Qichen Fu

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

Pansoma improves somatic variant calling using pangenome graphs, enhancing accuracy by avoiding reference bias and preserving graph-specific variant representations.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

This study shows that using graph-based pangenomes and inferred donor-specific assemblies improves somatic variant detection compared to GRCh38.

The paper develops a pangenomic method to create a benchmark resource for somatic variant detection using HapMap mixtures, identifying millions of variants across different genomic regions.