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      Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin

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          Abstract

          Tumours most often arise from progression of precursor clones within a single anatomical niche. In the bone marrow, clonal progenitors can undergo malignant transformation to acute leukaemia, or differentiate into immune cells that contribute to disease pathology in peripheral tissues 14 . Outside the marrow, these clones are potentially exposed to a variety of tissue-specific mutational processes, although the consequences of this are unclear. Here we investigate the development of blastic plasmacytoid dendritic cell neoplasm (BPDCN)—an unusual form of acute leukaemia that often presents with malignant cells isolated to the skin 5 . Using tumour phylogenomics and single-cell transcriptomics with genotyping, we find that BPDCN arises from clonal (premalignant) haematopoietic precursors in the bone marrow. We observe that BPDCN skin tumours first develop at sun-exposed anatomical sites and are distinguished by clonally expanded mutations induced by ultraviolet (UV) radiation. A reconstruction of tumour phylogenies reveals that UV damage can precede the acquisition of alterations associated with malignant transformation, implicating sun exposure of plasmacytoid dendritic cells or committed precursors during BPDCN pathogenesis. Functionally, we find that loss-of-function mutations in Tet2, the most common premalignant alteration in BPDCN, confer resistance to UV-induced cell death in plasmacytoid, but not conventional, dendritic cells, suggesting a context-dependent tumour-suppressive role for TET2. These findings demonstrate how tissue-specific environmental exposures at distant anatomical sites can shape the evolution of premalignant clones to disseminated cancer.

          Abstract

          Blastic plasmacytoid dendritic cell neoplasm (BPDCN) arises from clonal (premalignant) haematopoietic precursors in the bone marrow, and BPDCN skin tumours first develop at sun-exposed anatomical sites and are distinguished by clonally expanded mutations induced by ultraviolet radiation.

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          Fast and accurate short read alignment with Burrows–Wheeler transform

          Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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            Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.

            The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics.
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              Welcome to the Tidyverse

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                Author and article information

                Contributors
                gabriel_griffin@dfci.harvard.edu
                volker_hovestadt@dfci.harvard.edu
                pvangalen@bwh.harvard.edu
                andrew_lane@dfci.harvard.edu
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                7 June 2023
                7 June 2023
                2023
                : 618
                : 7966
                : 834-841
                Affiliations
                [1 ]GRID grid.65499.37, ISNI 0000 0001 2106 9910, Department of Pathology, , Dana-Farber Cancer Institute, ; Boston, MA USA
                [2 ]GRID grid.66859.34, ISNI 0000 0004 0546 1623, Broad Institute of MIT and Harvard, ; Cambridge, MA USA
                [3 ]GRID grid.62560.37, ISNI 0000 0004 0378 8294, Department of Pathology, , Brigham and Women’s Hospital, ; Boston, MA USA
                [4 ]GRID grid.65499.37, ISNI 0000 0001 2106 9910, Department of Medical Oncology, , Dana-Farber Cancer Institute, ; Boston, MA USA
                [5 ]GRID grid.62560.37, ISNI 0000 0004 0378 8294, Division of Hematology, , Brigham and Women’s Hospital, ; Boston, MA USA
                [6 ]GRID grid.65499.37, ISNI 0000 0001 2106 9910, Department of Cancer Biology, , Dana-Farber Cancer Institute, ; Boston, MA USA
                [7 ]Department of Dermatology, Center for Cutaneous Oncology, Dana-Farber Cancer Institute and Brigham and Women’s Hospital, Boston, MA USA
                [8 ]GRID grid.38142.3c, ISNI 000000041936754X, Department of Cell Biology, , Harvard Medical School, ; Boston, MA USA
                [9 ]GRID grid.38142.3c, ISNI 000000041936754X, Ludwig Center at Harvard, , Harvard Medical School, ; Boston, MA USA
                [10 ]GRID grid.65499.37, ISNI 0000 0001 2106 9910, Department of Pediatric Oncology, , Dana-Farber Cancer Institute, ; Boston, MA USA
                [11 ]GRID grid.2515.3, ISNI 0000 0004 0378 8438, Division of Hematology/Oncology, , Boston Children’s Hospital, ; Boston, MA USA
                Author information
                http://orcid.org/0000-0002-4042-6757
                http://orcid.org/0000-0003-3841-6637
                http://orcid.org/0000-0001-8422-0008
                http://orcid.org/0000-0002-7340-3359
                http://orcid.org/0000-0002-2301-0426
                http://orcid.org/0000-0001-6475-8345
                http://orcid.org/0000-0002-3480-6649
                http://orcid.org/0000-0002-0735-1570
                http://orcid.org/0000-0001-7380-0226
                Article
                6156
                10.1038/s41586-023-06156-8
                10284703
                37286599
                b1b69c7b-397a-4265-b061-b0baa463cd18
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 21 January 2021
                : 2 May 2023
                Categories
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                Custom metadata
                © Springer Nature Limited 2023

                Uncategorized
                genomic analysis,leukaemia,haematopoietic stem cells
                Uncategorized
                genomic analysis, leukaemia, haematopoietic stem cells

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