Lightnews — Scholar-powered news

Human-specific gene expansions contribute to brain evolution

Human Pangenome Reference Consortium @humanpangenome.bsky.social · 11d

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...

A complete human genome and functional modeling in zebrafish pinpoint gene expansions that may underlie the evolutionary innovations of the human brain.

www.cell.com

1 5

Human Pangenome Reference Consortium @humanpangenome.bsky.social · 12d

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!

3 4

Human Pangenome Reference Consortium @humanpangenome.bsky.social · 18d

👣 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...

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...

Regulatory Transposable Elements in the Encyclopedia of DNA Elements

1 3

Human Pangenome Reference Consortium @humanpangenome.bsky.social · 20d

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

3

Human Pangenome Reference Consortium @humanpangenome.bsky.social · 26d

~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...

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...

www.biorxiv.org

2

Human Pangenome Reference Consortium @humanpangenome.bsky.social · 27d

#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...

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

www.ashg.org

Lossless Pangenome Indexing Using Tag Arrays

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Sep 5

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...

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...

2 3

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Sep 4

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/

Partners

Exploring gene content with pangene graphs

1

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Aug 29

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...

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

academic.oup.com

1 3

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Aug 27

🔍 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...

HPRC Data Explorer

data.humanpangenome.org

2 2

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Aug 22

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...

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...

www.biorxiv.org

ASHG 2025 Workshop: The Human Pangenome: Data, Tools, and Workflows

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Aug 20

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...

Introducing participants to the new Human Pangenome Reference, how samples were chosen to maximize variation, & technologies used to build the pangenome

www.ashg.org

6 8

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Aug 15

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...

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-...

65 Genomes Expand Our Picture Of Human Genetics

1

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Aug 13

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-...

Researchers closely examined the genomes of 65 individuals to paint a more complex, and more complete, picture of human genetic diversity.

www.sciencefriday.com

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Aug 8

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...

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...

3 4

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Aug 6

🚌 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

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Aug 1

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...

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 ...

ASHG 2025 Workshop: The Human Pangenome: Data, Tools, and Workflows

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Jul 28

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...

Introducing participants to the new Human Pangenome Reference, how samples were chosen to maximize variation, & technologies used to build the pangenome

www.ashg.org

4 3

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Jul 18

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.

Population Sampling and Representation

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Jul 11

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/

Highly accurate assembly polishing with DeepPolisher

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Jul 9

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...

An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

genome.cshlp.org

2

Human Pangenome Reference Consortium @humanpangenome.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...

2

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Jun 25

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...

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.

www.cell.com

1

Human Pangenome Reference Consortium @humanpangenome.bsky.social · Jun 18

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...

Release Timeline