Mining Cancer Transcriptomes: Bioinformatic Tools and the Remaining Challenges

作者: Thomas Milan , Brian T. Wilhelm

DOI: 10.1007/S40291-017-0264-1

关键词:

摘要: The development of next-generation sequencing technologies has had a profound impact on the field cancer genomics. With enormous quantities data being generated from tumor samples, researchers have to rapidly adapt tools or develop new ones analyse raw maximize its value. While much this effort been focused improving specific algorithms get faster and more precise results, accessibility final for research community remains significant problem. Large amounts exist but are not easily available who lack resources experience download reanalyze them. In article, we focus RNA-seq analysis in context genomics discuss bioinformatic explore these data. We also highlight importance developing intuitive provide easier access public related issues sharing patient privacy.

参考文章(73)
Yongpeng Zhang, Linsen Li, Jun Xiao, Yanli Yang, Zexuan Zhu, FQZip: Lossless Reference-Based Compression of Next Generation Sequencing Data in FASTQ Format Springer, Cham. pp. 127- 135 ,(2015) , 10.1007/978-3-319-13356-0_11
Cancer Genome Atlas Research Network, None, Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia The New England Journal of Medicine. ,vol. 368, pp. 2059- 2074 ,(2013) , 10.1056/NEJMOA1301689
Gabor Marth, Erik Garrison, Haplotype-based variant detection from short-read sequencing arXiv: Genomics. ,(2012)
Marta Melé, Pedro G Ferreira, Ferran Reverter, David S DeLuca, Jean Monlong, Michael Sammeth, Taylor R Young, Jakob M Goldmann, Dmitri D Pervouchine, Timothy J Sullivan, Rory Johnson, Ayellet V Segrè, Sarah Djebali, Anastasia Niarchou, The GTEx Consortium, Fred A Wright, Tuuli Lappalainen, Miquel Calvo, Gad Getz, Emmanouil T Dermitzakis, Kristin G Ardlie, Roderic Guigó, None, The human transcriptome across tissues and individuals Science. ,vol. 348, pp. 660- 665 ,(2015) , 10.1126/SCIENCE.AAA0355
Jae-Woong Min, Woo Jin Kim, Jeong A Han, Yu-Jin Jung, Kyu-Tae Kim, Woong-Yang Park, Hae-Ock Lee, Sun Shim Choi, None, Identification of Distinct Tumor Subpopulations in Lung Adenocarcinoma via Single-Cell RNA-seq PLOS ONE. ,vol. 10, pp. e0135817- ,(2015) , 10.1371/JOURNAL.PONE.0135817
Stephen T. Sherry, Minghong Ward, Karl Sirotkin, dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Research. ,vol. 9, pp. 677- 679 ,(1999) , 10.1101/GR.9.8.677
Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru, Guillaume Rizk, Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph. BMC Bioinformatics. ,vol. 16, pp. 288- 288 ,(2015) , 10.1186/S12859-015-0709-7
Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo, Jill P Mesirov, GenePattern 2.0. Nature Genetics. ,vol. 38, pp. 500- 501 ,(2006) , 10.1038/NG0506-500
Thomas J Hardcastle, Krystyna A Kelly, baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data BMC Bioinformatics. ,vol. 11, pp. 422- 422 ,(2010) , 10.1186/1471-2105-11-422
Antonija Kreso, John E. Dick, Evolution of the Cancer Stem Cell Model Cell Stem Cell. ,vol. 14, pp. 275- 291 ,(2014) , 10.1016/J.STEM.2014.02.006