Intratumor heterogeneity mediated through chromosome instability was associated with an increased risk of recurrence or death, a finding that supports the potential value of chromosome instability as a prognostic predictor. (Funded by Cancer Research UK and others; TRACERx ClinicalTrials.gov number, NCT01888601 .).

The pan-cancer analysis of whole genomes The expansion of whole-genome sequencing studies from individual ICGC and TCGA working groups presented the opportunity to undertake a meta-analysis of genomic features across tumour types. To achieve this, the PCAWG Consortium was established. A Technical Working Group implemented the informatics analyses by aggregating the raw sequencing data from different working groups that studied individual tumour types, aligning the sequences to the human genome and delivering a set of high-quality somatic mutation calls for downstream analysis (Extended Data Fig. 1). Given the recent meta-analysis

SummaryImmune evasion is a hallmark of cancer. Losing the ability to present neoantigens through human leukocyte antigen (HLA) loss may facilitate immune evasion. However, the polymorphic nature of the locus has precluded accurate HLA copy-number analysis. Here, we present loss of heterozygosity in human leukocyte antigen (LOHHLA), a computational tool to determine HLA allele-specific copy number from sequencing data. Using LOHHLA, we find that HLA LOH occurs in 40% of non-small-cell lung cancers (NSCLCs) and is associated with a high subclonal neoantigen burden, APOBEC-mediated mutagenesis, upregulation of cytolytic activity, and PD-L1 positivity. The focal nature of HLA LOH alterations, their subclonal frequencies, enrichment in metastatic sites, and occurrence as parallel events suggests that HLA LOH is an immune escape mechanism that is subject to strong microenvironmental selection pressures later in tumor evolution. Characterizing HLA LOH with LOHHLA refines neoantigen prediction and may have implications for our understanding of resistance mechanisms and immunotherapeutic approaches targeting neoantigens.Video Abstract

Cancer develops through a process of somatic evolution 1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of mutational processes 3. Here, by whole-genome sequencing analysis of 2,658 cancers as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) 4 , we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of samples. A nearly fourfold diversification of driver genes and increased genomic instability are features of later stages. Copy number alterations often occur in mitotic crises, and lead to simultaneous gains of chromosomal segments. Timing analyses suggest that driver mutations often precede diagnosis by many years, if not decades. Together, these results determine the evolutionary trajectories of cancer, and highlight opportunities for early cancer detection. Similar to the evolution in species, the approximately 10 14 cells in the human body are subject to the forces of mutation and selection 1. This process of somatic evolution begins in the zygote and only comes to rest at death, as cells are constantly exposed to mutagenic stresses, introducing 1-10 mutations per cell division 2. These mutagenic forces lead to a gradual accumulation of point mutations throughout life, observed in a range of healthy tissues 5-11 and cancers 12. Although these mutations are predominantly selectively neutral passenger mutations, some are proliferatively advantageous driver mutations 13. The types of mutation in cancer genomes are well studied, but little is known about the times when these lesions arise during somatic evolution and where the boundary between normal evolution and cancer progression should be drawn. Sequencing of bulk tumour samples enables partial reconstruction of the evolutionary history of individual tumours, based on the catalogue of somatic mutations they have accumulated 3,14,15. These inferences include timing of chromosomal gains during early somatic evolution 16 , phylogenetic analysis of late cancer evolution using matched primary and metastatic tumour samples from individual patients 17-20 , and temporal ordering of driver mutations across many samples 21,22 .

SummaryCancer develops through a process of somatic evolution. Here, we use whole-genome sequencing of 2,778 tumour samples from 2,658 donors to reconstruct the life history, evolution of mutational processes, and driver mutation sequences of 39 cancer types. The early phases of oncogenesis are driven by point mutations in a small set of driver genes, often including biallelic inactivation of tumour suppressors. Early oncogenesis is also characterised by specific copy number gains, such as trisomy 7 in glioblastoma or isochromosome 17q in medulloblastoma. By contrast, increased genomic instability, a nearly four-fold diversification of driver genes, and an acceleration of point mutation processes are features of later stages. Copy-number alterations often occur in mitotic crises leading to simultaneous gains of multiple chromosomal segments. Timing analysis suggests that driver mutations often precede diagnosis by many years, and in some cases decades, providing a window of opportunity for early cancer detection.

downstream of the source element, in a process called 3′ transduction 7-9. L1 retrotransposons can also promote the somatic transmobilization of Alu elements, SINE-VNTR-Alu (SVA) elements and processed pseudogenes, which are copies of mRNAs that have been reverse transcribed into DNA and inserted into the genome with the machinery of active L1 elements 10-12. Approximately 50% of human tumors contain somatic retrotranspositions of L1 elements 7,13-15. Previous analyses indicate that although a fraction of somatically acquired L1 insertions in cancer may influence gene function, the majority of retrotransposon integrations in a single tumor represent passenger mutations with little or no effect on cancer development 7,13. Nonetheless, L1 elements are capable of promoting other types of genomic structural alterations in the germline and somatically, in addition to canonical L1 insertion events 16-18 ; the effect of these alterations remains largely unexplored in the context of human cancer 19,20 .

All normal somatic cells are thought to acquire mutations. However, characterisation of the patterns and consequences of somatic mutation in normal tissues is limited. Uterine endometrium is a dynamic tissue that undergoes cyclical shedding and reconstitution and is lined by a gland-forming epithelium. Whole genome sequencing of normal endometrial glands showed that most are clonal cell populations derived from a recent common ancestor with mutation burdens differing from other normal cell types and manyfold lower than endometrial cancers. Mutational signatures found ubiquitously account for most mutations.Many, in some women potentially all, endometrial glands are colonised by cell clones carrying driver mutations in cancer genes, often with multiple drivers. Total and driver mutation burdens increase with age but are also influenced by other factors including body mass index and parity. Clones with drivers often originate during early decades of life. The somatic mutational landscapes of normal cells differ between cell types and are revealing the procession of neoplastic change leading to cancer.

Cancer chromosomal instability (CIN) results from dynamic changes to chromosome number and structure. The resulting diversity in somatic copy number alterations (SCNA) may provide the variation necessary for cancer evolution. Multi-sample phasing and SCNA analysis of 1421 samples from 394 tumours across 24 cancer types revealed ongoing CIN resulting in pervasive SCNA heterogeneity. Parallel evolutionary events, causing disruption to the same genes, such as BCL9, ARNT/HIF1B, TERT and MYC, within separate subclones were present in 35% of tumours. Most recurrent losses occurred prior to whole genome doubling (WGD), a clonal event in 48% of tumours. However, loss of heterozygosity at the human leukocyte antigen locus and loss of 8p to a single haploid copy recurred at significant subclonal frequencies, even in WGD tumours, likely reflecting ongoing karyotype remodeling. Focal amplifications affecting 1q21 (BCL9, ARNT), 5p15.33 (TERT), 11q13.3 (CCND1), 19q12 (CCNE1) and 8q24.1 (MYC) were frequently subclonal and exhibited an illusion of clonality within single samples. Analysis of an independent series of 1024 metastatic samples revealed enrichment for 14 focal SCNAs in metastatic samples, including late gains of 8q24.1 (MYC) in clear cell renal carcinoma and 11q13.3 (CCND1) in HER2-positive breast cancer. CIN may enable ongoing selection of SCNAs, manifested as ordered events, often occurring in parallel, throughout tumour evolution.