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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 2d

#ASHG2025 kicks off next week!

Keep an eye out for IGVF presentations and posters throughout the meeting.

See you in Boston!

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 7d

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...

Human brain vascular multi-omics elucidates disease-risk associations

Reid et al. develop MultiVINE-seq to map thousands of non-coding disease variants to genes in human brain vascular cells. Cerebrovascular disease variants compromise vessel integrity, whereas Alzheime...

www.cell.com

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 14d

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...

PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations

Chemical and genetic perturbations, such as those induced by small molecules and CRISPR, effect complex changes in the molecular states of cells. Despite advances in high-throughput single-cell pertur...

pmc.ncbi.nlm.nih.gov

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 15d

ASHG 2025 is coming up! 🎉

Keep an eye out for IGVF talks and posters throughout the meeting.

We'll see you in Boston!

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 21d

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/...

GitHub - EngreitzLab/scE2G: Pipeline to run scE2G

Pipeline to run scE2G. Contribute to EngreitzLab/scE2G development by creating an account on GitHub.

github.com

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 23d

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

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 28d

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...

Leveraging sequences missing from the human genome to diagnose cancer

Cancer diagnosis using cell-free DNA (cfDNA) has the potential to improve treatment and survival but has several technical limitations. In this study, we developed a prediction model based on neomers,...

pmc.ncbi.nlm.nih.gov

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · 29d

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.

Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Sep 3

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...

CAGI7 Challenge

genomeinterpretation.org

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Aug 29

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

GitHub - scverse/scanpy: Single-cell analysis in Python. Scales to >100M cells.

Single-cell analysis in Python. Scales to >100M cells. - scverse/scanpy

github.com

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Aug 27

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...

IGVF High-level Consortium Map

igvf.org

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Aug 22

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...

MPRAnalyze

MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quant...

bioconductor.org

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Aug 21

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

IGVF

Portal for the Impact of Genomic Variation on Function consortium

data.igvf.org

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Aug 15

🔍 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/...

GitHub - EngreitzLab/scE2G: Pipeline to run scE2G

Pipeline to run scE2G. Contribute to EngreitzLab/scE2G development by creating an account on GitHub.

github.com

Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Aug 13

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

Impact of Genomic Variation on Function (IGVF) Consortium

IGVF, Impact of Genomic Variation on Function, IGVF Consortium, Understanding how genomic variation affects genome function to influence phenotypes

igvf.org

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Aug 8

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...

Interface-guided phenotyping of coding variants in the transcription factor RUNX1

Single-gene missense mutations remain challenging to interpret. Here, we deploy scalable functional screening by sequencing (SEUSS), a Perturb-seq method, to generate mutations at protein interfaces o...

pmc.ncbi.nlm.nih.gov

Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Aug 8

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...

pmc.ncbi.nlm.nih.gov

Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Aug 6

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

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Aug 1

Process 30M reads in minutes with high performance and efficiency.

Kallisto is a fast, accurate tool for quantifying transcript abundances from RNA-seq data using pseudoalignment; no full alignment needed.

Explore it here: github.com/pachterlab/k...

GitHub - pachterlab/kallisto: Near-optimal RNA-Seq quantification

Near-optimal RNA-Seq quantification. Contribute to pachterlab/kallisto development by creating an account on GitHub.

github.com

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Jul 28

A recent study demonstrates how biophysical modeling of high-throughput perturbation data can reveal transcriptional dynamics, like bursting and splicing, that shape cell fate and disease response.

Explore the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...

Stochastic Modeling of Biophysical Responses to Perturbation

Recent advances in high-throughput, multi-condition experiments allow for genome-wide investigation of how perturbations affect transcription and translation in the cell across multiple biological ent...

pmc.ncbi.nlm.nih.gov

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Jul 11

Part of the IGVF single-cell analysis workflow - the IGVF-chromap tool offers a command-line interface for indexing and aligning single-cell ATAC-seq data using the Chromap pipeline.

Explore the tool: github.com/IGVF/atomic-...

atomic-workflows/modules/igvf-chromap at main · IGVF/atomic-workflows

Workflows for pre-processing sequencing data from sequence census assays - IGVF/atomic-workflows

github.com

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Jul 9

Click editing is a recently developed platform that combines RNA-guided nickases and DNA-dependent polymerases to install precise genome edits, including substitutions, insertions, and deletions, with high efficiency and minimal indels.

Here’s how…
pmc.ncbi.nlm.nih.gov/articles/PMC...

Click editing enables programmable genome writing using DNA polymerases and HUH endonucleases

Genome editing technologies based on DNA-dependent polymerases (DDPs) could offer several benefits compared with other types of genome editors for installing diverse edits. Here, we develop click edit...

pmc.ncbi.nlm.nih.gov

Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Jul 3

🎉 Big milestone for our sister consortium, SMaHT!

Congrats on the paper in Nature, this is a huge step in mapping somatic variation!

smahtnetwrk.bsky.social @smahtnetwrk.bsky.social · Jul 3

The SMaHT marker paper is now live in @nature.com 🧬

This landmark study characterizes somatic variation across 19 tissue types from 150 nondiseased donors, laying the groundwork for future discoveries in health, aging, and disease.

Read the full paper: www.nature.com/articles/s41...

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Jun 25

🛠️ Topyfic is a Python library for applying reproducible LDA (rLDA) to single-cell and bulk RNA-seq data, helping identify consistent gene expression programs and key regulators like transcription factors across conditions.

Explore the tool: github.com/mortazavilab...

GitHub - mortazavilab/Topyfic: Topyfic: Reproducible latent dirichlet allocation (LDA) using leiden clustering and harmony for single cell epigenomics data

Topyfic: Reproducible latent dirichlet allocation (LDA) using leiden clustering and harmony for single cell epigenomics data - mortazavilab/Topyfic

github.com

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Impact of Genomic Variation on Function @igvfconsortium.bsky.social · Jun 18

IGVF is uncovering how genomic variation impacts genome function and phenotype through mapping, modeling, and resource generation to advance research across the community.

Learn more: igvf.org

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