A Closer Look at the Complete Genome

The HG002 resource expands accuracy assessment into sex chromosomes and structurally complex genomic regions

August 20, 2026
3 min

The Pathologist

Overview

Researchers have developed a nearly complete diploid genome benchmark, T2T-HG002 version 1.1, which covers 99.4% of the diploid genome without detectable errors. This benchmark provides a resource for genomic assessments, particularly in challenging regions that traditional reference-based methods struggle to evaluate.

Background

The development of accurate genomic benchmarks is crucial for sequencing and genomic analysis methods. Existing reference genomes often fall short in repetitive and structurally complex regions, leading to gaps in variant detection. The new benchmark provides a comprehensive resource for laboratories to assess genomic methods.

Data Highlights

The T2T-HG002 version 1.1 benchmark covers 99.4% of the diploid genome, with 99.35% free of detectable errors. It includes 701.4 Mb of high-confidence autosomal sequence not present in previous benchmarks.

Key Findings

The T2T-HG002 benchmark covers 99.4% of the diploid genome.
99.35% of the genome is free of detectable errors.
701.4 Mb of high-confidence autosomal sequence was added compared to GIAB version 4.2.1.
Genome Quality Checker software was developed to evaluate genomic methods against the benchmark.
Conventional variant calling against GRCh38 covers approximately 93% of HG002, while de novo assembly covers 99.94%.
Copy-number differences were identified in genes such as DUSP22 and GSTM1 between maternal and paternal genomes.