efficiently identify long stretches of shared DNA between pairs of individuals from array SNP data.

REF: Whole population, genome-wide mapping of hidden relatedness. Genome res. 2009


Genotype phasing by entropy minimization.

REF: Highly scalable genotype phasing by entropy minimization. IEEE/ACM TCBB. 2008