Complete genomes alert! @glennislogsdon.bsky.social, @christinebeck.bsky.social, and I were on @scifri.bsky.social today talking about "Complex genetic variation in nearly complete human genomes"
📄 www.nature.com/articles/s41...
📻 www.sciencefriday.com/segments/65-...

This is a highly collaborative effort with outstanding colleagues:
🙏 Dr. Seishi Ogawa, @yotarochi.bsky.social, @glennislogsdon.bsky.social, @thinks.lol, Masahiro Sugawa, Yoshitaka Sakamoto, and many others.
We hope this work helps reshape how we study centromere variation and its link to disease.

Finally, using ascairn, we analyzed 142 TCGA brain tumor whole genomes with 1p/19q co-deletion (class-defining centromere translocation).
We found that these events are dicentric, and that centromere haplogroups may influence the occurence of 1p/19q co-deletion!

We applied ascairn to over 3,300 WGS samples from the 1000 Genomes Project and Human Genome Diversity Project.
This revealed population-level differences in centromere haplogroups, providing new insights into human ancestry and migration. (4/n)

We developed a new algorithm, ascairn, to infer centromere haplogroups directly from short-read WGS data.
✅ Accuracy exceeds 95% for most chromosomes!
The tool is freely available here:
🔗 github.com/friend1ws/as...
(3/n)

We extracted rarely observed short nucleotide sequences (rare k-mers) from centromere assemblies generated by several pangenome consortia.
These rare k-mers act like “centromere SNPs”!
Rare k-mer profiles group centromere sequences into evolutionarily related haplogroups.
(2/n)

🚨New preprint out!
🧬Short reads can now decode centromeres.
🌍We reveal population-scale centromere haplogroups and their links to disease.
biorxiv.org/content/10.1... (1/n)

SSCVs are genomic variants that create novel splice sites and alter splicing. This updated resource supports variant interpretation and drug target discovery, especially with antisense oligonucleotides.
Details in our paper 👉 www.nature.com/articles/s41...

🧬 SSCV DB updated!
We screened 525,323 RNA-seq samples (up from 310,699 at the time of our SSCV paper) and identified 48,569 splice-site creating variants (SSCVs).
👉 sscvdb.io

#RNAseq #splicing #ASO

New from the lab by algorithm geek Hajime Suzuki! Genome assembly in centromeric regions is still challenging. By focusing on k-mer periodicity, Hajime implemented a novel hashing approach (github.com/ocxtal/mm2-ivh), which dramatically improves assembly in repetitive regions like centromeres!

Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!

📢 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...

Itō Shiori's award-winning documentary BLACK BOX DIARIES still can't be screened in Japan. A group of lawyers - Itō's former attorneys - say she didn't get permission for some of the footage. But is that true? Why are attorneys undermining their own former client?