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Next-generation sequencing: applications beyond genomes.

Marguerat S, Wilhelm BT, Bähler J - Biochem. Soc. Trans. (2008)

Bottom Line: These next-generation technologies make it feasible to sequence not only static genomes, but also entire transcriptomes expressed under different conditions.Below, we provide a snapshot of these exciting new approaches to understanding the properties and functions of genomes.Given that sequencing-based assays may increasingly supersede microarray-based assays, we also compare and contrast data obtained from these distinct approaches.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research UK, Fission Yeast Functional Genomics Group, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK. jurg@sanger.ac.uk

ABSTRACT
The development of DNA sequencing more than 30 years ago has profoundly impacted biological research. In the last couple of years, remarkable technological innovations have emerged that allow the direct and cost-effective sequencing of complex samples at unprecedented scale and speed. These next-generation technologies make it feasible to sequence not only static genomes, but also entire transcriptomes expressed under different conditions. These and other powerful applications of next-generation sequencing are rapidly revolutionizing the way genomic studies are carried out. Below, we provide a snapshot of these exciting new approaches to understanding the properties and functions of genomes. Given that sequencing-based assays may increasingly supersede microarray-based assays, we also compare and contrast data obtained from these distinct approaches.

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Related in: MedlinePlus

Sequence census data applied to cDNA allow genome-wide measurements of transcript levels (RNA-Seq)The sequence score defines the number of times each base of the reference genome sequence is hit by a sequence read (top panel). Sequence scores (based on normalized read numbers) are then plotted along the genome (bottom panel). Based on data from our fission yeast transcriptome analysis [48].
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Figure 2: Sequence census data applied to cDNA allow genome-wide measurements of transcript levels (RNA-Seq)The sequence score defines the number of times each base of the reference genome sequence is hit by a sequence read (top panel). Sequence scores (based on normalized read numbers) are then plotted along the genome (bottom panel). Based on data from our fission yeast transcriptome analysis [48].

Mentions: In addition to established analyses of genome sequences, next-generation sequencing is triggering new assays and applications that should greatly advance our understanding of genome function (Figure 1) [27]. The principle behind these alternative applications, which have been termed ‘sequence census’ methods, is simple: complex DNA or RNA samples are directly sequenced to determine their content. With reference genomes available, short sequence reads are sufficient to map their locations (except for repeated regions), and once mapped, millions of sequence hits are simply counted to determine their genomic distribution (Figure 2). This concept is based on previous approaches such as serial analysis of gene expression [28] and massively parallel signature sequencing [29]. Next-generation sequencing, however, delivers much more information at affordable costs, and it is easy to implement for a wider range of applications. Below, we will survey initial studies that analyse genome function exploiting sequence census methods, which will increasingly supersede microarray-based approaches (Figure 1).


Next-generation sequencing: applications beyond genomes.

Marguerat S, Wilhelm BT, Bähler J - Biochem. Soc. Trans. (2008)

Sequence census data applied to cDNA allow genome-wide measurements of transcript levels (RNA-Seq)The sequence score defines the number of times each base of the reference genome sequence is hit by a sequence read (top panel). Sequence scores (based on normalized read numbers) are then plotted along the genome (bottom panel). Based on data from our fission yeast transcriptome analysis [48].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2563889&req=5

Figure 2: Sequence census data applied to cDNA allow genome-wide measurements of transcript levels (RNA-Seq)The sequence score defines the number of times each base of the reference genome sequence is hit by a sequence read (top panel). Sequence scores (based on normalized read numbers) are then plotted along the genome (bottom panel). Based on data from our fission yeast transcriptome analysis [48].
Mentions: In addition to established analyses of genome sequences, next-generation sequencing is triggering new assays and applications that should greatly advance our understanding of genome function (Figure 1) [27]. The principle behind these alternative applications, which have been termed ‘sequence census’ methods, is simple: complex DNA or RNA samples are directly sequenced to determine their content. With reference genomes available, short sequence reads are sufficient to map their locations (except for repeated regions), and once mapped, millions of sequence hits are simply counted to determine their genomic distribution (Figure 2). This concept is based on previous approaches such as serial analysis of gene expression [28] and massively parallel signature sequencing [29]. Next-generation sequencing, however, delivers much more information at affordable costs, and it is easy to implement for a wider range of applications. Below, we will survey initial studies that analyse genome function exploiting sequence census methods, which will increasingly supersede microarray-based approaches (Figure 1).

Bottom Line: These next-generation technologies make it feasible to sequence not only static genomes, but also entire transcriptomes expressed under different conditions.Below, we provide a snapshot of these exciting new approaches to understanding the properties and functions of genomes.Given that sequencing-based assays may increasingly supersede microarray-based assays, we also compare and contrast data obtained from these distinct approaches.

View Article: PubMed Central - PubMed

Affiliation: Cancer Research UK, Fission Yeast Functional Genomics Group, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK. jurg@sanger.ac.uk

ABSTRACT
The development of DNA sequencing more than 30 years ago has profoundly impacted biological research. In the last couple of years, remarkable technological innovations have emerged that allow the direct and cost-effective sequencing of complex samples at unprecedented scale and speed. These next-generation technologies make it feasible to sequence not only static genomes, but also entire transcriptomes expressed under different conditions. These and other powerful applications of next-generation sequencing are rapidly revolutionizing the way genomic studies are carried out. Below, we provide a snapshot of these exciting new approaches to understanding the properties and functions of genomes. Given that sequencing-based assays may increasingly supersede microarray-based assays, we also compare and contrast data obtained from these distinct approaches.

Show MeSH
Related in: MedlinePlus