A T2T Benchmark Reveals How Reference Choice Shapes Human Genome Interpretation
- 1Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation
Abstract
The completion of telomere-to-telomere (T2T) human genomes has expanded the accessible landscape of human genetic variation, yet benchmark resources remain limited to conventional high-confidence regions defined by existing reference frameworks. Here, we generated a near-perfect diploid T2T genome (T2T-LIN) from a Chinese individual and established assembly-based truth sets by comparison with T2T-YAO, an ancestry-matched near-perfect T2T reference genome. The benchmark showed a heterozygous/homozygous SNV ratio of ~2, consistent with expectations under Hardy-Weinberg equilibrium, and enabled genome-wide evaluation of reference-dependent biases. We 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. Benchmarking previously inaccessible repetitive and structurally complex regions revealed substantial limitations of current variant callers that were masked by conventional metrics. The T2T-LIN and YAO-LIN benchmarks establish a T2T-era framework for evaluating reference-dependent genome interpretation and variant discovery across nearly the complete human genome.
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BibTeX
@misc{huang2026benchmark,
title = {{A T2T Benchmark Reveals How Reference Choice Shapes Human Genome Interpretation}},
author = {Z. Huang and Y. Chu and Y. Tian and C. Shao and J. Wang and X. Zhang and J. Chen and Z. Jia and L. Li and J. Li and G. Lin and K. Zhang and S. E. Antonarakis and Y. Kang and J. Huang},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.07.749735},
url = {https://www.biorxiv.org/content/10.64898/2026.09.07.749735v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - A T2T Benchmark Reveals How Reference Choice Shapes Human Genome Interpretation
AU - Z. Huang
AU - Y. Chu
AU - Y. Tian
AU - C. Shao
AU - J. Wang
AU - X. Zhang
AU - J. Chen
AU - Z. Jia
AU - L. Li
AU - J. Li
AU - G. Lin
AU - K. Zhang
AU - S. E. Antonarakis
AU - Y. Kang
AU - J. Huang
PY - 2026
DA - 2026/09/07
PB - bioRxiv
DO - 10.64898/2026.09.07.749735
UR - https://www.biorxiv.org/content/10.64898/2026.09.07.749735v1
AB - The completion of telomere-to-telomere (T2T) human genomes has expanded the accessible landscape of human genetic variation, yet benchmark resources remain limited to conventional high-confidence regions defined by existing reference frameworks. Here, we generated a near-perfect diploid T2T genome (T2T-LIN) from a Chinese individual and established assembly-based truth sets by comparison with T2T-YAO, an ancestry-matched near-perfect T2T reference genome. The benchmark showed a heterozygous/homozygous SNV ratio of ~2, consistent with expectations under Hardy-Weinberg equilibrium, and enabled genome-wide evaluation of reference-dependent biases. We 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. Benchmarking previously inaccessible repetitive and structurally complex regions revealed substantial limitations of current variant callers that were masked by conventional metrics. The T2T-LIN and YAO-LIN benchmarks establish a T2T-era framework for evaluating reference-dependent genome interpretation and variant discovery across nearly the complete human genome.
ER -