Human Pangenome Reference Consortium

65 Genomes Expand Our Picture Of Human Genetics Researchers closely examined the genomes of 65 individuals to paint a more complex, and more complete, picture of human genetic diversity.

Tune in to @scifri.bsky.social as experts discuss the analysis of 65 genomes from individuals around the world and how this work advances our understanding of human genetics and genome function.

🎧 Listen here: www.sciencefriday.com/segments/65-...

Phased nanopore assembly with Shasta and modular graph phasing with GFAse Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive r...

A new method using the Shasta assembler and GFAse tool improves the phasing of Oxford Nanopore Technologies (ONT) sequence data, enabling chromosome-scale phasing with higher accuracy and reduced complexity.

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

🚌 School’s back in session, and like dedicated students everywhere, our ELSI team is working hard to explore the ethical, legal, and social implications of building a more comprehensive human reference genome.

Meet the team behind it: www.humanpangenome.org/elsi-team/

WashU Epigenome Browser update 2025 The WashU Epigenome Browser (https://epigenomegateway.wustl.edu/) is a web-based tool for exploring genomic data and providing visualization, investigation, and analysis of epigenomic datasets. Since ...

The WashU Epigenome Browser update brings faster performance, a new UI, and new tools for long-read & single-cell methylation data, plus genome assembly comparisons like hg38 vs chm13.

Uncover the hard work behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...

ASHG 2025 Workshop: The Human Pangenome: Data, Tools, and Workflows Introducing participants to the new Human Pangenome Reference, how samples were chosen to maximize variation, & technologies used to build the pangenome

Join HPRC at ASHG 2025 for a workshop on the Human Pangenome: data, tools & workflows.

📅 Oct 14 10AM–12PM | Learn how to access, analyze & work with the pangenome.

Details:
www.ashg.org/product/ashg...

From the western hemisphere to the east 🌐 ... HPRC brings together institutions from across the globe.

Though separated by distance, we’re united by one common goal - building a pangenome reference that captures the full scope of human genomic variation.

A more complete understanding of human genetics starts with accurate, high-quality reference genomes.

HPRC is building a reference that reflects the breadth of human genetic variation, supporting better prediction, diagnosis, and treatment.

Learn more: humanpangenome.org/samples/

An emerging polishing pipeline, DeepPolisher, improves genome assemblies by reducing indel errors and correcting false homozygosity.

Applied to 180+ HPRC assemblies, it cut errors by 54% and significantly boosted overall quality.

Here’s how…
genome.cshlp.org/content/35/7...

🎉 Big milestone for our sister consortium, SMaHT!

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

Neotelomeres and telomere-spanning chromosomal arm fusions in cancer genomes revealed by long-read sequencing Long-read genome sequencing describes the existence and structures of neotelomeres and telomere-spanning chromosome arm fusions in cancer samples. Short-read sequences of 3,651 cancer samples were used to infer the frequency of these telomeric alterations across 40 cancer types.

Long- and short-read sequencing reveal four key telomere repeat changes shaping cancer genome evolution, offering a new model to study complex repetitive elements in somatic genomes.

Uncover the research behind it:
www.cell.com/cell-genomic...

See how HPRC is progressing…
From the first draft in 2023 to an expanded and refined collection in 2025, with a comprehensive release planned for 2026.

View the full release timeline: humanpangenome.org/release-time...

LungMAP Portal Ecosystem: Systems-level Exploration of the Lung An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire of molecular omics, cellular imaging, and pathological datasets. To centraliz...

Innovative tools and data shaping the future of lung research are here.

The expanded LungMAP portal connects multi-omics, imaging, and pathology data across species, enabling deeper insight into lung development and disease.

Explore the resource: pmc.ncbi.nlm.nih.gov/articles/PMC...

HPRC Associate Members have the unique opportunity to work collaboratively to advance human genomics.

From researchers to industry partners, HPRC welcomes additional academic and organizational participation!

Learn more about our Associate Members: humanpangenome.org/associate-me...

This upcoming #WorldEnvironmentDay, we’re reflecting on how HPRC’s work contributes to a more sustainable future.

By deepening our understanding of human genetic variation, we’re supporting better outcomes and helping move toward more efficient, targeted healthcare.🌱🌍

Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies - Genome Biology Background In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evalua...

A new method helps recover abundant, but frequently overlooked microbial genomes, even with HiFi reads.

Bringing us one step closer to complete metagenomes.

Uncover the science behind it:
genomebiology.biomedcentral.com/articles/10....

With the support of incredible partner institutions, HPRC is creating a human pangenome reference and resource that represents global genomic variation…

One initiative at a time.

Ethics choices during the Human Genome Project reflected their policy world, not ours Since human genomic data produced in the 1990s are still a significant part of the reference genome, decades-old decisions pertinent to the creation of these data persist. Here, we discuss how histori...

How did 1990s policy shape today’s genomics ethics?

A recent study traces how early HGP decisions still impact consent, IRBs & efforts like the human pangenome.

Uncover the story behind it: www.cell.com/cell-genomic...

Release 2️⃣ data is now available.

Access sequencing data, assemblies, and alignments through our interactive data explorer!

data.humanpangenome.org

Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection More than 50% of families with suspected rare monogenic diseases remain unsolved after whole genome analysis by short read sequencing (SRS). Long-read sequencing (LRS) could help bridge this diagnosti...

Research highlights how long-read sequencing is helping close the diagnostic gap for rare diseases.

Using a nanopore-based pipeline, researchers resolved 11 rare disease cases, uncovering variants and epigenetic changes missed by short-read approaches.

www.medrxiv.org/content/10.1...

📢 HPRC Release 2 is here!

Now with phased genomes from 200+ individuals, a 5x increase from Release 1.

Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️:

humanpangenome.org/hprc-data-re...

HPRC is building a reference that better reflects global genomic variation.

We're well on our way to advancing assembly technology and tools to power next-gen genomic research!

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads has enabled the completion of a human genome and spurred similar efforts to complete the geno...

A promising single-platform alternative to multi-tech T2T workflows.

A recent study shows ONT Duplex reads + Pore-C mapping can produce high-accuracy, chromosome-scale genome assemblies.

Explore the findings: www.biorxiv.org/content/10.1...

❤️ Our working groups are the heart of HPRC! ❤️

Driving everything from technology and T2T assemblies to ethics, outreach, and pangenome development.

Meet the teams shaping the future of human genomics:
humanpangenome.org/working-grou...

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing...

Severus, a new method advancing variant screening improves somatic structural variant detection using long-read sequencing & a phased breakpoint graph approach.

It outperforms existing approaches across multiple datasets, uncovering complex rearrangements.

www.medrxiv.org/content/10.1...

How do we define key terms at the Human Pangenome Reference Consortium?

Our glossary was crafted specifically for the consortium’s work, ensuring clarity across teams and research.

Uncover the full list here:
humanpangenome.org/definitions/

Genotyping sequence-resolved copy-number variations using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes Copy-number variable (CNV) genes are important in evolution and disease, yet sequence variation in CNV genes is a blindspot for large-scale studies. We present a method, ctyper, that leverages pangeno...

CNV genes play a crucial role in evolution & disease but historically have been a challenge to analyze.

Ctyper uses HPRC pangenomes to map CNV gene sequences with high accuracy, improving genotyping & disease insights like SMA diagnosis.

Uncover the science: www.biorxiv.org/content/10.1...

Collaboration is how we establish and conquer our common goals. April 1-4 in Cambridge, MA, we’re coming together to advance the GA4GH Road Map and shape the future of genomics.

We look forward to next week and to fostering partnerships and advancing common goals. 🎉

Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders ARC-SV enables highly accurate detection and characterization of localized complex rearrangements of multiple DNA segments. Applying ARC-SV across human populations and brain cohorts uncovers connecti...

Novel research uses HPRC pangenome assemblies to uncover complex structural variations (cxSVs) as a central part of human genetic variation.

ARC-SV detects cxSVs linked to brain function, evolution, and psychiatric disorders.

Uncover the research behind it: www.cell.com/cell/abstrac...

🗓️ The deadline to register for in-person attendance at GA4GH Connect is Wednesday, March 18!

Join us April 1-4 in Cambridge, MA to collaborate, share insights, and help shape the future of the GA4GH Roadmap. We’ll see you there!

broadinstitute.swoogo.com/connect25bos/

Panacus: fast and exact pangenome growth and core size estimation AbstractMotivation. Using a single linear reference genome poses a limitation to exploring the full genomic diversity of a species. The release of a draft

New research introduces Panacus, a pangenome graph tool that quantifies shared sequences and genomic variability across samples.

Panacus efficiently processes GFA files and generates interactive visualizations, enabling deeper insights into pangenome growth and core genome size.

shorturl.at/Va66Q