Human Pangenome Reference Consortium

YouTube video by Human Pangenome Reference Consortium The Human Pangenome Reference Consortium (HPRC) Q&A

This season, we’re grateful for the chance to share the work, voices, and perspectives of the HPRC community.

Our new Q&A video features members from across the consortium reflecting on the technologies, collaborations, and insights shaping the human pangenome.

Watch here: youtu.be/bJ7wkbwd5oU?...

Locityper enables targeted genotyping of complex polymorphic genes - Nature Genetics Locityper is a general-purpose genotyper that can efficiently genotype and analyze a diverse set of genes, such as hyperpolymorphic HLA genes, using both short-read and long-read whole-genome sequenci...

💡 Novel work supported by HPRC members highlights Locityper, a tool bringing accurate genotyping to some of the most challenging regions of the human genome.

Fast and precise, it outperforms current pipelines and scales to biobank-sized cohorts.

More at:
www.nature.com/articles/s41...

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 regions of the genome, long-read sequencing ...

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.

Learn more: pmc.ncbi.nlm.nih.gov/articles/PMC...

Curious about the work behind the Human Pangenome Reference Consortium?

Discover how researchers worldwide are working together to build a more complete reference of human genetic variation.

Learn more at humanpangenome.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!

Co-opted transposons help perpetuate conserved higher-order chromosomal structures Transposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include binding sites for architectural proteins, such as CTCF, RAD21, and SMC3, that are involved in ...

Transposable elements (TEs) do more than regulate genes; they help shape and preserve 3D genome structure across species.

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

We're live at #ASHG2025!

Don't forget to look out for HPRC member presentations, happening this week.

Next week, we're headed to #ASHG2025!

HPRC members will be sharing their latest research and insights throughout the week.

See who's presenting ⬇️

🌍 Researchers from around the world are joining forces through the Human Pangenome Reference Consortium to develop a more comprehensive and dynamic pangenome resource.

Learn more about our mission: humanpangenome.org

Human-specific gene expansions contribute to brain evolution A complete human genome and functional modeling in zebrafish pinpoint gene expansions that may underlie the evolutionary innovations of the human brain.

A complete telomere-to-telomere genome sequence reveals 213 human-specific gene families, including candidates shaping brain evolution.

Functional studies highlight roles for GPR89B and FRMPD2B in brain expansion and synapse signaling.

Read more in Cell:
www.cell.com/cell/abstrac...

HPRC will see you at #ASHG!

Join our workshop, The Human Pangenome: Data, Tools, and Workflows, on Oct 14 (10–12 pm) + look out for HPRC member presentations throughout the meeting.

Check out the presentations highlighted below, with more to come!

BWT construction and search at the terabase scale Burrows–Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome dat...

👣 A big step forward for pangenome research.

New tool ropebwt3 makes large-scale BWT indexing feasible, scaling to hundreds of human genomes & terabases of bacterial assemblies.

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

The Human Pangenome Reference Consortium is building a more complete and inclusive reference for human genetics, one that better reflects human variation and drives new discoveries.

Our story: humanpangenome.org

Regulatory Transposable Elements in the Encyclopedia of DNA Elements Transposable elements (TEs) make up about half of the human genome and many have the biochemical hallmarks of tissue- or cell type-specific cis -regulatory elements. While some TEs have been rigorousl...

~25% of human candidate cis-regulatory elements (cCREs) are derived from transposable elements, further shaping gene regulation, TF binding, and GWAS variant enrichment.

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

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

#ASHG25 is a little over a month away!

As you plan your schedule, don’t forget to pencil in time for the HPRC workshop on Tuesday, October 14, from 10am - 12pm.

Details and registration below:
www.ashg.org/product/ashg...

Lossless Pangenome Indexing Using Tag Arrays Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due t...

A scalable indexing framework for pangenome graphs enables efficient, lossless, and haplotype-aware queries. Tested on HPRC graphs, it preserves accuracy while improving scalability.

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

Collaboration drives progress.

From Coriell and the Genome Reference Consortium to Google and GA4GH, HPRC partners bring essential expertise to building the human pangenome.

Learn more about our partnerships:
humanpangenome.org/partners/

Exploring gene content with pangene graphs AbstractMotivation. The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although

Pangene, an innovative computational tool, maps gene orientation, order & copy-number changes across genomes. Applied to the human pangenome, it reveals both known variation & complex haplotypes.

Read more:
academic.oup.com/bioinformati...

🔍 Explore the Human Pangenome!

Our interactive Data Explorer makes it easy to navigate sequencing, assemblies, annotations, and alignments from the HPRC.

Start exploring the data here:
data.humanpangenome.org/raw-sequenci...

Highly accurate assembly polishing with DeepPolisher Accurate genome assemblies are essential for biological research, but even the highest quality assemblies retain errors caused by the technologies used to construct them. Base-level errors are typical...

Accurate genome assemblies just got better. DeepPolisher improves base-level accuracy, cutting errors by 50%+ and indels by >70%, applied to 180 HPRC assemblies.

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

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

Headed to #ASHG25?

Don’t miss HPRC’s workshop on the Human Pangenome: Data, Tools & Workflows.

📅 Oct 14 | 10AM–12PM

Learn how to access data & use pangenome tools!

www.ashg.org/product/ashg...

Whole-Genome Sequencing Reveals Individual and Cohort Level Insights into Chromosome 9p Syndromes Previous genomic efforts on chromosome 9p deletion and duplication syndromes have utilized low resolution strategies (i.e., karyotypes, chromosome microarrays). We present the first large-scale whole-...

The largest WGS study of 9p-related syndromes to date analyzes 100 individuals, revealing key genes, structural variation mechanisms, and insights into development.

Learn more...
pmc.ncbi.nlm.nih.gov/articles/PMC...

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...