Adrienne Margaret Flanagan

Chromosomal instability shapes spatial and temporal phenotypic diversity in a malignant peripheral nerve sheath tumour

This study uses single-cell and spatial multi-omics to analyze a malignant peripheral nerve sheath tumor, revealing chromosomal instability drives phenotypic diversity and spatial-temporal evolution.

Murine osteosarcoma recapitulates the driver landscape and genomic complexity of osteosarcoma evolution in humans

This study shows that a genetically engineered mouse model of osteosarcoma recapitulates the genomic complexity and driver mutations observed in human osteosarcoma.

Impact of tissue staining and scanner variation on the performance of pathology foundation models: a study of sarcomas and their mimics

Across 14 sarcoma and mimic subtypes, six pathology foundation models beat ResNet50 but lost accuracy under multi-institutional staining; adding 121 externally stained slides narrowed the gap.

A mouse model of PTEN Hamartoma Tumour Syndrome reveals that loss of the nuclear function of PTEN drives macrocephaly, lymphoid overgrowth, and late-onset cancer

This study shows that a specific PTEN mutation causes macrocephaly, lymphoid overgrowth, and late-onset cancer in mice by impairing nuclear PTEN functions, while maintaining normal PI3K/AKT signaling.

An optimised computational approach for the identification of somatic structural variants in cancer

The paper benchmarks structural variant callers in cancer genomics and recommends a consensus approach combining Delly, GRIDSS, Manta, and SvABA for improved performance.

SAVANA: reliable analysis of somatic structural variants and copy number aberrations in clinical samples using long-read sequencing

SAVANA improves detection of somatic structural variants and copy number aberrations in cancer using long-read sequencing with higher sensitivity and specificity than existing tools.

ATF4-Mediated Metabolic Stress Response as a Therapeutic Vulnerability in Chordoma

This study identifies ATF4-mediated metabolic stress response as a therapeutic target in chordoma, showing that EPRS inhibitors reduce cell viability and inhibit tumor growth in vivo.

Cancer-independent, second somatic NF1 mutation of normal tissues in neurofibromatosis type 1

The paper identifies second somatic NF1 mutations in normal tissues of neurofibromatosis type 1 patients through whole genome and exome sequencing, showing positive selection of truncating mutations in these tissues.

The history of chromosomal instability in genome doubled tumors

This paper introduces GRITIC, a method to time genomic gains in tumors, finding that copy number gains often accumulate after genome duplication.

A Genetic Model for Central Chondrosarcoma Evolution Correlates with Patient Outcome

The paper presents a genetic model of central chondrosarcoma using genomic and epigenomic data to identify mutations and methylation patterns associated with patient outcomes.

An efficient and adaptable workflow for editing disease-relevant single nucleotide variants using CRISPR/Cas9

The paper describes a workflow for efficient single nucleotide variant editing using CRISPR/Cas9, showing how experimental conditions affect editing efficiency and introducing methods for screening and quality control.

A pan-cancer landscape of somatic substitutions in non-unique regions of the human genome

The paper analyzes somatic substitutions in non-unique regions of the human genome across 2,658 cancers, revealing hidden mutations in coding sequences and regulatory elements.

Drivers underpinning the malignant transformation of giant cell tumour of bone

This study identifies genomic and methylation patterns associated with benign metastases and malignant transformation in giant cell tumour of bone.

PGP-UK: a research and citizen science hybrid project in support of personalized medicine

PGP-UK explores citizen science in genomics by recruiting participants, sharing data, and developing tools to advance personalized medicine.