Monday, September 5, 2011

Shaping Cancer Diagnosis: Looking at the Horizon of Next Generation Sequencing and Targeted Resequencing

Two articles in this week's issue of Genetic Engineering & Biotechnology News reviewed recent trends in the next-generation sequencing and targeted resequencing technologies.  These advances are expected to further impact cancer diagnostics and treatment decision-making.

Harry Glorikain and Brian Clancy of Scientia Advisors described business trends in next-generation sequencing:

  1. The shift of sequencing service (or activity) from small labs to large labs, companies and consortia will continue to accelerate, and so will be the outsourcing of sequencing service.
    Since the capital cost of increasingly desktop-based high-throughput sequencers continues to drop, the value chain involved in consumables and sample preparation and logistics will take center stage.
  2. Overall, the share of cost of instrumentation and tools to informatics will decrease.  Increasingly larger portion of budget will be allocated to IT infrastructure, data crunching, analysis and presentation in format that is accessible to doctors.  There will be a push towards industry-wide standardization driven by FDA guidelines.
  3. Over time, genome-wide sequencing will replace other methods as the first diagnosis tool for cancer (genome-first cancer-care paradigm)--such a paradigm, Glorikain and Clancy say, has a potential to act as disruptive technology, replacing entire clinical labs, immuno and molecular diagnostic labs and people, causing the equivalent of powerlooms making weavers redundant.

Richard Stein talked about the advances in targeted resequencing technology and re-iterated its advantages over whole-genome sequencing.

  1. Targeted resequencing uses 80-mer oligos to capture and sequence human exomes.  Targeted resequencing can be used to provide validation of genetic mutations.  The first generation technology, developed by Hanlee Ji of Stanford, and publicly and openly available at the Human OligoExome website (, is capable of resequencing one megabase sequence from just tens of nanograms of DNA.
  2. An extension of targeted resequencing is targeted RNA-Seq.  Targeted RNA-Seq allows analysis of cDNA libraries, providing a view of human transcriptome.  This one tool provides information of multiple aspects of gene expression and RNA biology: alternative splicing, presence and quantification of novel fusion transcripts, and allele-specific expression.
  3. A related technology being developed by Helicos BioSciences based in Cambridge, Mass., uses DNA shearing and single-strand DNA capture technique (on a flow cell matrix,) followed by sequencing.  The capture step obviates the need to amplify DNA isolated from clinical samples.  This technology also allows identification of large deletions or insertions.

Articles quoted:
  • Sequencing trends worth watching. Glorikian H and Clancy B. Genetic Engineering & Biotechnology News. Sept. 01, 2011. 31(15)18-20 | FullText |
  • Targeted resequencing hits bull's eye. Stein RA. Genetic Engineering & Biotechnology News. Sept. 01, 2011. 31(15)32-34 | FullText |
About Targeted Resequencing
Several genomic companies have developed their preferred workflow and protocols.  Some general references are below:

(From: Nature Methods 7, June 2010 | Link | Febit Biomed GmbH, Heidelberg, Germany)

  • Targeted resequencing of candidate genes using selector probes.  Johansson H et al. Nucleic Acids Res. 2011 Jan;39(2):e8 | PubMed | FreeFullText |
  • Overlapping pools for high-throughput targeted resequencing. Prabhu S and Pe'er I. Genome Res. 2009 Jul;19(7):1254-1261. | PubMed | FreeFullText |
  • Targeted resequencing for large-scale genomic studies: accelerating NGS throughput using molecular barcodes.  Nature Methods 7 June 2010 | DOI | FreeFullText |
  • Targeted Resequencing.  By Stuart Brown. Next-Gen Sequencing (blog). May 08, 2009 | Link |

Diagnostic Trailblazers in San Diego Advancing CDx, PGx and PM Goals in Cancer.  March 20, 2011. Johansson H, & et al (2011). Targeted resequencing of candidate genes using selector probes. Nucleic acids research, 39 (2) PMID: 21059679


  1. This is very comprehensive. I have been looking for those resource site. Thank you for the highly detailed information.

  2. With its unprecedented throughput, scalability, and speed, NGS Next Generation Sequencing enables researchers to study biological systems at a level never before possible. Today's complex genomic research questions demand a depth of information beyond the capacity of traditional DNA sequencing technologies. Next-generation sequencing has filled that gap and become an everyday research tool to address these questions. Next generation high-throughput sequencers are given for metagenomics, exome & dna pyro-sequencing for multi-omic & bioinformatic. Keep Learning.