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The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data setsExpand
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry andExpand
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Mutational heterogeneity in cancer and the search for new cancer-associated genes
Michael S. Lawrence*, Petar Stojanov*, Paz Polak*, Gregory V. Kryukov, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Chip Stewart, Craig H. Mermel, Steven A. Roberts, Adam Kiezun, Peter S.Expand
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Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
Detection of somatic point substitutions is a key step in characterizing the cancer genome. However, existing methods typically miss low-allelic-fraction mutations that occur in only a subset of theExpand
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Integrated genomic characterization of endometrial carcinoma
  • D. Levine, Gad Stacey B. Kristian Eric Andrey Carrie Mike Cyriac Getz Gabriel Cibulskis Lander Sivachenko Sougnez L, +271 authors H. Sofia
  • Biology, Medicine
  • Nature
  • 1 May 2013
We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array- and sequencing-based technologies. Uterine serous tumours and ∼25% ofExpand
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The Mutational Landscape of Head and Neck Squamous Cell Carcinoma
The mutational profile of head and neck cancer is complex and may pose challenges to the development of targeted therapies. Head and neck squamous cell carcinoma (HNSCC) is a common, morbid, andExpand
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A Landscape of Driver Mutations in Melanoma
Despite recent insights into melanoma genetics, systematic surveys for driver mutations are challenged by an abundance of passenger mutations caused by carcinogenic UV light exposure. We developed aExpand
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Integrated Genomic Analyses of Ovarian Carcinoma
A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients’ lives. The Cancer Genome Atlas project has analysedExpand
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Somatic mutations affect key pathways in lung adenocarcinoma
Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborativeExpand
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Absolute quantification of somatic DNA alterations in human cancer
We describe a computational method that infers tumor purity and malignant cell ploidy directly from analysis of somatic DNA alterations. The method, named ABSOLUTE, can detect subclonal heterogeneityExpand
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