Lei Song

Stratifying Lung Adenocarcinoma Risk with Multi-ancestry Polygenic Risk Scores in East Asian Never-Smokers

The paper develops and validates multi-ancestry polygenic risk scores for LUAD in East Asian never-smokers, showing improved risk prediction compared to East Asian-only models.

Shared and distinct genetic etiologies for different types of clonal hematopoiesis

The paper identifies shared genetic architecture across different types of clonal hematopoiesis and finds that overlapping mutations increase hematological malignancy risk.

A real-world pan-cancer catalogue of mutational signatures from 111,711 tumors

This paper introduces SATS, a framework for mutational signature analysis in targeted sequencing data, and presents a pan-cancer catalogue of mutational signatures from 111,711 tumors.

Population analyses of mosaic X chromosome loss identify genetic drivers and widespread signatures of cellular selection

This study identifies genetic drivers and cellular selection signatures of mosaic X chromosome loss in women using large-scale population data and polygenic scores.

MicrobiomeGWAS: a tool for identifying host genetic variants associated with microbiome composition

The paper introduces microbiomeGWAS, a tool to identify host genetic variants associated with microbiome composition using beta diversity metrics and corrects for statistical biases in pairwise distance data.

Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies

The paper establishes reference samples with high-coverage whole-genome sequencing to create truth sets for somatic mutation and germline variant detection using NGS technologies.

Genetic and Epigenetic Intratumor Heterogeneity Impacts Prognosis of Lung Adenocarcinoma

This study quantifies genetic and epigenetic intratumor heterogeneity in lung adenocarcinoma and links it to poor prognosis.

SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics

SummaryAUC approximates the AUC of polygenic risk scores using only summary statistics from validation datasets, enabling efficient evaluation of PRS models.

viGEN: An open source pipeline for the detection and quantification of viral RNA in human tumors

viGEN detects and quantifies viral RNA and variants in tumor samples using RNA-seq data, showing successful detection of HPV in cervical cancer and HBV in liver cancer.

Winners curse correction and variable thresholding improve performance of polygenic risk modeling based on summary-level data from genome-wide association studies

This paper improves polygenic risk scores by applying winners curse correction and variable thresholds to GWAS summary data, enhancing prediction accuracy for some diseases.