2026-08-06 ジョンズ・ホプキンス大学（JHU）
＜関連情報＞
- https://hub.jhu.edu/2026/08/06/complete-human-genome-johns-hopkins/
- https://www.cell.com/cell/fulltext/S0092-8674(26)00703-8
- https://www.cell.com/cell-genomics/fulltext/S2666-979X(26)00143-6
- https://www.cell.com/cell-genomics/fulltext/S2666-979X(26)00141-2
A complete diploid human genome benchmark for personalized genomics 個別化ゲノム解析のための完全な二倍体ヒトゲノムベンチマーク
Nancy F. Hansen ∙ Nathan Dwarshuis ∙ Hyun Joo Ji ∙ … ∙ Sergey Koren ∙ Justin M. Zook ∙ Adam M. Phillippy
Cell Published: August 6, 2026
DOI:https://doi.org/10.1016/j.cell.2026.06.016
Highlights
- A telomere-to-telomere diploid assembly of HG002 achieves near-perfect accuracy
- Personalized diploid genome annotation reveals haplotype-specific gene variation
- Companion software evaluates sequence, assembly, and variant accuracy genome-wide
- New benchmark facilitates transition to genome inference and personalized genomics
Summary
Human genome sequencing typically relies on mapping reads to a reference genome to call variants, but this approach introduces technical biases, excluding duplicated and structurally polymorphic regions of the genome. To overcome this, we present a telomere-to-telomere genome benchmark with near-perfect accuracy across 99.4% of the diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), which were absent from prior benchmarks. We annotated genes and repeats on both haplotypes, including 19,956 protein-coding genes on the maternal haplotype and 19,190 on the paternal haplotype, and developed new methods to measure the accuracy of reads, phased variant call sets, and assemblies against a diploid reference. Genome-wide analyses show that de novo assembly resolves 2%–7% more sequence and outperforms variant calling accuracy by an order of magnitude, expanding the reach of genomic medicine to the entire genome and enabling a new era of personalized genomics.
ラットのテロメアからテロメアまでのゲノムアセンブリとパンゲノム Telomere-to-telomere genome assembly and a pangenome for the rat
Kai Li ∙ Julia L. Ciosek ∙ Sergey Koren ∙ … ∙ Melissa L. Smith ∙ Theodore S. Kalbfleisch ∙ Peter A. Doris
Cell Genomics Published:August 6, 2026
DOI:https://doi.org/10.1016/j.xgen.2026.101281
Highlights
- A telomere-to-telomere (T2T) assembly of a rat genome
- Novel genes were identified using gene prediction software and long-read RNA-seq
- Sex chromosomes indicated loss of PAR genes and meiosis between Xp and Yq
- Demonstrate rat strain genomic relationships by creating an 8-strain pangenome
Summary
We report a complete rodent telomere-to-telomere genome assembly from the brown rat, Rattus norvegicus. Annotation was enriched with multi-tissue long-read RNA sequencing and uncovered numerous novel genes. Assembly of both sex chromosomes reveals the absence of gene coding in the presumed pseudo-autosomal regions and the presence of centromeric satellite repeats on distal chromosome Y (chrY). We provide evidence of meiotic conjunction between Xp and Yq. The genome assembly reveals several expanded autosomal regions enriched for testis-expressed genes. Finally, we have generated a pangenome from recent high-quality assemblies of 8 distinct inbred rat strain genomes. This allows the strain-specific distribution of structural variation to be examined. Non-allelic homologous recombination has produced multiple copies of several genes with evidence of transcription from duplicated copies.
Verkko-Filletを使用して、キリンのゲノムをテロメアからテロメアまで完全に解読する Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet
Juhyun Kim ∙ Benjamin D. Rosen ∙ Sarah E. Fumagalli ∙ … ∙ Adam M. Phillippy,,, ∙ Sergey Koren ∙ Arang Rhie
Cell Genomics Published:August 6, 2026
DOI:https://www.cell.com/cell-genomics/fulltext/S2666-979X(26)00141-2
Highlights
- Verkko-Fillet enables interactive curation of complex genome assembly graphs
- Improved path continuity increases genome assembly accuracy and quality
- A diploid T2T giraffe genome resolves major reference errors
Summary
High-quality reference genomes are critical for studying the biology of the genome, but current methods often leave gaps and errors, especially in repetitive regions. These issues arise from challenges in genome graph curation and are not fully resolvable by standard polishing approaches. To address this, we developed Verkko-Fillet, a Python-based interactive framework for inspecting, editing, and refining genome assembly graphs. It integrates multiple data sources and provides tools for visualization, gap filling, and structural correction. Applied to a giraffe and the benchmark human genome, Verkko-Fillet improves a draft assembly (Q61.5) to a complete telomere-to-telomere genome (Q73.6), increasing both contiguity and accuracy. This work highlights the importance of graph-based curation for producing a finished, gapless genome assembly suitable for downstream analyses.
