In the Spotlight: Bioinformatics

During 2012, next generation sequencing (NGS) has attracted great attention in the biomedical research community, especially for personalized medicine. Also, third generation sequencing has become available. Therefore, state-of-art sequencing technology and analysis are reviewed in this Bioinformatics spotlight on 2012. Next-generation sequencing (NGS) is high-throughput nucleic acid sequencing technology with wide dynamic range and single base resolution. The full promise of NGS depends on the optimization of NGS platforms, sequence alignment and assembly algorithms, data analytics, novel algorithms for integrating NGS data with existing genomic, proteomic, or metabolomic data, and quantitative assessment of NGS technology in comparing to more established technologies such as microarrays. NGS technology has been predicated to become a cornerstone of personalized medicine. It is argued that NGS is a promising field for motivated young researchers who are looking for opportunities in bioinformatics.

[1]  Wing Hung Wong,et al.  Statistical inferences for isoform expression in RNA-Seq , 2009, Bioinform..

[2]  Heng Li,et al.  A survey of sequence alignment algorithms for next-generation sequencing , 2010, Briefings Bioinform..

[3]  Yongchao Liu,et al.  CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform , 2012, Bioinform..

[4]  Chris Williams,et al.  RNA-SeQC: RNA-seq metrics for quality control and process optimization , 2012, Bioinform..

[5]  Gunnar Rätsch,et al.  rQuant.web: a tool for RNA-Seq-based transcript quantitation , 2010, Nucleic Acids Res..

[6]  T. Dallman,et al.  Performance comparison of benchtop high-throughput sequencing platforms , 2012, Nature Biotechnology.

[7]  Gabor T. Marth,et al.  Rapid whole-genome mutational profiling using next-generation sequencing technologies. , 2008, Genome research.

[8]  Sylvain Foissac,et al.  A General Definition and Nomenclature for Alternative Splicing Events , 2008, PLoS Comput. Biol..

[9]  M. Metzker Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[10]  Bernard P. Puc,et al.  An integrated semiconductor device enabling non-optical genome sequencing , 2011, Nature.

[11]  Nicolas Servant,et al.  A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis , 2013, Briefings Bioinform..

[12]  Ion I. Mandoiu,et al.  Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data , 2010, WABI.

[13]  Brian E. Howard,et al.  Towards Reliable Isoform Quantification Using RNA-Seq Data , 2009, BIBM.

[14]  E. Wang,et al.  Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.

[15]  S. Ranade,et al.  Stem cell transcriptome profiling via massive-scale mRNA sequencing , 2008, Nature Methods.

[16]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[17]  M. Stephens,et al.  RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.

[18]  Robert A. Edwards,et al.  Quality control and preprocessing of metagenomic datasets , 2011, Bioinform..

[19]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[20]  Amy E. Hawkins,et al.  DNA sequencing of a cytogenetically normal acute myeloid leukemia genome , 2008, Nature.

[21]  S. Letovsky,et al.  Quantification of the yeast transcriptome by single-molecule sequencing , 2009, Nature Biotechnology.

[22]  T. Dallman,et al.  Corrigendum: Performance comparison of benchtop high-throughput sequencing platforms , 2012, Nature Biotechnology.

[23]  Timothy B. Stockwell,et al.  Evaluation of next generation sequencing platforms for population targeted sequencing studies , 2009, Genome Biology.

[24]  Tao Jiang,et al.  Inference of Isoforms from Short Sequence Reads , 2010, RECOMB.

[25]  S. Turner,et al.  Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations , 2003, Science.

[26]  Steven J. M. Jones,et al.  Alternative expression analysis by RNA sequencing , 2010, Nature Methods.

[27]  Jian‐Kang Zhu Epigenome Sequencing Comes of Age , 2008, Cell.

[28]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[29]  X. Chen,et al.  Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases , 2008, Cell Research.

[30]  R. Vossen,et al.  Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms , 2008, Nucleic acids research.

[31]  Steven M. Johnson,et al.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. , 2008, Genome research.

[32]  Allen D. Delaney,et al.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing , 2007, Nature Methods.

[33]  David T. Okou,et al.  Microarray-based genomic selection for high-throughput resequencing , 2007, Nature Methods.

[34]  R. Durbin,et al.  Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P

, 2022 .

[35]  Sanghyuk Lee,et al.  Accurate quantification of transcriptome from RNA-Seq data by effective length normalization , 2010, Nucleic Acids Res..

[36]  Robert C. Thompson,et al.  NGSQC: cross-platform quality analysis pipeline for deep sequencing data , 2010, BMC Genomics.

[37]  S. Turner,et al.  Real-Time DNA Sequencing from Single Polymerase Molecules , 2009, Science.

[38]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[39]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[40]  M. Ronaghi,et al.  A Sequencing Method Based on Real-Time Pyrophosphate , 1998, Science.

[41]  Wei Li,et al.  RSeQC: quality control of RNA-seq experiments , 2012, Bioinform..

[42]  Kenny Q. Ye,et al.  Sensitive and accurate detection of copy number variants using read depth of coverage. , 2009, Genome research.

[43]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[44]  K. Zhao,et al.  Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq , 2009, Nucleic acids research.

[45]  Terry Speed,et al.  Normalization of cDNA microarray data. , 2003, Methods.

[46]  J. Foekens,et al.  Methylated genes as new cancer biomarkers. , 2009, European journal of cancer.