José Soto

The paper presents a pipeline to call mitochondrial DNA variants in gnomAD, reporting population frequencies for 10,850 unique mtDNA variants across 56,434 individuals.

From 125,748 exomes and 15,708 genomes, 443,769 high-confidence predicted loss-of-function variants yield LOEUF, a continuous gene intolerance score tracking mouse lethality, cell essentiality, and disease associations.

The paper develops an expression-based annotation metric to improve rare variant interpretation by filtering false-positive loss-of-function variants and identifying pathogenic variants in highly expressed exons.

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 analyzes loss-of-function variants in LRRK2 across large genomic datasets to assess the safety of partial LRRK2 inhibition as a Parkinson's disease therapy.

The paper analyzes multi-nucleotide variants (MNVs) in 125,748 exomes and 15,708 genomes, identifying their distribution, mutational origins, and functional implications.

The paper discovers and validates 50,000 high-quality SNPs in Nile tilapia through whole-genome resequencing of 326 individuals, useful for genomic selection and trait analysis.

The paper introduces a benchmark dataset of validated somatic mutations derived from cell lineage, providing a large collection of true somatic variation for use in mutation discovery pipelines.

The paper uses whole-genome sequencing to fine-map sex determination genes in Nile tilapia, identifying anti-Mullerian hormone as a major gene.

This study performs GWAS and evaluates genomic selection for growth and fillet yield in Nile tilapia using imputed SNP panels, finding imputation improves genomic prediction accuracy.