Breast cancer (BC) comprises multiple distinct subtypes that differ genetically, pathologically, and clinically. Here, we describe a robust protocol for long-term culturing of human mammary epithelial organoids. Using this protocol, >100 primary and metastatic BC organoid lines were generated, broadly recapitulating the diversity of the disease. BC organoid morphologies typically matched the histopathology, hormone receptor status, and HER2 status of the original tumor. DNA copy number variations as well as sequence changes were consistent within tumor-organoid pairs and largely retained even after extended passaging. BC organoids furthermore populated all major gene-expression-based classification groups and allowed in vitro drug screens that were consistent with in vivo xeno-transplantations and patient response. This study describes a representative collection of well-characterized BC organoids available for cancer research and drug development, as well as a strategy to assess in vitro drug response in a personalized fashion.

Metastatic cancer is a major cause of death and is associated with poor treatment efficacy. A better understanding of the characteristics of late-stage cancer is required to help adapt personalized treatments, reduce overtreatment and improve outcomes. Here we describe the largest, to our knowledge, pan-cancer study of metastatic solid tumour genomes, including whole-genome sequencing data for 2,520 pairs of tumour and normal tissue, analysed at median depths of 106× and 38×, respectively, and surveying more than 70 million somatic variants. The characteristic mutations of metastatic lesions varied widely, with mutations that reflect those of the primary tumour types, and with high rates of whole-genome duplication events (56%). Individual metastatic lesions were relatively homogeneous, with the vast majority (96%) of driver mutations being clonal and up to 80% of tumour-suppressor genes being inactivated bi-allelically by different mutational mechanisms. Although metastatic tumour genomes showed similar mutational landscape and driver genes to primary tumours, we find characteristics that could contribute to responsiveness to therapy or resistance in individual patients. We implement an approach for the review of clinically relevant associations and their potential for actionability. For 62% of patients, we identify genetic variants that may be used to stratify patients towards therapies that either have been approved or are in clinical trials. This demonstrates the importance of comprehensive genomic tumour profiling for precision medicine in cancer.In recent years, several large-scale whole-genome sequencing (WGS) analysis efforts have yielded valuable insights into the diversity of the molecular processes that drive different types of adult 1,2 and paediatric 3,4 cancer and have fuelled the promises of genome-driven oncology care 5 . However, most analyses were done on primary tumour material, whereas metastatic cancers-which cause the bulk of the disease burden and 90% of all cancer deaths-have been less comprehensively studied at the whole-genome level, with previous efforts focusing on tumourspecific cohorts 6-8 or at a targeted gene panel 9 or exome level 10 . As cancer genomes evolve over time, both in the highly heterogeneous primary tumour mass and as disseminated metastatic cells 11,12 , a better understanding of metastatic cancer genomes will be highly valuable to improve on adapting treatments for late-stage cancers.Here we describe the pan-cancer whole-genome landscape of metastatic cancers based on 2,520 paired tumour (106× average depth) and normal (blood, 38×) genomes from 2,399 patients ( Supplementary Tables 1 and 2, Extended Data Fig. 1). The sample distribution over age and primary tumour types broadly reflects the incidence of solid cancers in the Western world, including rare cancers (Fig. 1a). Sequencing data were analysed using an optimized bioinformatic pipeline based on open source tools (Methods, Supplementary Information) and identified a total of 59,472,629 single nucleotide varian...

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Organoids are self‐organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here, we describe a method to establish long‐term‐expanding human airway organoids from broncho‐alveolar resections or lavage material. The pseudostratified airway organoids consist of basal cells, functional multi‐ciliated cells, mucus‐producing secretory cells, and CC10‐secreting club cells. Airway organoids derived from cystic fibrosis (CF) patients allow assessment of CFTR function in an organoid swelling assay. Organoids established from lung cancer resections and metastasis biopsies retain tumor histopathology as well as cancer gene mutations and are amenable to drug screening. Respiratory syncytial virus (RSV) infection recapitulates central disease features, dramatically increases organoid cell motility via the non‐structural viral NS2 protein, and preferentially recruits neutrophils upon co‐culturing. We conclude that human airway organoids represent versatile models for the in vitro study of hereditary, malignant, and infectious pulmonary disease.