Genomics
treatment. Many other potential approaches to sequencing (eg Oxford Nanopore Technologies) are at various stages of development towards full commercial release, generating considerable excite- ment and raising hopes of even more spectacular improvements. It seems that the emergence of ‘third-generation’ sequencing platforms and of novel approaches to sequencing chemistry will ensure that the sequencing revolution is likely to continue apace. HTStec’s Next-Generation Sequencing Trends 2012 survey and report1 published in December 2012 set out to explore end-user experiences, prac- tices, preferences and metrics in NGS and to understand future requirements. The report also details interest in purchasing new instruments, alternative purchasing scenarios and expectations for ‘third generation’ sequencing platforms. We now report on some of the survey findings and dis- cuss them with reference to the latest developments in NGS.
Where is sequencing being done? The location where most survey respondents’ next generation sequencing (NGS) activities were undertaken was in their own lab, using instru- ments belonging to their organisation (34%). However, a substantial proportion of respondents carried out their NGS activities at commercial fee- for-service providers (CROs) (24%), or at a central facility using instruments jointly operated by their own organisation and collaborators (22%). Other locations for respondents’ NGS activities included at a third-party collaborator’s lab (11%), at a third-party not-for-profit facility (7%) and at other (undefined) places of sequencing (1%) (Figure 1).
What sequencers are most used? Survey respondents are using a wide range of NGS instrument platforms to generate sequencing data. The most used NGS instrument platform was the Illumina HiSeq 2000/1000 with 39% of respon- dents using. This was followed by 35% using the Roche 454 GS FLX+, 31% Illumina MiSeq, 28% Ion Torrent PGM, 26% Illumina Genome Analyser IIx, 20% Illumina Hiseq 2500/1500, 12% ABI SOLiD 5500, 12% Roche 454 GS Junior, 5% Pacific Biosciences RS, 3% Illumina HiScan SQ, 3% ABI SOLiD 4Hq, 1% Intelligent BioSystems/Azco MAX-Seq and 1% Intelligent BioSystems/Azco Mini-Seq (1%) (Figure 2). Most survey respondents either had access to one sequencing unit in their lab (34%), or they used the sequencers at a collaborator or service facility and did not know the exact number of
Drug Discovery World Spring 2013
Figure 3: Sequencing units available to survey respondents in their own lab/sequencing facility
0% 5% 10% 15% 20% 25% 30% 35% 40%
35% 34%
13% 7% 4% N/A None 1 © HTStec 2012
Figure 4: Next-generation sequencing applications most run today
Targeted resequencing mRNA-seq
Whole transcriptome sequencing
De novo whole genome assembly
Metagenomics Small RNA-seq
DNA methylation analysis ChIP-seq
CLIP-seq © HTStec 2012 8%
0% 5% 10% 15% 20% 25% 30% 35% 40% 45% 50% % Running
20% 16% 30% 23% 35% 43% 49% 47% 2 3
3% 1% 1% 0% 1% 0% 1% 1% 4
5 6 to 10 11 to 15 15-20 20-25 25-50 >50
Figure 5: Primary focus of survey respondents NGS investigations
Microbial genomics Cancer
Other human genetic disease Bioinformatics Other
Regulation of gene expression (including epigenetics) Developmental biology
Pathogen genomics/genetics Molecular ecology
Neurological disease Metabolic disease
Developing sequencing technologies
Human evolution
0% 1%
0% © HTStec 2012
5% 10% 15% 20% % Investigating
3% 3%
5% 5%
6% 13% 12%
11% 11%
17% 15%
31
% Responding
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