Bryce van de Geijn

SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease

Kushal K. Dey, Steven Gazal, Bryce van de Geijn, Samuel Sungil Kim et autres

We assess contributions to autoimmune disease of genes whose regulation is driven by enhancer regions (enhancer-related) and genes that regulate other genes in trans (candidate master-regulator). We link these genes to SNPs using several SNP-to-gene (S2G) strategies and apply heritability analyses to …

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Functionally informed fine-mapping and polygenic localization of complex trait heritability

Omer Weissbrod, Farhad Hormozdiari, Christian Benner, Ran Cui et autres

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Evaluating the informativeness of deep learning annotations for human complex diseases

Kushal K. Dey, Bryce van de Geijn, Samuel Sungil Kim, Farhad Hormozdiari et autres

Deep learning models have shown great promise in predicting regulatory effects from DNA sequence, but their informativeness for human complex diseases is not fully understood. Here, we evaluate genome-wide SNP annotations from two previous deep learning models, DeepSEA and Basenji, by applying …

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SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease

Kushal K. Dey, Steven Gazal, Bryce van de Geijn, Samuel Sungil Kim et autres

Abstract Gene regulation is known to play a fundamental role in human disease, but mechanisms of regulation vary greatly across genes. Here, we explore the contributions to disease of two types of genes: genes whose regulation is driven by enhancer regions as …

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Genes with High Network Connectivity Are Enriched for Disease Heritability

Samuel Sungil Kim, Chengzhen L. Dai, Farhad Hormozdiari, Bryce van de Geijn et autres

Functionally-informed fine-mapping and polygenic localization of complex trait heritability

Omer Weissbrod, Farhad Hormozdiari, Christian Benner, Ran Cui et autres

Abstract Fine-mapping aims to identify causal variants impacting complex traits. Several recent methods improve fine-mapping accuracy by prioritizing variants in enriched functional annotations. However, these methods can only use information at genome-wide significant loci (or a small number of functional annotations), severely …

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Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability

Bryce van de Geijn, Hilary K. Finucane, Steven Gazal, Farhad Hormozdiari et autres

Regulatory variation plays a major role in complex disease and that cell type-specific binding of transcription factors (TF) is critical to gene regulation. However, assessing the contribution of genetic variation in TF-binding sites to disease heritability is challenging, as binding is often …

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Evaluating the informativeness of deep learning annotations for human complex diseases

Kushal K. Dey, Bryce van de Geijn, Samuel Sungil Kim, Farhad Hormozdiari et autres

Abstract Deep learning models have shown great promise in predicting genome-wide regulatory effects from DNA sequence, but their informativeness for human complex diseases and traits is not fully understood. Here, we evaluate the disease informativeness of allelic-effect annotations (absolute value of the …

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Functional disease architectures reveal unique biological role of transposable elements

Farhad Hormozdiari, Bryce van de Geijn, Joseph Nasser, Omer Weissbrod et autres

Transposable elements (TE) comprise roughly half of the human genome. Though initially derided as junk DNA, they have been widely hypothesized to contribute to the evolution of gene regulation. However, the contribution of TE to the genetic architecture of diseases remains unknown. …

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Genes with High Network Connectivity Are Enriched for Disease Heritability

Samuel Sungil Kim, Chengzhen L. Dai, Farhad Hormozdiari, Bryce van de Geijn et autres

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IMPACT: Genomic Annotation of Cell-State-Specific Regulatory Elements Inferred from the Epigenome of Bound Transcription Factors

Tiffany Amariuta, Yang Luo, Steven Gazal, Emma E. Davenport et autres

Despite significant progress in annotating the genome with experimental methods, much of the regulatory noncoding genome remains poorly defined. Here we assert that regulatory elements may be characterized by leveraging local epigenomic signatures where specific transcription factors (TFs) are bound. To link …

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Disease Heritability Enrichment of Regulatory Elements Is Concentrated in Elements with Ancient Sequence Age and Conserved Function across Species

Margaux L.A. Hujoel, Steven Gazal, Farhad Hormozdiari, Bryce van de Geijn et autres

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