Jonathan Baber
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View article: Heritable defects in telomere and mitotic function selectively predispose to sarcomas
Heritable defects in telomere and mitotic function selectively predispose to sarcomas Open
Cancer genetics has to date focused on epithelial malignancies, identifying multiple histotype-specific pathways underlying cancer susceptibility. Sarcomas are rare malignancies predominantly derived from embryonic mesoderm. To identify pa…
View article: Genetic immune escape landscape in primary and metastatic cancer
Genetic immune escape landscape in primary and metastatic cancer Open
Immune surveillance escape is a hallmark of tumorigenesis1. Multiple studies have characterized the immune escape landscape across several untreated early-stage primary cancer types2–4. However, whether late-stage treated metastatic tumors…
View article: Unscrambling cancer genomes via integrated analysis of structural variation and copy number
Unscrambling cancer genomes via integrated analysis of structural variation and copy number Open
Complex somatic genomic rearrangements and copy number alterations are hallmarks of nearly all cancers. We have developed an algorithm, LINX, to aid interpretation of structural variant and copy number data derived from short-read, whole-g…
View article: Genetic immune escape landscape in primary and metastatic cancer
Genetic immune escape landscape in primary and metastatic cancer Open
Immune surveillance escape is a hallmark of tumorigenesis 1 . Multiple studies have characterized the immune escape landscape across several untreated early-stage primary cancer types 2–4 . However, whether late-stage treated metastatic tu…
View article: Additional file 2 of GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
Additional file 2 of GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing Open
Additional file 2. Tables S1-S2. Table S1. Probe validation results. Table S2. Small duplication driver predictions.
View article: Unscrambling cancer genomes via integrated analysis of structural variation and copy number
Unscrambling cancer genomes via integrated analysis of structural variation and copy number Open
Complex somatic genomic rearrangement and copy number alterations (CNA) are hallmarks of nearly all cancers. Whilst whole genome sequencing (WGS) in principle allows comprehensive profiling of these events, biological and clinical interpre…
View article: GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing
GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing Open
GRIDSS2 is the first structural variant caller to explicitly report single breakends - breakpoints in which only one side can be unambiguously determined. By treating single breakends as a fundamental genomic rearrangement signal on par wi…
View article: GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number
GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number Open
We have developed a novel, integrated and comprehensive purity, ploidy, structural variant and copy number somatic analysis toolkit for whole genome sequencing data of paired tumor/normal samples. We show that the combination of using GRID…
View article: Pan-cancer whole genome analyses of metastatic solid tumors
Pan-cancer whole genome analyses of metastatic solid tumors Open
Metastatic cancer is one of the major causes of death and is associated with poor treatment efficiency. A better understanding of the characteristics of late stage cancer is required to help tailor personalised treatment, reduce overtreatm…