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Clinical Genomics Using NGS Approach

Video by Cambridge Healthtech about the impact of next generation sequencing on clinical genomics.

Nazneen Aziz of the College of American Pathologists and Konrad J. Karczewski of Stanford University are talking about analytical and bioinformatics standards, personal analysis, challenges and interpretation services.

Recently Launched Tools for Genomic Sequencing

Costs for DNA sequencing decreased tremendously the last years. New technologies and better methods cause that rapid drop in prices.
On the other hand, the field of sequencing is pushed forward with

  • methods to enrich nucleic acid samples,
  • kits that simplify library preparation from a variety of samples, and
  • services to assist the researcher with all aspects of sequencing.

Read more at the Nature Product Focus; the article was published in Nature 26 September 2013

Interview With Dr. Georg Gradl About Genome Sequencing

georg_gradl_lowBehind the scene…

You may know that Floragenex and Eurofins MWG Operon launched a new partnership to promote RAD sequencing.

As part of Floragenex’ series of interviews on genomic applications, they talked to our colleague and NGS expert Dr. Georg Gradl about his experiences with de novo genomic sequencing.

Check out the interview

Whole Genome Sequencing And You

What is a genome? What are the basics of how whole genome sequencing works? What are the potential benefits and risks? Or do you just want to learn a bit more about this technology?
Ths video was developed by researchers at Mount Sinai’s Department of Genetics and Genomic Sciences and Department of Emergency Medicine with funding from the Charles Bronfman Institute for Personalized Medicine.

Just take a cool drink and relax while watching the video.

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.

Amplicon Sequencing Strategy: What Is Your Technology Of Choice?

amplicon_sequencingWe asked for your favourite technology for amplicon sequencing.

Please find the results here:

  • The majority (41 people) voted for Illumina MiSeq due to the data output
  • 29 prefer Ion Torrent for amplicon sequencing
  • 24 favour Roche 454 because of the long reads
  • 6 people say that classical Sanger sequencing is their technology of choice
  • Just 4 are using other technologies

104 NGS experts took part in the voting.


High-Throughput Sequencing Machines By Platform

The High-Throughput Sequencing map by James Hadfield (Cancer Research UK, Cambridge) gives us a very interesting overview about sequencing activities around the world. We ran a survey to find out if your favourite machines correspond with the platforms listed by James in his overview.

Here are the results: Your personal favourites are nearly a perfect match with platforms in the genome centers worldwide. Great match!



The British Ash Tree Genome Project

ash_treeMid of March we wrote about the British Ash Tree Genome Project.

Yesterday, the School of Biological and Chemical Sciences, Queen Mary University of London launched a website explaining in detail their amazing project: Find there general information, data and tools. Further, an interview on the project from the Radio 4 Today programme on 21/12/12 can be heard here. More details on the project can be heard on NERC’s 5/2/13 Planet Earth podcast.


Genome Sequencing Analysis of Ash Tree – Supported by £2.4 Million

ash_treeTo conduct genome sequencing and analysis of Ash (Fraxinus excelsior), researchers in the UK received £2.4 million ($3.6 million / €2.8 million). The major aim of this project is to increase the understanding of the wide spreading fungal tree disease, which is widespread in northern Europe and has already been found at more than 300 sites across the UK (see Those fungi attack ash tress but some tress resists those attacks.

For this reason a lot of samples of the ash dieback fungus will be sequenced and – funded by an urgency grant from the Natural Environment Research Council – the complete genome sequence of Ash is aimed to be available by August.

Sequencing of the approximately 900 Mb plant genome will be performed applying the latest hybrid de novo sequencing strategy, recently proven to deliver excellent scaffolding and assembly results. This new golden standard in de novo sequencing employs a combination of Roche/454 FLX++ long read technology (software version 2.8 with read lengths up to 1,100 bp) and Illumina HiSeq 2000/2500 high throughput sequencing with several ultra-accurate long jumping distance libraries (LJD of 3kb, 8kb, 20kb and 40kb), supplemented by sequencing of Illumina shotgun libraries with different fragment sizes.

With the sequenced ash tree genome the researchers hope to hold clues to how some of the trees (2% are able to defend the disease) are able to resist attack, and knowledge about the genetic differences between resistant and non-resistant trees. This knowledge could be used to develop trees that can’t be infected.

Project leader, Dr. Richard Buggs from Queen Mary’s School of Biological and Chemical Sciences: “Sequencing the ash genome is a foundational step towards discovering the genetic basis of resistance to ash dieback – the future of ash trees in Britain may depend on this”.

Read more about that exciting project at GenomeWeb about the general project and at Eurofins MWG Operon about the genome sequencing.

The Galaxy of the Genomics Virtual Lab

The Genomics Virtual Lab (GVL) project – using the computing resources from the NeCTAR Research Cloud – is an Australian Government project conducted as part of the “Super Science” initiative. It is developing infrastructure supporting genome informatics research.

Their Galaxy-based NGS and HTS tutorials are really excellent:

You will love the precise explanations, the hands-on demonstration and the additional material like screenshots and in-depth information!