Journal Article10.1038/NRG2841
Advances in understanding cancer genomes through second-generation sequencing
TL;DR: This Review focuses on the methodological considerations for characterizing somatic genome alterations in cancer and the future prospects for these approaches.
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Abstract: Cancer is fundamentally a disease of the genome and so high-throughput sequencing technologies offer great potential for improving our understanding of the biology and treatment of cancer Experimental strategies, computational approaches and cancer-specific considerations for detecting different types of genomic alterations are discussed Cancers are caused by the accumulation of genomic alterations Therefore, analyses of cancer genome sequences and structures provide insights for understanding cancer biology, diagnosis and therapy The application of second-generation DNA sequencing technologies (also known as next-generation sequencing) — through whole-genome, whole-exome and whole-transcriptome approaches — is allowing substantial advances in cancer genomics These methods are facilitating an increase in the efficiency and resolution of detection of each of the principal types of somatic cancer genome alterations, including nucleotide substitutions, small insertions and deletions, copy number alterations, chromosomal rearrangements and microbial infections This Review focuses on the methodological considerations for characterizing somatic genome alterations in cancer and the future prospects for these approaches
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Citations
Rethinking future development of molecular therapies in hepatocellular carcinoma: A bottom-up approach
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Frontiers in Bladder Cancer Genomic Research.
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Interrogating genomic and epigenomic data to understand prostate cancer
TL;DR: This review of leading discoveries in prostate cancer research derived from the use of high-throughput approaches powered by microarrays and massively parallel next-generation sequencing (NGS) demonstrates the power of interrogating genomic and epigenomic data in understanding the plethora of mechanisms of transcriptional regulation.
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The somatic autosomal mutation matrix in cancer genomes
Nuri A. Temiz,Nuri A. Temiz,Duncan E. Donohue,Duncan E. Donohue,Albino Bacolla,Albino Bacolla,Karen M. Vasquez,David Neil Cooper,Uma Mudunuri,Joseph Ivanic,Regina Z. Cer,Regina Z. Cer,Ming Yi,Robert M. Stephens,Jack R. Collins,Brian T. Luke +15 more
TL;DR: A 32 × 12 mutation matrix that captures the nucleotide pattern two nucleotides upstream and downstream of the mutation, constructed from tumor-specific mutations derived from each of 909 individual cancer genomes harboring a total of 10,681,843 single-base substitutions is presented.
Re-alignment of the unmapped reads with base quality score
TL;DR: The results show that many reads which fail to be aligned by the most popular alignment tools (BWA and Bowtie2) can be correctly re-aligned by RAUR, with a similar Precision.
References
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TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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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.
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna,Matthew Hanna,Eric Banks,Andrey Sivachenko,Kristian Cibulskis,Andrew Kernytsky,Kiran V. Garimella,David Altshuler,Stacey Gabriel,Mark J. Daly,Mark A. DePristo +10 more
TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
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A method and server for predicting damaging missense mutations.
Ivan Adzhubei,Steffen Schmidt,Leonid Peshkin,Vasily Ramensky,Anna Gerasimova,Peer Bork,Alexey S. Kondrashov,Shamil R. Sunyaev +7 more
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