The complete sequence of a human genome

By Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, Nicolas Altemose, L. Uralsky, Ariel Gershman and 89 more. bioRxiv, 2021

2,469 citations recorded by the source corpus.

In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics. While these drafts and the updates that followed effectively covered the euchromatic fraction of the genome, the heterochromatin and many other complex regions were left unfinished or erroneous. Addressing this remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium has finished the first truly complete 3.055 billion base pair (bp) sequence of a human genome, representing the largest improvement to the human reference genome since its initial release. The new T2T-CHM13 reference includes gapless assemblies for all 22 autosomes plus Chromosome X, corrects numerous errors, and introduces nearly 200 million bp of novel sequence containing 2,226 paralogous gene copies, 115 of which are predicted to be protein coding. The newly completed regions include all centromeric satellite arrays and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies for the first time.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/81ab376d534890d70a3fc2bef9a12b224b420fdc

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Citations in the corpus

Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing (2021, neutral): “The function h() maps contig terminus pairs to Hi-C scores (see Methods). d, nX plots showing the minimum sequence length (y-axis, log scale) needed to constitute a particular percentage of the assembly (x-axis). e, Ideogram showing contig boundaries (alternating color and gray) within the final sca”
A draft human pangenome reference (2022, background): “The known homology between the short arms bolsters the possibility of ongoing sequence information exchange between non-homologous chromosomes (Nurk et al., 2022), which would be consistent with the patterns we observe.”
Nanopore sequencing technology, bioinformatics and applications (2021, neutral): “135 ).”
Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing (2022, neutral): “1 assembly is the first-ever published complete sequence of a human genome [11].”
CADD v1.7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions (2024, background): “GRCh38 and recent efforts by the T elomere-to-T elomere (T2T) consortium have clearly shown the limitations of a single reference genome ( 84 ).”
The UCSC Genome Browser database: 2023 update (2022, methodology): “0 assembly (34), we created a GenArk browser to display the sequence alongside various annotation tracks which were a combination of consortium-generated and in-house data.”
Ensembl 2023 (2022, background): “Nowhere is this more evident than the human genome itself, with the recent release of the CHM13 genome assembly from the Telomere to Telomere Consortium (T2T) (6), marking the first essentially complete human genome.”
DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing (2023, positive): “Using bidirectionalGated Recurrent Unit (GRU) and attentionneuralnetworks,ccsmethdetectsmethylationstatesofCpGs at both read level and genome-wide site level.”
GENCODE: reference annotation for the human and mouse genomes in 2023 (2022, background): “We have participated in the annotation of the developing human pangenome (e.g. 34), supporting the annotation of the T2T consortium’s CHM13 human cell line as- sembly.”