Targeted Resequencing (TPS/WES) Tops Next Gen Sequencing Survey

Oxford Gene Technology (NGS provider currently listed on Genohub) recently presented the results of their next gen sequencing survey which demonstrated targeted resequencing as the top use for next generation sequencing. The results are based on a survey of 596 researchers who responded regarding their current and expected use of NGS services. When compared to the results for whole genome sequencing the popularity of targeted resequencing is possibly attributed mostly to the lower cost of targeted resequencing. This infographic depicts the results:

OGT NGS Survey Results

OGT NGS Survey Results

Other interesting results point to a general data problem with 38% of respondents saying they lack trust in bioinformatics data. Bioinformatics also leads the field when researchers were asked about the biggest barrier to NGS usage (see below).

Barriers to NGS Usage

Barriers to NGS Usage

Undoubtedly this presents an immense opportunity for the bioinformatics sector to increase confidence in data accuracy and interpretation which could have a positive impact on the use of next gen sequencing as a whole.

You can find many more interesting survey results on the excellent infographic titled Oxford Gene Technology – NGS Survey 2013.

First XPRIZE Cancelled Due To Unexpected Innovation in Next Gen Sequencing

For the first time ever, an XPRIZE has been cancelled. The reason — unexpected innovation in next generation sequencing. The Archon Genomics XPRIZE announced in 2006, had promised to award $10 mil to the first team that was able to accurately sequence 100 whole human genomes at a cost of $10,000 or less per genome in a short period of time. The competition was cancelled as XPRIZE CEO Peter Diamandis and team felt it was not serving its intended purpose to incentivize technological innovation in gene sequencing.

As stated by Peter Diamandis, “Every XPRIZE is carefully designed to address a market failure and hopefully create a new industry to achieve breakthroughs and solutions once thought to be impossible.” Although the Archon Genomics XPRIZE was conceived according to this criteria, the XPRIZE team felt that innovation in gene sequencing has been progressing independently of the XPRIZE incentive, therefore voiding the need for the competition.

The rapid innovation in next generation sequencing has caused sequencing times to decrease and prices to plummet to around $5,000 per genome. The XPRIZE team feels as if the targets laid out by the competition will be met in the very near future with or without their incentive, and have opted to cancel the XPRIZE and return the money to sponsors. The announcement by Peter Diamandis can be read in its entirety on the Huffington Post.

The logic behind the XPRIZE cancellation seems clear, however it remains to be seen what backlash, if any, arises from scientists who may have spent considerable time and effort devoted to meeting this challenge. Although next gen sequencing instruments are developed by large companies such as Illumina ($1.15B revenue), which may not be driven by a competition like the XPRIZE, innovation in this field must also be attributed to the wider research community, of which a team may have conceivably won the competition independent of any large commercial enterprise. In fact, in his cancellation announcement, Peter Diamandis thanks George Church and the Wyss Institute at Harvard for registering for the competition. Does the XPRIZE lose some of its ability to incentivize future competitions because of this cancellation? We welcome your comments on the matter.

How to Select the Best Next Generation Sequencing Platform For Your Project

We often get questions from researchers on selecting the best next generation sequencing platforms for specific projects. We are glad to offer free consultation to researchers on inquiries such as these among others. We also offer a sequencing guide to get you started.

Another great resource is a YouTube talk by Dr Elaine Mardis, a professor of Genetics and Molecular Biology and the co-director of the Genome Institute at the Washington University School of Medicine. She begins by discussing next gen sequencing instrument similarities, such as library amplification, nucleotide detection, read lengths, and paired end sequencing. She then dives into the factors unique to individual next gen sequencing instruments by Roche 454, Life Technologies, Illumina, Ion Torrent, PacBio, and Oxford Nanopore. The discussion focuses on the benefits and dissimilarities among them associated with:

  • Paired end reads: linear vs circularized fragments
  • Sequencing technologies: DNA polymerase, DNA ligase, synthesis H+ detection, syntheses, and nanopore
  • Library amplification methods: emPCR, bridge amplification, and its absence in some 3rd gen platforms
  • Run times
  • Error rates
  • Read lengths

Below, you can view the video in its entirety which goes into quite some detail and discusses the best types of projects for each NGS platform.

4 Top Next Generation Sequencing Forums

Forums offer a great opportunity to mind share with like minded professionals across the globe. They offer a vehicle to ask and potentially receive quick answers to just about any industry related question. Forums also offer a vehicle for collaboration and improved decision making by harnessing the power of the crowd. So which are the top next gen sequencing forums? These 4 were selected for having the largest number of active members discussing next gen sequencing specifically.

Top Next Generation Sequencing Forums

  1. Seqanswers: A top list of NGS forums would not be complete without SEQanswers. This forum is dedicated solely to this topic. Seqanswers was founded to be an information resource and user-driven community focused on all aspects of next-generation genomics.
  2. Nature Network: Nature Network is a professional networking website for scientists around the world. It is not dedicated specifically to next generation sequencing but they do have many members active on the subject. Nature is an online meeting place where you and your colleagues can gather, share and discuss ideas, and keep in touch. It’s also where you can consult the community for answers to scientific questions or offer your expertise to help others.
  3. The Science Advisory Board: This forum has as its mission to improve communications between medical and life science professionals and the companies who provide this community with products and services. To accomplish this mission, The Science Advisory Board conducts studies about the products and services NGS professionals currently use. Companies value this information and use it to improve existing products and services or to develop new ones that better meet the needs of their customers.
  4. LinkedIn: Little explanation required. Here are the top 3 forums (based on the number of members)

Forums can be an extremely valuable tool in a career involving next generation sequencing (or otherwise), enabling both researchers and NGS providers a fantastic way to collaborate and build relationships. Undoubtedly there are other great next gen sequencing forums out there. If you have any you would like to share we would love to here about it!

Wyzer Biosciences Lists Services On the Genohub Next Generation Sequencing Market

Genohub would like to welcome Wyzer Biosciences to Genohub. The sequencing services listed by Wyzer will add more available options to the Genohub next generation sequencing market.

Wyzer listed next generation sequencing services for an Ion PGM 314 Chip.

Privately held, Wyzer Biosciences, Inc. was founded in 2011 and is located in dynamic Cambridge, MA, the home of Harvard, MIT and many other world-class educational and biotech institutions. Through their expertise in molecular biology they provide services to partners and collaborators in industry and academia that will aid them in their ongoing research. We look forward to matching Wyzer with the most compatible high throughput sequencing projects for their lab.

2 Ted Talks on the Next Generation Sequencing Impact

Here are a couple of great Ted Talks on the impact of next generation sequencing on a variety of areas that promise to fundamentally change our daily lives.

This is a good talk about the future of sequencing and the impact of massively parallel sequencing. The impact to patient care, food supply, health insurance, politics, and more are discussed.

Richard Resnick: Welcome to the genomic revolution:

http://embed.ted.com/talks/richard_resnick_welcome_to_the_genomic_revolution.html

 

More of an introductory discussion on gene sequencing. What is genomics? How will it affect our lives? In this intriguing primer on the genomics revolution, entrepreneur Barry Schuler says we can at least expect healthier, tastier food. He suggests we start with the pinot noir grape, to build better wines.

Barry Schuler: Genomics 101:

http://embed.ted.com/talks/barry_schuler_genomics_101.html

 

11 Top Next Generation Sequencing Blogs

Here is a compilation of some of the best next generation sequencing blogs for your reading pleasure:

CoreGenomics:

CoreGenomics is a personal blog written by James Hadfield who runs a genomics core facility in Cambridge. The core runs lots of next-generation sequencing and gene expression microarrays alongside other Genomic technologies.

Pathogens Genes and Genomes:

A heady mix of bacterial pathogenomics, next-generation sequencing, type-III secretion, bioinformatics and evolution.

Next-Gen Sequencing:

A working guide to the rapidly developing world of Next-Generation DNA sequencing, with an emphasis on bioinformatics.

BitesizeBio:

An eclectic blog of what could more adeptly be described as complete articles which are produced by a variety of authors with varying areas of focus.

Omics! Omics!:

A computational biologist, Dr Keith Robison’s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery.

Genomes Unzipped:

Genomes Unzipped is a group blog providing expert, independent commentary on the personal genomics industry.

In Between Lines of Code:

A blog on Biology, sequencing, bioinformatics and more, by Lex Nederbragt who works at the University of Oslo at the Centre for Ecological and Evolutionary Synthesis (CEES).

Kevin’s GATTACA World:

Kevin Gattaca’s blog with a focus on bioinformatics, genome science and next generation sequencing.

Next Generation Technologist:

A blog by Dale Yuzuki, who is a marketing professional who currently works for Life Technologies Corporation and offers a unique perspective on next generation sequencing.

Blog @ Illumina:

Of course no next gen sequencing blog list would be complete without including the most prolific next gen sequencing instrument company in the world.

RNA-SeqBlog:

A blog focused on transcriptome sequencing news.

We hope you enjoy some of the blogs on this list. Please comment if I missed any other terrific next gen sequencing blogs.