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
Cancer Genome Landscapes
Bert Vogelstein,Nickolas Papadopoulos,Victor E. Velculescu,Shibin Zhou,Luis A. Diaz,Kenneth W. Kinzler +5 more
TL;DR: This work has revealed the genomic landscapes of common forms of human cancer, which consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of "hills" (Genes altered infrequently).
Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies
Chetan Bettegowda,Chetan Bettegowda,Mark Sausen,Rebecca J. Leary,Isaac Kinde,Yuxuan Wang,Nishant Agrawal,Nishant Agrawal,Bjarne Bartlett,Bjarne Bartlett,Hao Wang,Brandon Luber,Rhoda M. Alani,Emmanuel S. Antonarakis,Nilofer S. Azad,Alberto Bardelli,Henry Brem,John L. Cameron,Clarence Lee,Leslie A. Fecher,Leslie A. Fecher,Gary L. Gallia,Peter Gibbs,Dung T. Le,Dung T. Le,Robert L. Giuntoli,Michael Goggins,Michael D. Hogarty,Matthias Holdhoff,Seung-Mo Hong,Seung-Mo Hong,Yuchen Jiao,Hartmut Juhl,Jenny J. Kim,Giulia Siravegna,Daniel A. Laheru,Calogero Lauricella,Michael Lim,Evan J. Lipson,Suely Kazue Nagahashi Marie,George J. Netto,Kelly S. Oliner,Alessandro Olivi,Louise Olsson,Gregory J. Riggins,Andrea Sartore-Bianchi,Kerstin Schmidt,le-Ming Shih,Sueli Mieko Oba-Shinjo,Salvatore Siena,Dan Theodorescu,Jeanne Tie,Timothy T. Harkins,Silvio Veronese,Tian Li Wang,Jon D. Weingart,Christopher L. Wolfgang,Laura D. Wood,Dongmei Xing,Ralph H. Hruban,Jian Wu,Peter J. Allen,C. Max Schmidt,Michael A. Choti,Victor E. Velculescu,Kenneth W. Kinzler,Bert Vogelstein,Nickolas Papadopoulos,Luis A. Diaz,Luis A. Diaz +69 more
TL;DR: The ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types was evaluated and suggested that ctDNA is a broadly applicable, sensitive, and specific biomarker that can be used for a variety of clinical and research purposes.
Snakemake--a scalable bioinformatics workflow engine.
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Frequent pathway mutations of splicing machinery in myelodysplasia
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