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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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Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.
The Cancer Genome Atlas Network recently cataloged recurrent genomic abnormalities in glioblastoma multiforme (GBM). We describe a robust gene expression-based molecular classification of GBM intoExpand
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The Structure of Haplotype Blocks in the Human Genome
Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose. As part of The SNPExpand
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The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity
The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical modelExpand
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EGFR Mutations in Lung Cancer: Correlation with Clinical Response to Gefitinib Therapy
Receptor tyrosine kinase genes were sequenced in non–small cell lung cancer (NSCLC) and matched normal tissue. Somatic mutations of the epidermal growth factor receptor gene EGFR were found in 15ofExpand
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From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high‐quality variant calls that can be used in downstream analyses.Expand
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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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The Somatic Genomic Landscape of Glioblastoma
We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutatedExpand
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A second generation human haplotype map of over 3.1 million SNPs
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations andExpand
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