Cancer genomics articles within Nature Communications

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  • Article
    | Open Access

    Rhabdomyosarcomas are tumours blocked in myogenic differentiation, which despite the expression of master muscle regulatory factors, including MYOD, are unable to differentiate. Here, the authors show that SNAI2 is upregulated by MYOD through super enhancers, binds to MYOD target enhancers, and arrests differentiation.

    • Silvia Pomella
    • , Prethish Sreenivas
    •  & Myron S. Ignatius

  • Article
    | Open Access

    In metastatic urothelial carcinoma, it has not been established whether circulating tumor DNA (ctDNA) can replace archival primary tissue to assess mutations and biomarkers. Here, the authors show high mutation concordance between ctDNA and tumour tissue, with high consistency in serial samples.

    • Gillian Vandekerkhove
    • , Jean-Michel Lavoie
    •  & Alexander W. Wyatt

  • Article
    | Open Access

    Predicting who will develop skin cancer is difficult. Here, the authors from 23andMe developed a polygenic risk score for skin cancer based on a questionnaire and genetic data from more than 210,000 individuals and suggest that the score could be used in early screening programmes.

    • Pierre Fontanillas
    • , Babak Alipanahi
    •  & Adam Auton

  • Article
    | Open Access

    The determination of whether cancer cell lines recapitulate the molecular features of corresponding patient tumours remains essential for the selection of appropriate cell line models for preclinical studies. The method developed here, Celligner, integrates cancer cell line and tumour RNA-seq datasets and reveals large differences in their concordance across cell lines and cancer types.

    • Allison Warren
    • , Yejia Chen
    •  & James M. McFarland

  • Article
    | Open Access

    The detection of aberrations in circulating tumour DNA represents a non-invasive method to survey the oncogenes and tumour suppressors that are modified within a patient’s cancer. Here, the authors analysed more than 10,000 patients using a targeted sequencing panel and report on the frequencies of the mutations that they found.

    • Yongliang Zhang
    • , Yu Yao
    •  & Qiang Zeng

  • Article
    | Open Access

    Molecular profiling of breast cancer in non-Caucasian populations remains underexplored. Here the authors report a high prevalence of HER2-subtypes and enriched immune score with improved survival and higher rates of TP53 somatic mutations with poorer survival in ER+ tumours in a Malaysian cohort.

    • Jia-Wern Pan
    • , Muhammad Mamduh Ahmad Zabidi
    •  & Soo-Hwang Teo

  • Article
    | Open Access

    RNA-sequencing data from tumours can be used to predict the prognosis of patients. Here, the authors show that a neural network meta-learning approach can be useful for predicting prognosis from a small number of samples.

    • Yeping Lina Qiu
    • , Hong Zheng
    •  & Olivier Gevaert

  • Article
    | Open Access

    The mechanisms underlying the growth of breast cancer metastasis in the brain are unclear. Here, the authors use an intracranial injection mouse model and single-cell analysis of patient circulating tumour cells to demonstrate that increased hypoxic and HIF1A signalling promotes tumour growth in the brain.

    • Richard Y. Ebright
    • , Marcus A. Zachariah
    •  & Shyamala Maheswaran

  • Article
    | Open Access

    The impact of variant calling algorithms on the analysis of intra-tumour heterogeneity has not been properly quantified. Here the authors measure the variability of 22 pipelines with different variant callers and clustering algorithms for subclonal reconstruction to inform future analyses.

    • Lydia Y. Liu
    • , Vinayak Bhandari
    •  & Paul C. Boutros

  • Article
    | Open Access

    The role of germline variation in human cancers is not fully understood. Here, the authors define the landscape of putative deleterious germline variants that abrogate tumor suppressor proteins in advanced urothelial cancer patients.

    • Aram Vosoughi
    • , Tuo Zhang
    •  & Bishoy M. Faltas

  • Article
    | Open Access

    Combinatorial treatments have become a standard of care for various complex diseases including cancers. Here, the authors show that combinatorial responses of two anticancer drugs can be accurately predicted using factorization machines trained on large-scale pharmacogenomic data for guiding precision oncology studies.

    • Heli Julkunen
    • , Anna Cichonska
    •  & Juho Rousu

  • Article
    | Open Access

    Adenocarcinoma at the gastroesophageal junction has a dismal prognosis and few drug options. Here, the authors present genomic and transcriptomic features and potential therapeutic targets and prognostic biomarkers of Chinese and Caucasian tumours, and reveal the molecular similarities.

    • Yuan Lin
    • , Yingying Luo
    •  & Dongxin Lin

  • Article
    | Open Access

    Xeroderma Pigmentosum group C (XP-C) is a rare genetic disorder characterised by deficient DNA repair leading to skin and internal cancer, but the latter is not well understood molecularly. Here the authors sequence genomes of non-skin cancers from XP-C patients to unravel its mutational patterns.

    • Andrey A. Yurchenko
    • , Ismael Padioleau
    •  & Sergey Nikolaev

  • Article
    | Open Access

    MYCN amplification is common in neuroblastomas. Here the authors analyse the MYCN amplicon structure and its epigenetic regulation by integrating short- and longread genomic and epigenomic data and find two classes of MYCN amplicons in neuroblastomas, one driven by local enhancers and the other by hijacking of distal regulatory elements.

    • Konstantin Helmsauer
    • , Maria E. Valieva
    •  & Richard P. Koche

  • Article
    | Open Access

    Cancers deficient in homologous recombination can benefit from treatment with poly ADP-ribose polymerase (PARP) inhibitors. Here, the authors generated a classifier that can predict homologous recombination deficiency from genomic data and suggest several cancer types that may benefit from PARP inhibitor treatment.

    • Luan Nguyen
    • , John W. M. Martens
    •  & Edwin Cuppen

  • Article
    | Open Access

    Non-coding cancer driver mutations that induce splicing variants exist, but are largely unexplored. Here, the authors find these non-coding mutations in known pan-cancer driver genes and show that they create new exons and might interact with pre-existing potential splice sites.

    • Song Cao
    • , Daniel Cui Zhou
    •  & Li Ding

  • Article
    | Open Access

    SMARCA4 is the core catalytic subunit of the mammalian SWI/SNF complex and is known to be mutated in many cancers. Here, the authors detect more than 10,000 SMARCA4 variants across different cancer subtypes and find hotspot mutations throughout the helicase domain, which reduce remodeling activity.

    • Tharu M. Fernando
    • , Robert Piskol
    •  & Robert L. Yauch

  • Article
    | Open Access

    The histone variant mutation H3.3-G34W occurs in the majority of giant cell tumor of bone (GCTB). By profiling patient-derived GCTB tumor cells, the authors show that this mutation associates with epigenetic alterations in heterochromatic and bivalent regions that contribute to an impaired osteogenic differentiation and the osteolytic phenotype of GCTB.

    • Pavlo Lutsik
    • , Annika Baude
    •  & Christoph Plass

  • Article
    | Open Access

    Acral melanoma occurs on the soles of the feet, palms of the hands and in nail beds. Here, the authors reports the genomic landscape of 87 acral melanomas and find that some tumors harbor a UV signature and that the tumors are diverse at the levels of mutational signatures, structural aberrations and copy number signatures.

    • Felicity Newell
    • , James S. Wilmott
    •  & Nicholas K. Hayward

  • Article
    | Open Access

    Genomic analysis of neuroblastoma has revealed important disease etiology. In this study, the authors assembled whole genome, exome and transcriptome data from over 700 neuroblastomas and identified molecular signatures correlated with age, and rare, potentially targetable variants overlooked in smaller cohorts.

    • Samuel W. Brady
    • , Yanling Liu
    •  & Jinghui Zhang

  • Article
    | Open Access

    Developing machine learning models that work equally well for all ethnic groups is of crucial importance to health disparity prevention and reduction. Here, using an extensive set of machine learning experiments on cancer omics data, the authors find that transfer learning can improve model performance for data-disadvantaged ethnic groups.

    • Yan Gao
    •  & Yan Cui

  • Article
    | Open Access

    The evolutionary progression from primary to metastatic prostate cancer is largely uncharted, and the implications for liquid biopsy are unexplored. Here, the authors use deep genomic sequencing and histopathological information to trace tumor evolution both within the prostate and during metastasis in ten men.

    • D. J. Woodcock
    • , E. Riabchenko
    •  & D. C. Wedge

  • Article
    | Open Access

    Working with cancer genomes from multiple projects can increase investigative power, but quality of sequences can vary. Here, the authors present a framework for comparing whole genome sequencing quality to help researchers guide downstream analyses and exclude poor quality samples.

    • Justin P. Whalley
    • , Ivo Buchhalter
    •  & Ivo G. Gut

  • Article
    | Open Access

    A molecular tumor board (MTB) is often used as a platform that integrates clinical and molecular parameters for clinical decision making. Here, the authors review the outcome of 715 cancer patients presented at their institution’s MTB, and demonstrate that patients who received a MTB-recommended regimen received therapy that was better matched to their alterations and achieved better clinical outcomes.

    • Shumei Kato
    • , Ki Hwan Kim
    •  & Razelle Kurzrock

  • Article
    | Open Access

    With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

    • Matthew H. Bailey
    • , William U. Meyerson
    •  & Christian von Mering

  • Article
    | Open Access

    Pancreatic ductal adenocarcinoma may be initiated by acinar metaplasia, but the molecular and cellular insights during this transition are unclear. Here the authors show, using single cell RNA-sequencing analyses, that mouse metaplastic acinar cells can be clustered into six cell types or states that are heterogeneous and have unique transcription programs.

    • Yehuda Schlesinger
    • , Oshri Yosefov-Levi
    •  & Oren Parnas

  • Article
    | Open Access

    Multiple algorithms exist for predicting heterogeneity and clonal architecture from the bulk sequencing of tumor tissue. Here, the authors report on an algorithm, FastClone, which was developed from a DREAM challenge and show that FastClone can accurately predict clonality in simulated data and data from colon cancer.

    • Yao Xiao
    • , Xueqing Wang
    •  & Yuanfang Guan

  • Article
    | Open Access

    The correct identification of copy-number aberrations (CNAs) in tumours can provide information for diagnosis, prognosis and therapeutic strategies. Here, the authors provide an algorithm, HATCHet, which quantifies CNAs using multiple samples from the same patient, providing more accurate information than studying one sample alone.

    • Simone Zaccaria
    •  & Benjamin J. Raphael

  • Article
    | Open Access

    Mongolia has the highest incidence of—and mortality from—hepatocellular carcinoma (HCC) in the world. Here, the authors examine the genomic and transcriptomic landscape of Mongolian HCC, uncover novel driver mutations, and suggest distinct disease etiologies.

    • Julián Candia
    • , Enkhjargal Bayarsaikhan
    •  & Xin Wei Wang

  • Article
    | Open Access

    There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

    • Constance H. Li
    • , Stephenie D. Prokopec
    •  & Christian von Mering

  • Article
    | Open Access

    Here, using methylCIBERSORT, the authors characterize the tumour-immune microenvironment of paediatric central nervous system (CNS) tumours and its association with tumour type and prognosis. These findings suggest that immuno-methylomic profiling may inform immunotherapy approaches in paediatric patients with CNS tumour.

    • Yura Grabovska
    • , Alan Mackay
    •  & Daniel Williamson

  • Article
    | Open Access

    Large-scale screens of chemical and genetic vulnerabilities in cancer are typically limited to simple readouts of cell viability. Here, the authors develop a method for profiling post-perturbation transcriptional responses across large pools of cancer cell lines, enabling deep characterization of shared and context-specific responses.

    • James M. McFarland
    • , Brenton R. Paolella
    •  & Aviad Tsherniak

  • Article
    | Open Access

    Gallbladder cancer incidence shows characteristic geographic patterns. Here the authors perform a genomic analysis of gallbladder cancers in patients from countries with high incidence (South Korea, India and Chile) and identify ELF3 and other significantly mutated genes not previously associated with gallbladder cancer.

    • Akhilesh Pandey
    • , Eric W. Stawiski
    •  & Somasekar Seshagiri

  • Article
    | Open Access

    The clinical benefit from immunotherapy response in patients with mutations of genes forming the chromatin remodelling complex PBAF remains controversial. Here the authors show that PBAF complex mutations are not associated with favourable response in pan-cancer cohorts of patients treated with immune-checkpoint blockade.

    • A. Ari Hakimi
    • , Kyrollis Attalla
    •  & Robert J. Motzer

  • Article
    | Open Access

    Here the authors show that stronger immune selection and immune editing in females and younger patients lead to the accumulation of poorly presented driver mutations in tumors. These results may explain why young and female patients are characterized by lower response rates to immune checkpoint blockade therapies.

    • Andrea Castro
    • , Rachel Marty Pyke
    •  & Hannah Carter

  • Article
    | Open Access

    Neoplastic pancreatic cysts are associated with invasive pancreatic cancer, but their origins and evolutionary relationships are unclear. Here, the authors present the evolutionary analysis of neoplastic cysts and report them as precursors of invasive pancreatic cancer, and that SMAD4/TGFBR2 alterations are likely drivers of invasion in a subset of cases.

    • Michaël Noë
    • , Noushin Niknafs
    •  & Laura D. Wood

  • Article
    | Open Access

    Chemotherapy resistance in recurrent gliomas is a large hurdle for successful therapy. Here, the authors show that some recurrent gliomas harbour O-6-methylguanine-DNA methyltransferase (MGMT) genomic rearrangements, and in vitro and in vivo these contribute to temozolomide resistance.

    • Barbara Oldrini
    • , Nuria Vaquero-Siguero
    •  & Massimo Squatrito

  • Article
    | Open Access

    The transcripts generated by frameshifts and indels in cancer are frequently degraded by nonsense mediated decay. Here, the authors show that some of these transcripts can escape this degradation mechanism and their prevalence correlates with tumour response to immunotherapy.

    • Kevin Litchfield
    • , James L. Reading
    •  & Charles Swanton

  • Article
    | Open Access

    Rare cancer mutations are often missed using recurrence-based statistical approaches, but are usually accompanied by changes in expression. Here the authors leverage this information to uncover several elusive candidate cancer-associated genes using topological data analysis.

    • Raúl Rabadán
    • , Yamina Mohamedi
    •  & Pablo G. Cámara

  • Article
    | Open Access

    ENCODE is a resource comprising thousands of functional genomic datasets. Here, the authors present custom annotation within ENCODE for cancer, highlighting a workflow that can help prioritise key elements in oncogenesis.

    • Jing Zhang
    • , Donghoon Lee
    •  & Mark Gerstein

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