Utilize the IGVF Data Portal to access research data, software, predictive models, and genomic resources generated by the IGVF Consortium. From raw sequencing data to analyzed results, discover data driving functional genomics: data.igvf.org

FastGxC enables fast, powerful mapping of context-specific eQTLs from bulk and single-cell RNA-seq data, improving trait interpretation while expanding candidate causal genes.  Explore the study: www.cell.com/cell-genomic...

FastGxC: Fast and powerful context-specific eQTL mapping in bulk and single-cell data

Krockenberger, Lu, et al. introduce FastGxC, a method that identifies how genetic variants regulate gene activity in specific tissues and cell types more efficiently than existing approaches. Applied ...

cell.com

Explore the IGVF YouTube channel for workshops, Q&A sessions, presentations, and more. Hear directly from consortium members and discover resources that support functional genomics research. Watch here: www.youtube.com/@igvf

Impact of Genomic Variation on Function

youtube.com

Understanding sequencing library structure is essential for accurate genomics data processing. seqspec provides a machine-readable specification that standardizes library descriptions, improving preprocessing, reproducibility, and assay comparisons.  Learn more: academic.oup.com/bioinformati...

IGVF is building resources to better understand how genomic variation influences genome function and human health through predictive modeling, functional characterization, mapping, networking, and shared data resources. Learn more about our initiative: www.igvf.org/about/

FastGxC is a tool for identifying context-specific genetic effects from single-cell and bulk RNA-seq data. By modeling repeated samples from the same individual, it improves detection power and remains robust even with missing data. Explore the tool: github.com/BalliuLab/Fa...

GitHub - BalliuLab/FastGxC

Contribute to BalliuLab/FastGxC development by creating an account on GitHub.

github.com

New preprint! 📢 PerturbPlan introduces an analytical framework for designing Perturb-seq and TAP-seq experiments, reducing power calculation runtimes by up to seven orders of magnitude and enabling interactive experimental design. www.biorxiv.org/content/10.6...

PerturbPlan: An analytical framework for designing Perturb-seq experiments

CRISPR screens with single-cell RNA-seq readouts provide a powerful tool for characterizing the functions of noncoding elements and genes. However, designing these experiments to balance statistical p...

biorxiv.org

A recent preprint presents an MPRA framework that assays cis-regulatory elements alongside their target promoter, providing a functional map of 1,214 CYP3A4 regulatory variants and insights into gene regulation, drug response, and disease. Read more: www.biorxiv.org/content/10.6...

Massively parallel reporter assays for CYP3A4 enhancer variants alongside their native promoter

Massively parallel reporter assays (MPRAs) enable high-throughput functional testing of thousands of cis -regulatory elements (CREs). However, conventional MPRAs typically use short CRE fragments comb...

biorxiv.org

Explore the IGVF YouTube channel for workshop recordings, research presentations, consortium updates, and insights from scientists working to understand how genomic variation impacts genome function. www.youtube.com/@igvf

Impact of Genomic Variation on Function

youtube.com

MPRA is an R package that provides tools for the differential analysis of Massively Parallel Reporter Assay (MPRA) data, helping researchers investigate regulatory element activity at scale. Explore MPRA: github.com/hansenlab/mpra

GitHub - hansenlab/mpra

Contribute to hansenlab/mpra development by creating an account on GitHub.

github.com

Looking for information on a gene, variant, or genomic region? The IGVF catalog brings together experimental data and computational predictions from the IGVF Consortium and other resources on a single searchable platform. catalog.igvf.org

Hear from Andreas Gschwind, PhD, as he highlights enhancer-gene mapping, CRISPR perturbation data, predictive models, and tools within the IGVF catalog.  youtu.be/jVxcwRXZYMc

Using the IGVF Catalog to Study Noncoding Variant Function

YouTube video by Impact of Genomic Variation on Function

youtu.be

How can researchers access and build on IGVF resources?  In this workshop presentation, Michael Love, PhD, highlights the IGVF data portal, catalog, APIs, and computational tools supporting reproducible functional genomics research. youtu.be/W6Mr7O7gUNY

Accessing and Building on the IGVF Data Portal and Catalog

YouTube video by Impact of Genomic Variation on Function

youtu.be

IGVF has adopted seqspec, a machine-readable standard helping improve reproducibility, transparency, and interoperability across functional genomics datasets. Learn how seqspec is supporting scalable data sharing and QC across IGVF: igvf.org/news/seqspec/

IGVF Adopts 'seqspec' to Advance Reproducibility and Data Standards in Functional Genomics

IGVF Adopts 'seqspec' to Advance Reproducibility and Data Standards in Functional Genomics

igvf.org

Roulette is a basepair-resolution model for predicting germline de novo mutation rates across the human genome, helping uncover mechanisms that shape mutagenesis, including the impact of Polymerase III transcription.  Explore the tool: github.com/vseplyarskiy...

GitHub - vseplyarskiy/Roulette: A mutation rate model at the basepair resolution identifies the mutagenic effect of Polymerase III transcription

A mutation rate model at the basepair resolution identifies the mutagenic effect of Polymerase III transcription - vseplyarskiy/Roulette

github.com

Hear from Karen Mohlke, PhD, as she introduces the IGVF Consortium and its efforts to build a functional genomics resource connecting genetic variation to genome function and disease.  Check out the full presentation: youtu.be/CbCILxe_eSI?...

Introduction to the IGVF Consortium and Functional Genomics Resource

YouTube video by Impact of Genomic Variation on Function

youtu.be

Why build a comprehensive variant effects catalog? Katherine Degner, PhD, explains how a trusted, centralized resource can help researchers explore how genes impact different tissues and cell types, all in one place. ▶️ youtu.be/Iof2mfE6sRM

Why is it important to build a comprehensive catalog of variant effects?

YouTube video by Impact of Genomic Variation on Function

youtu.be

Saturation genome editing of BARD1 variants resolves 95% of variants of uncertain significance, linking functional effects to cancer risk with high accuracy (AUC=0.99). Uncover the science behind it: www.medrxiv.org/content/10.1...

Saturation genome editing of BARD1 resolves VUS and provides insight into BRCA1-BARD1 tumor suppression

BARD1 variants are associated with hereditary breast cancer and neuroblastoma, yet, 98% of missense variants remain variants of uncertain significance (VUS). We applied Saturation Genome Editing (SGE)...

medrxiv.org

New preprint: Transcription factor collaboration shapes CD8+T cell states. Large-scale TF screens and single-cell profiling map regulatory programs and interactions (including RUNX–KLF2) that inform T cell exhaustion and potential cell therapy strategies. Read more: www.biorxiv.org/content/10.6...

Follow IGVF on YouTube for Q&As, research highlights, and insights from across the consortium. Subscribe and tune in: www.youtube.com/@igvf

Impact of Genomic Variation on Function

youtube.com

MPRAflow is a pipeline for analyzing MPRA sequencing data, generating count tables, linking variants to barcodes, and modeling variant effects from saturation mutagenesis experiments. Explore the tool: github.com/shendurelab/...

New research combines CRISPR activation, Perturb-seq, and in situ screening to uncover RNA-based mechanisms that enhance T cell–mediated killing of cancer and infected cells.  Read more: www.nature.com/articles/s41...

High-content CRISPR activation screens identify synthetically lethal RNA-based mechanisms to sensitize cancer cells to targeted T cell cytotoxicity - Nature Genetics

A series of in vitro and in vivo CRISPR activation screens combined with in situ Perturb-seq identify regulators of T cell-dependent cytotoxicity in melanoma.

nature.com

The IGVF Data Portal brings together datasets, tools, models, and protocols from across the consortium, from raw sequencing data to analyzed variant effects. Explore the resource: data.igvf.org

What’s one of the biggest challenges in genomics today? Lea Starita explains how variants of uncertain significance limit genetic medicine, and how IGVF is working to solve it using functional data and predictive models. ▶️ youtu.be/yEjEeIIkj9Q

What are the key problems in the field that IGVF is addressing?

YouTube video by Impact of Genomic Variation on Function

youtu.be

Looking for IGVF across social media? Visit our Linktree to find all IGVF platforms in one place and stay up to date on the latest research, tools, and consortium updates.  linktr.ee/IGVFConsortium

New preprint: Neuron–astrocyte interactions reshape neuronal gene regulation. Co-culture and CRISPR screens reveal regulatory elements and TF networks that control neuronal maturation and link to schizophrenia and Alzheimer’s disease. Read more: www.biorxiv.org/content/10.6...

What makes the IGVF Catalog exciting? Michael Love, PhD, explains how it moves beyond genome annotation to map networks linking variants, regulatory elements, genes, and phenotypes, offering a new way to understand genome function. 🎬 youtu.be/oC7a_IJw9X8

What excites you most about the IGVF catalog?

YouTube video by Impact of Genomic Variation on Function

youtu.be

The IGVF Mapping Working Group generates large-scale single-cell datasets, developing computational pipelines to help uncover how genetic variation influences human health and disease. Learn more about IGVF Working Groups: igvf.org/working-grou...

IGVF Working Groups

Code of Conduct of Impact of Genomic Variation on Function (IGVF) Consortium

igvf.org

How do noncoding variants drive immune disease? Using large-scale Perturb-seq in primary human CD4+ T cells, researchers map the chain from variant → CRE → gene → regulatory network, linking risk loci to shared disease programs. Read the preprint: www.biorxiv.org/content/10.6...

Handling large-scale single-cell data requires efficient tools. 🛠️ anndata is a Python package designed for working with annotated data matrices, offering sparse data support, lazy operations, and integration with PyTorch. Learn more: github.com/scverse/annd...

GitHub - scverse/anndata: Annotated data.

Annotated data. Contribute to scverse/anndata development by creating an account on GitHub.

github.com