Stephen Jacob Chanock

This study analyzes breast cancer GWAS across multiple ancestries, finding similar heritability and genetic correlations, and identifies shared regulatory and cellular contexts.

This study examines ecDNA in lung cancer, finding it in 18.9% of patients and associating it with worse survival and genomic instability.

This study identifies ZC3H18 mutations that stabilize endogenous retroviral RNA, linking ERV RNA accumulation to oncogenesis in zebrafish and human cell lines.

This study identifies novel genetic risk loci for pancreatic ductal adenocarcinoma in African ancestry individuals through admixture mapping and GWAS.

This study identifies subtype-specific mutational mechanisms and links them to host metabolic factors in endometrial cancer using genomic and transcriptomic data from 440 tumors.

The paper identifies functional variants and VNTRs at the 5p15.33 locus using fine-mapping, MPRA, and CRISPRi screens, revealing their role in cancer susceptibility through antagonistic pleiotropy.

This study identifies 14 susceptibility loci for Ewing sarcoma through a genome-wide association meta-analysis, revealing genetic interactions with somatic EWSR1::FLI1 fusions.

This paper develops a deep learning model to predict molecular alterations in never-smoker lung adenocarcinomas from histological images, achieving high accuracy for most features.

This study identifies three distinct evolutionary trajectories in lung adenocarcinomas using whole-genome sequencing, revealing that some never-smoking tumors follow smoking-like paths driven by KRAS mutations.

The paper identifies key transcription factors and their target proteins in renal cell carcinoma using multi-omic integration of ChIP-seq and GWAS data.

The paper identifies three subtypes of NS-LUAD using RNA-seq data and develops a 60-gene signature that predicts survival across subgroups.

This study identifies a unique mutational signature, SBS87, in testicular germ cell tumors (TGCTs) that resembles thiopurine-induced DNA damage and is associated with tumor latency and telomere elongation.

This study analyzes 1024 lung adenocarcinomas to identify evolutionary patterns and mutational mechanisms, revealing distinct trajectories linked to smoking, ancestry, and retrotransposition.

Geny improves KIR gene genotyping accuracy by combining expectation-maximization and integer linear programming to resolve ambiguities in sequencing data.

This study identifies VNTR6-1 and rs10069690 as regulators of TERT splicing and expression, influencing cancer risk and telomere dynamics through altered telomerase isoform ratios.

The paper fine-maps a PDAC GWAS signal at chr1p36.33 and identifies KLHL17 as a target gene regulated by JunB/D, with potential implications for inflammation and PDAC risk.

This study identifies 40 circulating proteins associated with cancer risk using MR and colocalization, highlighting potential therapeutic targets and adverse effects of protein-altering interventions.

The paper identifies two lung cancer subtypes defined by APOBEC mutagenesis levels and shows their association with different genetic mutations, aging, and immune responses.

This study identifies 447 new genetic variants associated with prostate-specific antigen levels across multiple ancestries and shows improved cross-ancestry prediction of PSA, with implications for personalized prostate cancer screening.

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

This study develops a polygenic score to adjust PSA levels, improving the detection of aggressive prostate cancer while reducing unnecessary biopsies.

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.

This study maps expression and splicing QTLs in East Africans and finds population-specific genetic variation related to immunity, metabolism, and pigmentation.

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

This study improves polygenic risk scores for colorectal cancer by combining Asian and European ancestry data, enhancing risk prediction across diverse racial and ethnic groups.

This study shows that time to first cigarette strongly influences lung tumor mutational burden, signatures, and survival in smokers.

ImmunoTyper-SR genotypes IGHV alleles from short read data and identifies associations between IGHV alleles and anti-type I IFN autoantibodies in COVID-19 patients.

The paper identifies a Neandertal introgressed haplotype in the OAS1 gene associated with increased risk of severe COVID-19 and shows it impairs SARS-CoV-2 clearance through genetic regulation of OAS1 expression.

The paper assesses breast cancer risks linked to rare missense variants in five susceptibility genes using logistic and mixture models, finding varying risk contributions across genes.