Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma
Cristina López,Kortine Kleinheinz,Sietse M. Aukema,Marius Rohde,Stephan H. Bernhart,Daniel Hübschmann,Rabea Wagener,Rabea Wagener,Umut H. Toprak,Umut H. Toprak,Francesco Raimondi,Markus Kreuz,Sebastian M. Waszak,Zhiqin Huang,Lina Sieverling,Nagarajan Paramasivam,Nagarajan Paramasivam,Julian Seufert,Stephanie Sungalee,Robert B. Russell,Julia Bausinger,Helene Kretzmer,Ole Ammerpohl,Anke K. Bergmann,Hans Binder,Arndt Borkhardt,Benedikt Brors,Alexander Claviez,Gero Doose,Lars Feuerbach,Andrea Haake,Martin-Leo Hansmann,Jessica I. Hoell,Michael Hummel,Jan O. Korbel,Chris Lawerenz,Dido Lenze,Bernhard Radlwimmer,Julia Richter,Philip Rosenstiel,Andreas Rosenwald,Markus Schilhabel,Harald Stein,Stephan Stilgenbauer,Peter F. Stadler,Monika Szczepanowski,Marc A. Weniger,Marc Zapatka,Roland Eils,Roland Eils,Peter Lichter,Markus Loeffler,Peter Möller,Lorenz Trümper,Wolfram Klapper,Steve Hoffmann,Ralf Küppers,Birgit Burkhardt,Matthias Schlesner,Reiner Siebert,Reiner Siebert +60 more
TL;DR: Interaction of structural, mutational, and transcriptional changes, which contribute to MYC oncogene dysregulation together with the pathognomonic IG-MYC translocation are unraveled.
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Abstract: Burkitt lymphoma (BL) is the most common B-cell lymphoma in children. Within the International Cancer Genome Consortium (ICGC), we performed whole genome and transcriptome sequencing of 39 sporadic BL. Here, we unravel interaction of structural, mutational, and transcriptional changes, which contribute to MYC oncogene dysregulation together with the pathognomonic IG-MYC translocation. Moreover, by mapping IGH translocation breakpoints, we provide evidence that the precursor of at least a subset of BL is a B-cell poised to express IGHA. We describe the landscape of mutations, structural variants, and mutational processes, and identified a series of driver genes in the pathogenesis of BL, which can be targeted by various mechanisms, including IG-non MYC translocations, germline and somatic mutations, fusion transcripts, and alternative splicing.
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References
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, 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.
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
39.8K
•Book
WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues
Stevens H. Swerdlow...
- 29 Sep 2017
TL;DR: Thank you very much for reading who classification of tumours of haematopoietic and lymphoid tissues, and maybe you have knowledge that, people have look hundreds of times for their chosen readings like this, but end up in malicious downloads.
15.1K
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
TL;DR: The ANNOVAR tool to annotate single nucleotide variants and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP is developed.
Comparative Protein Modelling by Satisfaction of Spatial Restraints
Andrej Sali,Tom L. Blundell +1 more
TL;DR: A comparative protein modelling method designed to find the most probable structure for a sequence given its alignment with related structures, which is automated and illustrated by the modelling of trypsin from two other serine proteinases.
13.4K
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