Floris Barthel

Glioblastoma is monitored mostly by MRI, which can miss early changes. Cell-free DNA (cfDNA) in blood is a promising alternative, but we know little about what governs its release. Our new paper in Neuro-Oncology, led by @sharvarimankame.bsky.social, dissects it. 🧵 doi.org/10.1093/neuonc/noag204

Huge credit to @sharvarimankame.bsky.social, who led this work, and to Hersh Nanda, Maria Kyriakidou, Mimi Mbegbu, Nanyun Tang and Michael Berens at @tgenresearch.bsky.social. Angad Beniwal, Matthew Dufault and Nhan Tran ran the mouse studies at @mayoclinic.org Arizona.

doi.orgCell-free DNA sequencing captures tumor dynamics, microenvironment interactions, and treatment pressures in glioblastomaMankame S, Beniwal AS, Dufault M, et al. Neuro-Oncology (2026), advance article. Open access.

Supported by a @theabta.bsky.social Discovery Award, the Ivy Foundation, the Lane Spyrow GBM Fellowship and Students Supporting Brain Tumor Research. 📄 Open access in Neuro-Oncology (@neuroonc.bsky.social): doi.org/10.1093/neuonc/noag204

In mice with orthotopic GBM43 tumors, plasma cfDNA was elevated over PBS-injected controls. Separating human from mouse reads, we found tumor-derived fragments were shorter than host fragments, and their copy number profile recapitulated the parental chr7 and chr9 gains.

Together: cfDNA composition depends on tumor proliferation, the microenvironment and treatment. Interpreting a liquid biopsy in GBM will require accounting for that context. Next up: testing these principles in patient samples. Stay tuned.

Fragment sizes told the same story. Astrocyte cfDNA showed a mononucleosomal peak (~185 bp) typical of apoptosis, GBM43 cfDNA lacked nucleosomal peaks, and co-cultures produced a multimodal pattern (174, 330, 486 bp) seen in neither monoculture.

Temozolomide (TMZ) changed the picture. In treated GBM43, cfDNA yield rose sharply and correlated with dead cell counts (R = 0.85), no longer with live cells (R = −0.04). Treated cfDNA showed nucleosomal laddering and a narrower pool of detectable variants.

To model the microenvironment, we co-cultured GBM43 with normal human astrocytes (NHAs). Variants unique to each cell type let us attribute cfDNA to its source: GBM43 variants were absent from astrocyte cfDNA, and NHA variants from tumor cfDNA.

Over 5 days, GBM43 outgrew the astrocytes and astrocyte death increased. In co-culture cfDNA, NHA-specific VAFs rose 2.4% per day while GBM43-specific VAFs fell 3.6% per day. Dying astrocytes diluted the tumor signal, much as host DNA does in patient plasma.

We cultured two patient-derived GBM lines, GBM43 and GBM12, and sampled the media every 24 h for 5 days to measure cell counts, cfDNA yield, fragment size and variants. All variants in each line's genomic DNA were detected in its cfDNA.

UC Santa Cruz Genomics Institute

We expected cfDNA to come mostly from dying cells. Instead, cfDNA yield correlated more strongly with live cell counts than with dead cell counts (GBM43: R = 0.88 vs 0.47). So cfDNA release in these models is not driven by apoptosis alone.

Floris Barthel reposted

Adam Phillippy

@aphillippy.bsky.social

6 Aug

For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]

Floris Barthel reposted

@ucscgenomics.bsky.social

6 Aug

We’ve sequenced a marmoset! Grad student @prajnahebbar.bsky.social & @benedictpaten.bsky.social led the effort, and expect it to enable scientists to learn more about genes that contribute to memory loss and Alzheimer's. 🔗https://news.ucsc.edu/2026/08/first-complete-marmoset-genome/

Floris Barthel reposted

Excited to share a big KaryoScope update this past week: the HKS k-mer backend is now integrated, and you can build databases for any features of interest. The complete @humanpangenome.bsky.social HG002 assembly (~6.3 Gbp) now annotates in 21 minutes on a MacBook Pro. 🧵

biorxiv.orgHierarchical genomic feature annotation with variable-length queriesK -mer-based methods are widely used for sequence classification in metagenomics, pangenomics, and RNA-seq analysis, but existing tools face important limitations: they typically require a fixed k -me...

The improved HKS index was developed by @jnalanko.bsky.social, @camillemrcht.bsky.social and Simon Puglisi. KaryoScope and its original KMC-derived data structure were developed by @trhyker.bsky.social, with our co-authors and @humanpangenome.bsky.social HKS: www.biorxiv.org/content/10.6...

biorxiv.orgKaryoScope: rapid, alignment-free sequence annotation for the pangenome eraThe pangenome era is producing long-read sequencing data and complete genome assemblies ([1][1]–[3][2]) at a pace that current annotation methods cannot match. Existing tools were each built for a sin...

If you build a KaryoScope database for your organism of interest, we would love to hear about it. 📄 www.biorxiv.org/content/10.6... 💻 github.com/barthel-lab/KaryoScope

Feature sets are not tied to a genome: any annotation that tiles a reference can become one. Here is a database we built for the Arabidopsis Col-CEN T2T reference, with chromosome, gene, region, and repeat feature sets, including the CEN180 satellite arrays.

Getting KaryoScope off the cluster and onto a personal computer is a milestone we cared about. Genome analysis belongs to everyone, not just institutions and corporations that have the resources to maintain high-performance compute clusters.

Some run statistics: peak 941% CPU across 10 threads, peak 10.2 GB RAM on an M1 Max. Broad plateaus are k-mer lookup, sharp bursts are hierarchy-aware smoothing, and each of the six feature sets appears as its own block.

gist.github.comReproduce KaryoScope v2.1 karyotyping of the T2T-HG002 v1.1 diploid assembly end to end (macOS / Apple Silicon, ~20 min at 8-10 threads, 16 GB+ RAM)Reproduce KaryoScope v2.1 karyotyping of the T2T-HG002 v1.1 diploid assembly end to end (macOS / Apple Silicon, ~20 min at 8-10 threads, 16 GB+ RAM) - reproduce_karyoscope_hg002.sh

Per feature set the cost is remarkably flat: 138 to 146 s of lookup each (chromosome, region, repeat, subtelomere, gene, acrocentric), plus a brief smoothing burst. Runtime scales linearly with feature sets queried. Try it yourself: gist.github.com/fpbarthel/6e9537f6c60188ba029bcbf397d2c6e9

Floris Barthel reposted

bioRxiv Genomics

@biorxiv-genomic.bsky.social

22 July

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation https://www.biorxiv.org/content/10.64898/2026.07.21.739710v1

Floris Barthel reposted

bioRxiv Bioinfo

@biorxiv-bioinfo.bsky.social

28 May

Fast Set Operations for Compact k-mer Sets https://www.biorxiv.org/content/10.64898/2026.05.24.727514v1

barthel-lab.orgthe barthel laboratory - studying telomere dysfunction in gliomagenesis and evolution at TGenThe Barthel Laboratory studies how telomere dysfunction drives structural genome evolution and shapes the molecular trajectory of cancer. Based at TGen in Phoenix, Arizona, we combine cytogenetics and...

26 May

Busy month at the lab. We've refreshed our site with four new preprints: arm-specific telomeres in astrocytoma (Jehangir), pancreatic cancer assembly (Wagner), telomere crisis in astrocytes (Mbegbu) and KaryoScope (Ranallo-Benavidez). Plus new(-ish) lab members Shea, Nick, Daniel, Griffin, and Divy.

Telomere crisis is an engine of genomic instability, driving the structural evolution of cancer genomes. Our new preprint finds this damage isn't random: it converges on the nucleolus and the chromosomes that build it. 🧵 www.biorxiv.org/content/10.6...

Together: telomere dysfunction preferentially destabilizes acrocentric chromosomes and disrupts the nucleolus they collectively build. The nucleolus emerges as a structural nexus linking telomere crisis to large-scale genome rearrangement.

Huge credit to co-first authors Mimi Mbegbu and Yi-An Chen, and to collaborators Pippa Cosper and Tianpeng Zhang. 📄 Preprint: www.biorxiv.org/content/10.6...

biorxiv.orgbiorxiv.org

To probe nuclear organization, we used Hi-C. Standard pipelines discard the rare inter-chromosomal contacts at acrocentric arms, so we recovered them with KaryoScope, our alignment-free tool. These contacts were persistently depleted in crisis cells. bsky.app/profile/flor...

Floris Barthel@florisbarthel.bsky.social

The human genome's most variable and clinically important regions (centromeres, telomeres, and acrocentric short arms) have been hardest to study at scale. Thrilled to share KaryoScope, our new preprint that brings them within reach. 🧵 www.biorxiv.org/content/10.6...

We expected broad genomic instability. Instead, telomere crisis zeroed in on the acrocentrics, consistent with findings from Beth Sullivan's lab over a decade ago using dominant-negative TRF2. doi.org/10.1371/jour... doi.org/10.1371/jour...

The rearrangements were strikingly dynamic. Chromosome 13 translocations were common early but transient, replaced by new partners at later passages, while whole-chromosome losses persisted. Crisis generates a shifting, subclonal landscape of damage.

Why acrocentrics? Their short arms carry the NORs that nucleate the nucleolus. In crisis cells, nucleoli broke down: compact spheres gave way to dispersed, necklace-like structures, with rDNA transcription and processing decoupled.

To capture it, we grew normal human astrocytes with HPV E6/E7 (inactivating p53 and Rb) but no telomerase, so cells divide through progressive telomere erosion. We tracked them longitudinally from senescence bypass through crisis, an otherwise inaccessible window.

Multicolor FISH revealed subclonal abnormalities largely invisible to short-read sequencing. The bias was striking: acrocentric chromosomes carried 41% of all abnormalities despite being 15% of the autosomal genome. Chr13 was abnormal in >92% of metaphases.

Annotation is the pangenome era's bottleneck, and KaryoScope is our step toward dissolving it: a framework that any annotation source can plug into. Tremendous thanks to @trhyker.bsky.social for leading this work, and to all co-authors.

📄 Paper: www.biorxiv.org/content/10.6... 💻 Code*: github.com/barthel-lab/KaryoScope *currently still set to private, opening to the public early next week as we wrap up the software release In the meantime, dive into the manuscript and share your comments and feedback.

biorxiv.orgbiorxiv.org

KaryoScope works on any sequence input, beyond diploid assemblies: long reads, short reads, Hi-C, RNA-seq, metagenomics. It detects SVs from individual long reads (manuscripts forthcoming) and dissects cancer genome assemblies (HG008): bsky.app/profile/florisbarthel.bsky.social/post/3mle3v75bpk2k

KaryoScope analyzes sequence data faster than instruments from @pacbio.bsky.social , @nanoporetech.com, Illumina, and @elembio.bsky.social (and others) produce it, on laptop-grade hardware. Real-time, on-instrument sequence annotation is within reach.

FSHD1, a muscular dystrophy, is caused by structural changes in D4Z4, a complex subtelomeric repeat array on chromosomes 4q and 10q. Across hundreds of @humanpangenome.bsky.social, KaryoScope first catalogs D4Z4 diversity, including configurations previously not described.

@khmiga.bsky.social and @glennislogsdon.bsky.social have charted centromeres. KaryoScope adds pangenome-scale variation: chr9 megabase inversion, chr3/chr5 repeat losses, FISH-validated. See also: www.science.org/doi/10.1126/... www.biorxiv.org/content/10.6...

Built on k-mer matching (short, fixed-length DNA fragments), KaryoScope annotates a complete diploid human genome at base-pair resolution in ~2 minutes, across repeats, satellite families, genes, and chromosome-end structure. ~300× faster than RepeatMasker.

Robertsonian translocations are complex chromosomal rearrangements of acrocentric chromosomes. @aphillippy.bsky.social, @thinks.lol, and Jen Gerton showed SST1 is the fusion substrate; KaryoScope confirms this from k-mers alone. See also: www.nature.com/articles/s41... www.nature.com/articles/s41...

🧵 Excited to contribute to a new preprint led by Justin Zook & the NIST/GIAB team: "A complete human pancreatic cancer genome": the first near-complete, haplotype-resolved tumor cell line assembly (HG008-T, hypodiploid PDAC). 📄 www.biorxiv.org/content/10.6...

Huge congrats to Justin Zook, @mishakolmogorov.bsky.social, @glennislogsdon.bsky.social, Chunlin Xiao & the full team, and to @trhyker.bsky.social for driving KaryoScope. A milestone resource for somatic variant benchmarking in repetitive regions of cancer genomes.

academic.oup.comHaplotype-resolved genome assemblies of BJ and IMR-90 human fibroblast cell lines reveal extensive structural variation and enable reanalysis of historical sequencing dataAbstract. We present chromosome-level, phased diploid genome assemblies of two widely used human fibroblast cell lines: BJ (46,XY) and IMR-90 (46,XX). Usin

Stay tuned for the official KaryoScope release (very soon, I promise!). For now please check out our recent paper in NAR that first featured our new method 🔬 academic.oup.com/nar/article/... #genomics #T2T #cancergenomics

That α-satellite fusion produced what turned out to be a putative functional dicentric chromosome: two CDRs ~1 Mbp apart on D7Z1 and D6Z1, beautifully characterized by CenMAP from the @glennislogsdon.bsky.social lab. 🔗 github.com/logsdon-lab/...

KaryoScope also resolved two reciprocal translocations (chr12↔15, chr18↔X), foldback inversions, acrocentric short-arm rearrangements, and complex multi-chromosomal events; all reconciled against dGH ground truth. Check out the pre-print for a complete overview of everything we observed.

Our lab contributed via KaryoScope, our k-mer-based sequence annotation tool. It produced an ISCN-annotated karyotype of the tumor assembly that was concordant with KromaTiD dGH SCREEN cytogenetics across all 35 tumor chromosomes.

KaryoScope resolved a striking chromoplexy event linking chr 3, 6, 7, and 11 into three hybrid tumor chromosomes, and pinpointed the chr6↔chr7 breakpoint deep inside the α-satellite array of both centromeres.