Stacey Gabriel

Himito is a graph-based toolkit for analyzing mitochondrial genomes using long reads, achieving superior performance in assembly and variant calling and revealing age-related patterns in the All of Us dataset.

The paper presents a large reference panel of 515,579 genomes to improve rare-variant imputation across underrepresented populations, enhancing accuracy for variants with frequencies as low as 0.002%.

The paper analyzes expression and splicing quantitative trait loci (e/sQTL) across multiple tissues in the TOPMed dataset and finds that secondary e/sQTL signals are still discoverable, with many GWAS signals colocalizing with these e/sQTL.

This study identifies 44 genetic loci associated with pulmonary artery diameter across COPD and population-based cohorts, highlighting shared causal variation between pulmonary and systemic vascular biology.

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.

The paper performs large-scale GWAS and RVAS on 392,030 whole genomes from All of Us, identifying 49,863 associations and 193 novel pLoF gene-phenotype links through meta-analysis with UK Biobank.

The paper integrates genomics and transcriptomics data from human heart samples to identify regulatory mechanisms linking genetic variation to dilated cardiomyopathy.

The paper analyzes over 800,000 human genomes to assess penetrance of clinically relevant variants, finding that 95% of pLoF variants in severe diseases have explanations for lack of disease manifestation.

The paper analyzes long-read sequencing data from the All of Us Research Program to identify structural variants and their associations with diseases in a large cohort of Black or African American participants.

This study uses whole-genome sequence data from diverse participants to identify novel genetic loci associated with brain structural volumes, highlighting the importance of diverse cohorts in uncovering genetic architecture.

The paper conducts proteome-wide and transcriptome-wide association studies for blood lipids, finding high-level consistency between proteome and transcriptome-lipid associations across tissues.

This paper resolves ring chromosomes, Robertsonian translocations, and complex structural variants using long-read sequencing and telomere-to-telomere assembly, revealing breakpoint structures and methylation changes.

This study identifies shared and distinct ultra-rare genetic risk factors for epilepsy subtypes using whole-exome sequencing of 20,979 patients and 33,444 controls.

The paper analyzes pathogenic variant frequencies in the All of Us cohort by ancestry, revealing disparities and potential biases in genomic data.

The paper maps interaction QTLs (iQTLs) for cell type, age, and other variables in blood multi-omic data to identify context-specific genetic regulatory effects.

Rare-variant depletion in 1kb windows of 76,156 gnomAD genomes, versus feature-adjusted mutation expectations, marks regulatory elements and outperforms seven alternative scores at flagging functional non-coding variants.

The paper develops a method to infer compound heterozygosity from exome sequencing data, achieving high accuracy in phasing rare variants for recessive disease diagnosis.

The paper identifies 83 rare lncRNA variant sets associated with blood lipid levels using WGS data from the TOPMed program and validates some in UK Biobank data.

The paper identifies impactful rare variants by integrating multi-omic data from MESA, showing that combining expression and protein data increases the detection of rare stop and frameshift variants.

This study shows that common splice-regulatory variants can reduce the pathogenicity of rare exonic variants by modulating mRNA splicing.

This paper introduces MAS-ISO-seq, a method to boost throughput of long-read RNA sequencing for isoform discovery, showing improved detection of differentially spliced genes and cell clustering in T cells.

This study performs a multi-ancestry GWAS on lung function and COPD, identifying 559 genes and 29 pathways, and showing genetic risk scores are associated with COPD across ancestries.

The paper presents a comprehensive catalog of structural variants across 138,134 individuals, identifying novel variants and their associations with cardio-metabolic and hematologic traits.

This paper improves multi-omics integration by enhancing orthogonality in canonical vectors and demonstrates transferability across cohorts for proteomics and methylomics data.

The paper performs whole genome sequence analysis of plasma lipid levels in 66,329 individuals, identifying new lipid-associated alleles, including rare non-coding variants.

The paper identifies ten new genes with coding variants linked to Crohn's disease risk using sequencing data from over 30,000 patients and 80,000 controls.

The paper tests for genetic interactions affecting causal variant effect sizes in gene expression and LDL-C across European and African American populations, finding significant evidence in gene expression but not LDL-C.

Open flow cell on a circular wafer with mostly natural nucleotides and no reversible terminators: about 300 bp reads at $1/Gb, 99.6% SNP accuracy on reference human genomes.

Exomes of 24,248 schizophrenia cases and 97,322 controls implicate ultra-rare damaging variants in 10 genes, including GRIN2A and GRIA3, with odds ratios of 3 to 50.

The paper describes the process of obtaining an FDA IDE for returning genomic results via WGS in the All of Us Research Program and presents validation results.