Aug 2026· Cell· Vol 189, pp. 4857 - 4875.e31· 8 citations· 148 references
Medicine
TL;DR
A telomere-to-telomere genome benchmark with near-perfect accuracy across 99.4% of the diploid HG002 genome is presented, expanding the reach of genomic medicine to the entire genome and enabling a new era of personalized genomics.
Abstract
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.
This Primer outlines the computational foundations of long-read whole-genome analysis in human genomics, spanning read processing, mapping, de novo assembly, multi-class variant detection, haplotype phasing, repeat analysis and epigenetic profiling, and highlights key analytical trade-offs between mapping-based and ass...
Xin-Chang Zheng, P. Sanio, Rui-Bang Luo et al.· Nature Reviews Methods Prime...· 0 citations
This work describes the full spectrum of genetic variation and shows that while 99% of the variants between any two genomes are single base-pair substitutions, 88% of the euchromatic variant base pairs are SVs, including insertions, deletions, duplications, and inversions.
J. Lin, J. Gustafson, J. Wertz et al.· medRxiv· 1 citation
The highly repetitive regions of the human genome were long underrepresented from reference assemblies, limiting study of their biological function. Long-read sequencing and improved assembly algorithms have since resolved many of these regions, from centromeres to ribosomal DNA arrays, revealing structural variation i...
Kar-Tong Tan, Ryan Jun Xiang Ong, Brandon Bing Rui Kee et al.· bioRxiv· 0 citations
It is found that reference choice substantially influences genome interpretation: ancestry-matched linear T2T references provided the most faithful representation of individual genomic variation and enabled more accurate genome reconstruction than unmatched linear, diploid and graph-based references.
AlignMarkers is a robust bioinformatics pipeline designed to accurately place molecular markers on genome assemblies without requiring information on initial positions on a reference genome, using sequence alignment.
TruPath Genome achieves high-resolution detection of SNVs and indels alongside long-range phasing for CNVs and structural variant (SV) refinement and facilitates telomere-to-telomere assemblies and pangenome development, advancing the understanding of genome biology at an unprecedented scale.
