Tag Archives: sequence capture

Global Next Generation Sequencing Market in Clinical Applications

A brand new market research by BCC Research was announced yesterday: “Next Generation Sequencing Emerging Clinical Applications & Global Markets”.

The report wants to provide an in-depth analysis of the clinical next generation sequencing (NGS) industry. The approach of analysing the industry is taken in terms of workflow (e.g. sequencers, sequence capture, informatics) and key indications where NGS diagnostics will have market share by 2018.

Key findings of the NGS market research:ngs_survey

  • The global market for sequencing products was nearly $3 billion in 2011. It is forecast to grow at a compound annual growth rate (CAGR) of 17.5% to reach $6.6 billion by 2016.
  • Sequencing instruments and consumables made up the largest market segment in 2011, with revenues of nearly $1.6 billion.  BCC expects this market to grow to $2.2 billion by 2016, a CAGR of 7.3%.
  • The sequencing services market was $838 million in 2010, which reached nearly $988 million in 2011. Sequencing services comprise the fastest-growing market segment with a 29% CAGR estimated to reach $3.5 billion by 2016.

The research examines the markets for NGS diagnostics for the years 2012, 2013 and 2018.
Unfortunately the report costs about $5450. More details on BCC Research.

As soon as there are details and results available, we will share them with you.

Comparison of Exome Enrichment Technologies in Nature Biotechnology

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Very recently researchers from Stanford University systematically investigated performance of the most widely used exome enrichment platforms:

  1. Roche/NimbleGen’s Seq Cap EZ Exome Library v2.0 (44 Mbp)
  2. Agilent’s Sure Select Human All Exon (50 Mbp)
  3. Illumina’s Tru Seq Exome (61 Mbp)

One of the findings of the study is: When comparing coverage efficiency at constant read depth (80 million reads each) NimbleGen Sequence capture is by far better than the other two platforms. With NimbleGen sequence capture 98.6 % of all targeted bases were covered at least 10x, while Agilent’s Sure Select and Illumina’s Tru Seq covered only 89.6 % and 90.0 % of all bases at least 10x. In my opinion, the different target sizes of the exomes should have been taken into account. In this case the read depth should have been normalized according to the exome sizes. Independent of the missing normalisation it is however clearly shown in the paper that the NimbleGen technology enriched a much higher percentage of the targeted bases than the other two products..

Other criteria that were compared are the off-target enrichment rate (NimbleGen performed best) as well as the enrichment bias owing to GC content (Agilent performed best).

The decision, which platform is best for a specific scientific question should also be influenced by the individual target regions covered by different Exome kits. Agilent’s and NimbleGen’s exomes share 38 Mbp of their target regions. Apart from that Agilent’s Exome covers better Ensembl genes, while NimbleGen’s Exome covers a greater portion of miRNAs. Illumina’s exome, although displaying low coverage efficiency, is designed to capture UTRs in addition, which by now are almost not covered by the other designs and is therefore the choice, if those regions are of interest.

Differences in the performance come from the different oligonucleotide designs. I therefore postulate similar key parameters when using the customised versions of the capture technologies.

DSRG Study: Independent Comparison of Custom Target Enrichment Methods

The DNA Sequencing Research Group (DSRG) from the Association of Biomolecular Resource Facilities (ABRF) has made it its task to provide material that helps researchers to evaluate performance relating to this topic. Recently the group has compared capture technologies for the enrichment of selected genomic regions from genomic DNA. The technologies that were compared are the Agilent SureSelect Enrichment method as well as the array and in-solution (Seq Cap EZ Choice) capture technologies from Roche NimbleGen.

Please have a look yourself which technology performed best in the comparison.