DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome
Timothy J. Ley,Elaine R. Mardis,Li Ding,Bob Fulton,Michael D. McLellan,Ken Chen,David J. Dooling,Brian H. Dunford-Shore,Sean McGrath,Matthew T. Hickenbotham,Lisa Cook,Rachel Abbott,David E. Larson,Daniel C. Koboldt,Craig Pohl,Scott M. Smith,Amy Hawkins,Scott Abbott,Devin P. Locke,LaDeana W. Hillier,Tracie L. Miner,Lucinda Fulton,Vincent Magrini,Todd Wylie,Jarret Glasscock,Joshua J. Conyers,Nathan Sander,Xiaoqi Shi,John R. Osborne,Patrick Minx,David Gordon,Asif T. Chinwalla,Yu Zhao,Rhonda E. Ries,Jacqueline E. Payton,Peter Westervelt,Michael H. Tomasson,Mark A. Watson,Jack Baty,Jennifer Ivanovich,Sharon Heath,William D. Shannon,Rakesh Nagarajan,Matthew J. Walter,Daniel C. Link,Timothy A. Graubert,John F. DiPersio,Richard K. Wilson +47 more
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TLDR
This study establishes whole-genome sequencing as an unbiased method for discovering cancer-initiating mutations in previously unidentified genes that may respond to targeted therapies.Abstract:
Acute myeloid leukaemia is a highly malignant haematopoietic tumour that affects about 13,000 adults in the United States each year. The treatment of this disease has changed little in the past two decades, because most of the genetic events that initiate the disease remain undiscovered. Whole-genome sequencing is now possible at a reasonable cost and timeframe to use this approach for the unbiased discovery of tumour-specific somatic mutations that alter the protein-coding genes. Here we present the results obtained from sequencing a typical acute myeloid leukaemia genome, and its matched normal counterpart obtained from the same patient's skin. We discovered ten genes with acquired mutations; two were previously described mutations that are thought to contribute to tumour progression, and eight were new mutations present in virtually all tumour cells at presentation and relapse, the function of which is not yet known. Our study establishes whole-genome sequencing as an unbiased method for discovering cancer-initiating mutations in previously unidentified genes that may respond to targeted therapies.read more
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
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Sequencing technologies-the next generation
TL;DR: A technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments is presented.
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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
TL;DR: This work presents a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation and demonstrates that this method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping.
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VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
Daniel C. Koboldt,Qunyuan Zhang,David E. Larson,Dong Shen,Michael D. McLellan,Ling Lin,Christopher A. Miller,Elaine R. Mardis,Li Ding,Richard K. Wilson +9 more
TL;DR: An analysis tool for the detection of somatic mutations and copy number alterations in exome data from tumor-normal pairs is presented and new light is shed on the landscape of genetic alterations in ovarian cancer.
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The cancer genome
Michael R. Stratton,Michael R. Stratton,Peter J. Campbell,Peter J. Campbell,P. Andrew Futreal +4 more
TL;DR: This work has shown that the complete DNA sequence of large numbers of cancer genomes will be possible to obtain and will provide a detailed and comprehensive perspective on how individual cancers have developed.
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