Join NHGRI on Friday, October 30, for a pre-application webinar on upcoming IGVF funding opportunities. Learn about program goals, objectives, and the application review process, with a Q&A session to follow. Submit questions and learn more: grants.nih.gov/news-events/...

As ASHG 2026 wraps up tomorrow, stop by the 2:30 - 4:30PM poster session to explore research from IGVF members. Visit the IGVF at ASHG page for poster details! igvf.org/news/igvf-as...

IGVF ASHG 2026 Presentations

IGVF ASHG 2026 Presentations

igvf.org

ASHG 2026 is in full swing! IGVF consortium members will be sharing their research throughout the meeting. Check out the schedule below for additional information on IGVF member presentations.

Explore FRACTEL, a computational tool that identifies significant discoveries at the element level by combining individual p-values using Robust Rank Aggregation (RRA). Access the tool: github.com/Gersbachlab-...

GitHub - Gersbachlab-Bioinformatics/FRACTEL: Framework for Rank Aggregation of CRISPR Tests within ELements

Framework for Rank Aggregation of CRISPR Tests within ELements - Gersbachlab-Bioinformatics/FRACTEL

github.com

ASHG 2026 is just one week away! IGVF members will be presenting their research throughout the meeting. Stay tuned for more details to help you plan your time at ASHG and connect with IGVF.

Calling researchers in functional genomics, computational biology, imaging, and generative AI to explore the CM4AI AnVIL Cell Map Prediction DREAM Challenge, launching October 19! Participants will develop models to predict protein localization in cells. www.synapse.org/Synapse:syn7...

CM4AI-AnVIL DREAM Challenge

'CM4AI-AnVIL DREAM Challenge' (Synapse ID: syn77349038) is a project on Synapse. Synapse is a platform for supporting scientific collaborations centered around shared biomedical data sets.

synapse.org

IGVF researchers developed a scalable approach to interpret uncertain genetic variants. Using experimental and predictive evidence, the team reclassified 75% of 16,115 VUS and preclassified 62% of >90,000 unobserved variants. www.biorxiv.org/content/10.6...

A scalable approach to resolving variants of uncertain significance

Over 90% of missense variants across ∼4,000 disease-associated genes are variants of uncertain significance (VUS). Experimental variant effect measurements provide critical evidence about pathogenicit...

biorxiv.org

Explore the IGVF outreach page for workshops, informational videos, and links to the IGVF Data Portal, resources, and Catalog. igvf.org/outreach/

IGVF Education & Outreach

IGVF Education & Outreach

igvf.org

SEEK-VEC is a new framework for finding hidden patterns in count-based data. By combining multiple topic models, it helps identify key terms, uncover relationships, and assess results, especially when signals are weak. www.biorxiv.org/content/10.6...

SEEK-VEC: Augmenting topic modeling with spectral ensemble learning

Count data are ubiquitous across many applications in which understanding latent patterns is of interest. Topic modeling is a powerful tool for detecting latent structure in count data. However, stand...

biorxiv.org

The Integrative Analysis Working Group brings together multimodal IGVF data to define variant function, resolve assay discrepancies, characterize pleiotropic effects, and develop models to predict and interpret variant function.  Explore this and other 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 specific is a gene to a cell type, tissue, or condition? This preprint introduces ember, a principled approach to measuring gene specificity, with applications across mouse tissues and human PBMCs. Uncover the science behind it: www.biorxiv.org/content/10.1...

Determining gene specificity from multivariate single-cell RNA sequencing data

An important application of single-cell genomics experiments is to identify genes specific to biological categories or experimental conditions. Although numerous approaches have been proposed to ident...

biorxiv.org

MPRAsnakeflow enables standardized, reproducible processing and analysis of MPRA data. Developed by the IGVF Consortium, the tool and community standards support robust integration of diverse datasets for regulatory genomics. genome.cshlp.org/content/earl...

How do genetic variants affect secreted proteins? A new study introduces MultiSTEP, a scalable method for measuring variant effects in coagulation factor IX. The approach assessed >8,500 F9 missense variants and helped reclassify 63.1% of VUSs. pubmed.ncbi.nlm.nih.gov/40514537/

Multiplex and multimodal mapping of variant effects in secreted proteins via MultiSTEP - PubMed

Despite widespread advances in DNA sequencing, the functional consequences of most genetic variants remain poorly understood. Multiplexed assays of variant effect can measure the function of variants at scale but cannot readily be applied to the ~10% of human genes encoding secreted proteins. Here w …

pubmed.ncbi.nlm.nih.gov

Explore pySpade, a computational tool for whole-transcriptome analysis of single-cell perturbation datasets. Using Cell Ranger output, pySpade identifies differential expression and generates hit tables and Manhattan plots. github.com/Hon-lab/pySp...

GitHub - Hon-lab/pySpade: Single cell Perturbations - Analysis of Differential gene Expression

Single cell Perturbations - Analysis of Differential gene Expression - Hon-lab/pySpade

github.com

Our interactive high-level consortium map lets you explore the experiments, teams, and technologies that make up IGVF.  Explore the map to see the connections between experiments, teams, and technologies.  igvf.org/high-level-c...

IGVF High-level Consortium Map

IGVF High-level Consortium Map

igvf.org

Demuxafy streamlines demultiplexing and doublet detection for droplet-based scRNA-seq, giving users the flexibility to choose and efficiently run methods best suited to their dataset. Explore the tool:  demultiplexing-doublet-detecting-docs.readthedocs.io/en/latest/

An open-source framework for exploring functional genomic regions through an interactive web app or command-line tool. Design and analyze CRISPR-Cas, CRISPRi, and CRISPRa tiling screens with CRISPR-SURF. Explore the tool: github.com/pinellolab/C...

GitHub - pinellolab/CRISPR-SURF

Contribute to pinellolab/CRISPR-SURF development by creating an account on GitHub.

github.com

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