The complete sequence of a human genome

Abstract

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures

“…Some of these events were captured in a single long ONT read connecting a telomere to various SV rearrangements, reminiscent of SV mutations stabilized by independent telomere fusions. The assignment of telomeric repeats to chromosomal haplotypes also highlighted the need for continuous reference improvements, as some of these events could only be unambiguously resolved using the new CHM13 telomere-to-telomere (T2T) assembly 31 . A comparable analysis on short-read data failed to resolve the telomere-associated complex rearrangements, and only three out of the five SV to telomere junctions showed confident telomeric repeat motifs in an unmapped mate or a soft-clipped read, which underscores the critical need for long-read sequencing to investigate telomere-associated structural rearrangements, which are considered a key cancer mutational process in association with telomere crisis 28 .…”

“…We use the control genome to filter out likely mapping artifacts due to incomplete reference sequences by masking alignments from the control genome that show both a telomeric repeat and a unique alignment outside a telomere region. In case of mapping ambiguities, we used the CHM13 telomere-to-telomere (CHM T2T) assembly 31 as an alternative reference sequence. The method to detect telomere fusions is implemented in our long-read alignment toolkit lorax as a new sub-command.…”

“…Telomere fusions can also stabilize altered chromosomes after catastrophic events such as chromothripsis 30 , which would suggest an alternative sequence of events, with chromothripsis and templated insertion threads causing unprotected break sites healed through telomere addition. Another telomere crisis event observed in the primary tumor likely fused chromosome 19 to the telomere of chromosome 16q, an event that could only be resolved unambiguously using the CHM13 telomere-to-telomere (CHM T2T) assembly 31 as a reference sequence (Figure S13). We further investigated whether eroded telomeres were preferentially fused with genomic loci active in transcription as has been suggested previously 32 , but our small number of telomere fusions do not provide sufficient evidence.…”

Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions

“…Crop genome sequencing projects were focussed on almost homozygous cultivars (Jaillon et al, 2007) or even doubled haploid lines when possible (Dohm et al, 2014). Even human genome initiatives that are usually a few years ahead of plant sciences, have only recently managed to produce a complete haploid genome assembly (Nurk et al, 2021). This implies that two separate genome sequences need to be assembled to represent the two haplotypes of heterozygous genotypes.…”

Truvari: Refined Structural Variant Comparison Preserves Allelic Diversity

“…To approach the central question of when to match a pair of SVs, we start with a set of 36 previously established, haplotype-resolved, long-read assemblies and call SVs [16,17]. We called SVs against three references -hg19, GRCh38 and the newly published chm13 -to observe how references impact the calling and analysis of the SVs [18][19][20]. First, to ensure a high accuracy of SV calling, we compared the NA24385 sample on hg19 against Genome in a Bottle (GIAB) v0.6 Tier1 SVs using Truvari bench (see methods).…”