Xuefang Zhao

The paper constructs a high-resolution human pangenome structural variant resource, identifies disease-associated SVs, and demonstrates its utility in filtering variants from probands and associating SVs with traits in a large cohort.

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

This study evaluates the diagnostic yield of short-read and long-read sequencing in rare diseases, finding limited added value from long-read sequencing despite increased variant discovery.

This study identifies novel genetic drivers of orofacial clefts by analyzing de novo variants in 2,497 trios and integrating findings across subtypes and syndromic status.

gnomAD v4 (730,947 exomes) brings LOFTEE-2 loss-of-function annotation (0.90 precision, strict mode), missense-aware constraint, and LLM-mined literature evidence combined with constraint to rank disease genes.

The paper investigates the functional role of recursive splicing in CADM2, showing that its deletion leads to altered gene expression and behavioral changes in neurodevelopmental disorders.

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

The paper develops a cell type-aware framework to identify non-coding variants in Mendelian disorders by integrating single-cell multi-omic data and applying it to congenital cranial dysinnervation disorders.

The paper harmonizes diverse human genomes from multiple datasets to create a new reference panel with improved variant coverage and population structure analysis.

The paper estimates the diagnostic yield of sequencing 418 genes in OFC cases and controls, finding a higher prevalence of likely pathogenic variants in cases.

The paper presents a high coverage whole genome sequencing resource of 3,202 samples, including 602 trios, generated from the expanded 1000 Genomes Project.

This study identifies 3,154 high-confidence structural variants in Parkinson's disease using short-read sequencing and validates some with long-read data, highlighting limitations of short-read methods.

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.

The paper reports de novo structural mutation rates and gamete-of-origin biases using genome sequencing of 2,396 families, finding higher rates in autism cases and paternal origin dominance.

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

This study evaluates genome sequencing as a single diagnostic approach for fetal structural anomalies, showing it detects nearly all variants from standard tests and provides higher diagnostic yield than individual tests.

The paper compares structural variant detection using short-read and long-read sequencing in three trios, showing lrWGS finds more SVs but srWGS has high concordance in non-repetitive regions.

The paper functionally annotates rare structural variants in the human brain by integrating SV calling with RNA-seq data to assess their regulatory effects and prioritize pathogenic deletions.

Short-read genome sequencing of 14,891 diverse genomes yields 433,371 structural variants (SVs) for gnomAD; loss-constrained genes also resist duplication, and clinical SV carrier rates are benchmarked.

The paper uses whole-genome and RNA sequencing from the human prefrontal cortex to identify genetic variants and transcriptomic changes associated with neurodevelopment and neuropsychiatric disorders.

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

VaPoR validates structural variations using long-read sequencing data with high accuracy and efficiency, outperforming manual methods.

SVelter reconstructs complex structural genomic rearrangements by iteratively rearranging genome regions and scoring them against sequencing data.