Sophie Parsa

Multi-omics in the All Of Us Research Program expands mapping genetic mechanisms in health and disease

The paper reports on the All of Us multi-omics cohort, identifying 182,246 QTLs and demonstrating rare variant effects across proteomic and transcriptomic data.

Integrating 730,947 exome sequences with clinical literature improves gene discovery

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.

Variant scoring performance across selection regimes depends on variant-to-gene and gene-to-disease components

This study evaluates variant scoring methods across different selection regimes, showing their performance depends on variant-to-gene and gene-to-disease factors.

A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner

The paper introduces BGE, a sequencing method that combines low-pass whole genome and deep whole exome data, showing high accuracy and cost-effectiveness for genetic variant discovery.

Functional Separation of mRNA Domains Coordinates Pluripotent Cell Behavior

The paper shows that different mRNA domains (CDS and 3UTR) have distinct functional roles in pluripotent cells, with 3UTR affecting colony structure and CDS impacting transcriptional control.