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

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

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...

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...

What drives the science behind IGVF? In this IGVF Q&A, members share how the team is tackling long-standing genomics challenges and building a comprehensive catalog of variant effects to advance human health & research. Tune in: youtu.be/zPzGIjSQJ4U?...

A new preprint from IGVF introduces a scalable workflow to address variants of uncertain significance (VUS). Across 40 genes, the approach reclassified 75% of 16,115 VUS and preclassified >90K variants—moving clinical genomics forward. Read more:  www.biorxiv.org/content/10.6...

SIMBA enables joint embedding of cells and their defining features into a shared latent space. This attribute supports single-cell and multimodal analysis, batch correction, and multi-omic integration.  Learn more: simba-bio.readthedocs.io/en/latest/

IGGSy 2026 is coming! July 5 - 9, join researchers from around the world to explore genome graphs, pangenomics, and metagenomics, including a dedicated Human Pangenome Project session with keynotes from speakers of varied specializations. Registration open now! iggsy.org

Recent IGVF research benchmarks Perturb-seq in human stem cells, enabling scalable analysis of gene and enhancer function during differentiation and disease. Uncover the science behind it: www.cell.com/stem-cell-re...

How does IGVF research move us closer to understanding human health and disease? Charles Gersbach, PhD, explains how mapping the function of genetic variation is key to unlocking better treatments, from cancer and fibrosis to neurodegeneration and aging. ▶️ youtu.be/R6Q3yavjGDs

A recent preprint introduces MaveMD, a clinical interface for MaveDB that integrates MAVE data with ClinVar and ClinGen to support variant classification and reduce VUS uncertainty. Uncover the science behind it:  www.medrxiv.org/content/10.1...

Momentum and connections is exactly right! Excited to see the impact highlighted in the 2025 Annual Report. 👏🏼

Large-scale perturbation of transcription factors and enhancers reveals regulatory networks shaping human heart development and congenital heart disease.  A new reference map helps interpret CHD genes and variants.   Uncover the research behind it: www.biorxiv.org/content/10.6...

Understanding how genomic variation shapes disease opens the door to entirely new therapeutic strategies. Hear from Jesse Engreitz, PhD, and other IGVF members in the full Q&A. ▶️ youtu.be/zPzGIjSQJ4U

Cells sense matrix stiffness through mechanoenhancers, genomic elements that tune gene activity in response to mechanical signals. Editing these enhancers can reshape cell behavior, pointing to new therapeutic possibilities. Read more: www.science.org/doi/10.1126/...

Cheers to another year of discovery! 🎇 As we wrap up 2025 and look toward 2026, we’re excited to share voices from across IGVF. Tune in to our IGVF Q&A featuring consortium members reflecting on this year’s work and what’s ahead: youtu.be/zPzGIjSQJ4U

Monod is a Python package for single-cell RNA-seq that integrates nascent and mature RNA using biophysical models, revealing regulatory dynamics beyond average expression. Learn more: www.nature.com/articles/s41...

Kallisto utilizes pseudoalignment to quickly estimate transcript abundances from RNA-seq data and can handle tens of millions of reads in minutes, all while maintaining high accuracy. Explore the tool: github.com/pachterlab/k...

NEW from IGVF: our NAR paper highlighting the IGVF Catalog, an open resource for exploring how genomic variation impacts function. Use the resource, explore the data, and tell us what you think! academic.oup.com/nar/advance-...

We're proud to recognize this year’s IGVF Team Science Award winners, leaders and teams whose work strengthens the entire consortium. Congratulations to each of our award recipients 👏🏽

Feeling extra grateful this November for the IGVF community! Thank you for your collaboration, dedication, and the incredible work you do to advance our understanding of human health and disease.

IGVF @ CAGI7! This year’s meeting features several talks from IGVF members, all aligned with our efforts to link genomic variation to function. Keynote by Douglas Fowler (UW). Late registration ends Dec 1. genomeinterpretation.org/cagi7.html

Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies” shorturl.at/H3Qww This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon. Bluetorial below.

Incredible work from the IGVF community! A major step forward for scalable CRT discovery, and a significant contribution to understanding gene regulation in human neurons.

🔍 scE2G is a computational pipeline for predicting genome-wide enhancer–gene regulatory links using single-cell ATAC-seq or paired ATAC + RNA-seq (multiome) data. Learn more & access the tool here: github.com/EngreitzLab/...

From data to discovery, IGVF is working to understand how genomic variation influences genome function and phenotype. Learn more about our work at www.igvf.org

Wishing everyone a spook-tacular Halloween! 👻 Whether you’re celebrating or just enjoying a well-earned weekend, we hope it’s a wickedly wonderful one!

RSV remains a global health challenge. Using CRISPR knockout screens and single-cell RNA-seq, researchers identified key host factors and responses that drive infection. Read more: pmc.ncbi.nlm.nih.gov

From all fields and corners of the map, IGVF members came together in Durham, NC. United by one mission, to understand how genomic variation influences function. A huge thank you to the Durham Bulls Athletic Park for welcoming us and hosting a fantastic night of food, fun, and practice home runs! ⚾

#ASHG2025 kicks off next week! Keep an eye out for IGVF presentations and posters throughout the meeting. See you in Boston!

How do genetic variants in brain vascular cells shape neurological disease risk? With MultiVINE-seq, researchers mapped thousands of risk variants, revealing distinct mechanisms for cerebrovascular vs. neurodegenerative disorders—including Alzheimer’s. www.cell.com/neuron/fullt...

How do cells respond to chemical and genetic perturbations? A recent study introduces PerturbNet, a deep generative model that predicts how unseen drugs, CRISPR edits, or even missense mutations alter single-cell gene expression. Read the full publication: pmc.ncbi.nlm.nih.gov/articles/PMC...

ASHG 2025 is coming up! 🎉 Keep an eye out for IGVF talks and posters throughout the meeting. We'll see you in Boston!

scE2G is a computational pipeline for predicting genome-wide enhancer–gene regulatory links using single-cell ATAC-seq or multiome data. Explore the tool here: github.com/EngreitzLab/...

The IGVF Consortium began with one mission: to understand how genomic variation shapes genome function and influences health. Together, we’re building lasting resources for the research community. igvf.org

Neomer-based classifiers "short DNA sequences from tumor mutations”, show high accuracy in detecting cancer, even at early stages, and distinguishing subtypes. Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...

IGVF uses state-of-the-art experimental and computational approaches to model, predict, characterize, and map genome function. Together, these efforts are building a catalog that reveals how genomic variation influences genome function and phenotypes.

Deadline extended! 🏁 The submission deadlines for TCS2 and ATP7B in CAGI7 are now September 15. A big thanks to our collaborators in the Fowler and Roth groups for their leadership on this effort. genomeinterpretation.org/cagi7-challe...

Scanpy is a scalable Python toolkit for analyzing single-cell gene expression data. From preprocessing & visualization to clustering, trajectory inference, and differential expression testing, Scanpy can handle datasets with over 1M cells. Learn more & access the tool: github.com/scverse/scanpy

See how IGVF comes together 🧩 Our High-Level Consortium Map highlights the experiments, teams & technologies driving discovery on how genomic variation impacts function. Explore the map: igvf.org/high-level-c...

MPRAnalyze offers a powerful statistical framework for Massively Parallel Reporter Assays (MPRAs) to study enhancer activity. From quantifying activity to comparing across conditions, it helps researchers uncover how enhancers drive gene regulation. bioconductor.org/packages/rel...

The IGVF Data Portal serves as the central hub for research data from the consortium, encompassing raw sequences, analyzed effects, software, and predictive models. Explore how genomic variation impacts function and phenotype. data.igvf.org

🔍 scE2G is a computational pipeline for predicting genome-wide enhancer–gene regulatory links using single-cell ATAC-seq or paired ATAC + RNA-seq (multiome) data. Learn more & access the tool here: github.com/EngreitzLab/...

IGVF is bringing together discoveries from across the network into a lasting, openly available catalog of how genomic variants influence genome function and phenotypes. A resource that will continue to power future research. Explore our goals and the impact ahead: igvf.org

Using the SEUSS Perturb-seq method, researchers mapped 115 RUNX1 mutations in leukemia cells, revealing wild-type-like, loss-of-function, and hypomorphic types. Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...

Using the SEUSS Perturb-seq method, researchers mapped 115 RUNX1 mutations in leukemia cells, revealing wild-type-like, loss-of-function, and hypomorphic types. Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...

Thousands of genomic variants are linked to disease, but how do they actually function? IGVF is building a catalog of experimental and computational insights to uncover the impact of variants. 🔎 We’re on the case: igvf.org