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Open AccessCrowd-sourced benchmarking of single-sample tumor subclonal reconstruction
Subclonal reconstruction algorithms use bulk DNA sequencing data to quantify parameters of tumor evolution, allowing an assessment of how cancers initiate, progress and respond to selective pressures. We launc...
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Open AccessIntra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole-genome sequencing with histopathological features
Extension of prostate cancer beyond the primary site by local invasion or nodal metastasis is associated with poor prognosis. Despite significant research on tumour evolution in prostate cancer metastasis, the...
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Open AccessCancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine
Prostate cancer (PrCa) genomic heterogeneity causes resistance to therapies such as androgen deprivation. Such heterogeneity can be deciphered in the context of evolutionary principles, but current clinical tr...
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Open AccessAuthor Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition
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Open AccessThe genomic landscape and clonal evolutionary trajectory of classical hairy cell leukemia
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Open AccessAuthor Correction: The evolutionary history of 2,658 cancers
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Open AccessThe architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates
Up to 80% of cases of prostate cancer present with multifocal independent tumour lesions leading to the concept of a field effect present in the normal prostate predisposing to cancer development. In the prese...
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Open AccessAfrican-specific molecular taxonomy of prostate cancer
Prostate cancer is characterized by considerable geo-ethnic disparity. African ancestry is a significant risk factor, with mortality rates across sub-Saharan Africa of 2.7-fold higher than global averages1. The c...
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Article
Open AccessClonal diversification and histogenesis of malignant germ cell tumours
Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells. They are uniquely able to recapitulate embryonic and extraembryonic tissues, which carries progno...
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Open AccessIn utero origin of myelofibrosis presenting in adult monozygotic twins
The latency between acquisition of an initiating somatic driver mutation by a single-cell and clinical presentation with cancer is largely unknown. We describe a remarkable case of monozygotic twins presenting...
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Article
Open AccessAPOBEC3 mutational signatures are associated with extensive and diverse genomic instability across multiple tumour types
The APOBEC3 (apolipoprotein B mRNA editing enzyme catalytic polypeptide 3) family of cytidine deaminases is responsible for two mutational signatures (SBS2 and SBS13) found in cancer genomes. APOBEC3 enzymes a...
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Open AccessWhole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes
Black women across the African diaspora experience more aggressive breast cancer with higher mortality rates than white women of European ancestry. Although inter-ethnic germline variation is known, differenti...
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Genomic and evolutionary classification of lung cancer in never smokers
Lung cancer in never smokers (LCINS) is a common cause of cancer mortality but its genomic landscape is poorly characterized. Here high-coverage whole-genome sequencing of 232 LCINS showed 3 subtypes defined b...
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A unified haplotype-based method for accurate and comprehensive variant calling
Almost all haplotype-based variant callers were designed specifically for detecting common germline variation in diploid populations, and give suboptimal results in other scenarios. Here we present Octopus, a ...
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Open AccessPromises and challenges of adoptive T-cell therapies for solid tumours
Cancer is a leading cause of death worldwide and, despite new targeted therapies and immunotherapies, many patients with advanced-stage- or high-risk cancers still die, owing to metastatic disease. Adoptive T-...
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Open AccessRe-evaluating experimental validation in the Big Data Era: a conceptual argument
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A practical guide to cancer subclonal reconstruction from DNA sequencing
Subclonal reconstruction from bulk tumor DNA sequencing has become a pillar of cancer evolution studies, providing insight into the clonality and relative ordering of mutations and mutational processes. We pro...
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Genomic copy number predicts esophageal cancer years before transformation
Recent studies show that aneuploidy and driver gene mutations precede cancer diagnosis by many years1–4. We assess whether these genomic signals can be used for early detection and pre-emptive cancer treatment us...
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Open AccessMalignant transformation and genetic alterations are uncoupled in early colorectal cancer progression
Colorectal cancer (CRC) development is generally accepted as a sequential process, with genetic mutations determining phenotypic tumor progression. However, matching genetic profiles with histological transiti...
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Open AccessMulti-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases
Metastatic melanoma carries a poor prognosis despite modern systemic therapies. Understanding the evolution of the disease could help inform patient management. Through whole-genome sequencing of 13 melanoma m...
