Kate Downes

Incorporating alternative Polygenic Risk Scores into the BOADICEA breast cancer risk prediction model

This paper evaluates methods to incorporate alternative polygenic risk scores into the BOADICEA breast cancer risk prediction model, finding that retrospective likelihood approaches provide more accurate estimates.

Recommendations for clinical interpretation of variants found in non-coding regions of the genome

This paper provides recommendations for interpreting non-coding variants in clinical settings, adapting existing guidelines to account for their role in disease.

Transcriptional, epigenetic and metabolic signatures in cardiometabolic syndrome defined by extreme phenotypes.

The paper identifies molecular and metabolic signatures of cardiometabolic syndrome using extreme phenotype groups and shows changes after bariatric surgery.

Whole-genome sequencing of rare disease patients in a national healthcare system

This study uses whole-genome sequencing in a national healthcare system to diagnose rare diseases and discover new aetiological variants, identifying 95 Mendelian associations and 4 novel non-coding disease-causing variants.

Elucidating mechanisms of genetic cross-disease associations: an integrative approach implicates protein C as a causal pathway in arterial and venous diseases

The paper identifies a genetic variant in PROCR that influences protein C and factor VII levels, linking it to both reduced coronary artery disease risk and increased venous thromboembolism risk through opposing inflammatory and thrombotic mechanisms.

Genetic Analyses of Blood Cell Structure for Biological and Pharmacological Inference

This study performs GWAS on blood cell flow-cytometry phenotypes, identifies variant-trait associations, and links them to cellular structures and disease mechanisms.

Cell type specific novel lincRNAs and circRNAs in the BLUEPRINT haematopoietic transcriptomes atlas.

The paper identifies novel long non-coding RNAs and circular RNAs in hematopoietic cells using BLUEPRINT consortium data, highlighting their cell type specificity.

Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility

The paper identifies how variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility and cell count differences.

Diagnostic high-throughput sequencing of 2,390 patients with bleeding, thrombotic and platelet disorders

The paper reports a diagnostic HTS test for bleeding, thrombotic, and platelet disorders, identifying molecular diagnoses in 897 out of 2,390 patients.

DNA methylation oscillation defines classes of enhancers

The paper identifies DNA methylation oscillations as a marker for enhancer classification, showing high predictive power compared to other methods.

Comparative analysis of neutrophil and monocyte epigenomes

This study compares the epigenomes of neutrophils and monocytes to identify regulatory elements and chromatin states, revealing differences in enhancer activity and DNA methylation.

Chromosome contacts in activated T cells identify autoimmune disease candidate genes

The paper identifies autoimmune disease candidate genes by integrating promoter capture Hi-C data with genetic associations in activated CD4+ T cells.

Genome-wide Analysis of Differential Transcriptional and Epigenetic Variability Across Human Immune Cell Types

The paper measures and compares transcriptional and epigenetic variability across immune cell types and finds neutrophils exhibit higher variability linked to immune pathways and environmental exposure.