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Genomics


Figure 1: Location of survey respondents’ sequencing activities


In own lab, using instruments belonging to my organisation


At a commercial fee-for-service provider (CRO)


At a central facility, using instruments jointly operated by my organisation and collaborators


Other place(s) of sequencing At a third-party not-for-profit facility At a third-party collaborator’s lab


11% 7% 1%


0% 5% 10% 15% 20% 25% 30% 35% % Responding


© HTStec 2012 24% 22% 34%


base is then detected using an imaging-based sys- tem. Sequence data from each array feature is amassed through alternating cycles of enzyme- based biochemistry and imaging. Eventually the sequences corresponding to each array cluster (known as reads) are aligned to assemble the con- tiguous DNA sequence.


Figure 2: Use of different NGS instruments to generate sequencing data


Roche 454 GS FLX+ Illumina HiSeq 2000/1000


Ion Torrent PGM Illumina MiSeq


Illumina Genome Analyzer IIx Illumina HiSeq 2500/1500


ABI SOLiD 4Hq Illumina HiScan SQ Pacific Biosciences RS Roche 454 GS Junior ABI SOLiD 5500


Intelligent BioSystems/Azco Mini-seq Intelligent BioSystems/Azco MAX-Seq


ABI SOLiD PI Helicos Heliscope Polonator G.007


12% 12%


5%


0% 0% 0% 1% 1% 3% 3%


0% 5% 10% 15% 20% 25% 30% 35% 40% % Using


© HTStec 2012 20% 31% 28% 26% 39% 35%


In the past decade, the rapid development of NGS technology has transformed the landscape of genomic research. Technological innovation has resulted in a dramatic reduction in the cost of sequencing. The ability to acquire affordable sequence data has enabled NGS technology to expand beyond the confines of large research cen- tres into many smaller labs. When combined with the availability of the reference genomes for a growing number of organisms, this has precipitat- ed an explosion in genomic research. Researchers across many fields are using NGS technology to answer questions to diverse biologi- cal problems, ranging from analysis of genes com- monly mutated in types of cancer to which gene loci promote speciation. A growing suite of appli- cations of NGS has helped to reveal the intricacy of networks controlling gene expression. These approaches have provided insights into the epigenome, transcriptome and a multitude of pro- tein-DNA interactions, hinting at the high levels of regulatory sophistication operating in cells. Recent research has even highlighted the importance of the expanses of non-coding DNA within the genome – which are far more extensive than coding regions, and were previously labelled as ‘junk’ DNA. Although clearly a valuable tool for the investi- gation of a range of biological phenomena, the interpretation and analysis of the vast amounts of data being generated through NGS now represents a significant challenge. Similarly, improvements in read length and accuracy are desirable. In response to budgetary constraints in many research environ- ments, efforts are also being focused on streamlin- ing the sample preparation processes for numerous applications, and enhancing the efficiency of run- ning a sequencing instrument.


A growing trend in sequencing has been the development of instruments capable of operating at higher speeds and producing longer read lengths. Some so-called ‘third generation’ sequencing plat- forms incorporate innovations such as single-mole- cule real-time sequencing, whereas others build upon existing approaches. It is expected that the further improvements offered by ‘third-generation’ platforms will facilitate transfer of sequencing into areas such as the clinical environment, where it could transform aspects of disease detection and


30 Drug Discovery World Spring 2013


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