Analysis of oaks using RAD-Seq

Excellent paper just out that dissects the phylogeny of North American oak trees using RAD-Seq.sequences-per-individual

A phylogenetic study of the American Oak clade based on RAD-seq data has recently be published by PLoS ONE. The study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23-33 million year-old clade.
Associated with the paper is a new R package for downstream analysis of phylogenetic RADseq data, RADami

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data >>

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Are you a NGS expert?

Some months ago we asked you for how long you have been involved with next generation sequencing.

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Almost 200 people sent their feedback and gave us a very interesting insight in their experience with NGS. To take this into account, we want to further align our posts with the focus topics of our readers.

Feel free to send me your comments and suggestions to make ngs-expert.com even more valuable for you.

The next step after sequencing: Synthesis of a designer chromosome

Next generation sequencing allows deciphering genomes of any kind and size; But, what to do with all this information?

Now a group of scientists from the John Hopkins University in Baltimore around Jef Boeke and 79 other authors published that they have been able to synthesize one of the 16 chromosomes of the baker’s yeast. Instead of the natural 317,000 bases they have reduced the chromosome to 274,000 bases by leaving out what they regarded as redundant or not necessary to grow under cell culture conditions.

Yeast cells already today produce important substances in large fermenters. They are used for bio fuel production but also for the production of Artemisinin, a potent malaria drug.

By reducing the genome of such organisms, the perfect “factory” can be designed in the future that delivers high yield of the desired substance at a minimum cost and a minimum contamination with other undesired metabolic byproducts. The White Biotechnology is certainly a hope for our permanent growing population. A number of companies engaged in this field can be found here.

Why should I buy Illumina stock shares?

What is the impact for a company of winning an award? In case of Illumina you can cleary see it is about brand and market awareness. Only recently we reported about the award for Illumina of beeing the smartest company in 2013. Today we have a short interview for you that answers the question: why to buy stock shares for Illumina.

From my point of view the only risk of being a market leader in a highly dynamic area like next generation sequencing is, that you have a lot to loose. But Illumina is working on this. One example: only this year Illumina launched two new next generation sequencing instruments: the X-Ten for human whole genome sequencing and the Next500 – a mid-size sequencer that fills the gap between the HiSeq and the MiSeq. So let’s see what happens next…

Will Oxford Nanopore´s MinION hold its promises?

When I first heard of the Oxford Nanopore technology, it sounded rather exciting: The company proclaimed a new technology which enabled sequencing with extremely long read lengths of up to 100 kbp at a reasonable accuracy and in a very short time.

The technology is based on so-called “strand sequencing”. This technique involves a protein nanopore, in combination with a specific enzyme. This enzyme is designed to feed a single strand of DNA through the nanopore. The bases of the DNA strand are identified as they pass through the pore.

The sequencing systems are called “GridION” and “MinION”, with the GridION representing a high throughput system, and the MinION being a miniaturised system the size of a USB stick.

NewsFirst data for the GridION system have been presented in February 2012 at the AGBT conference. After that, there had been hardly any news from Oxford Nanopore for a long time. Then in November 2013, Oxford Nanopore announced an early access program for the MinION system on the ASHG meeting. They also gave demonstrations of the system to selected customers in the company´s labs. However, the company did not show any sequencing data yet. In February 2014, Oxford Nanopore has started to issue invitations to the early access program, and the first MinION systems should be shipped soon.

On the AGBT meeting in Feburary, the first MinION sequencing data, generated by Oxford Nanopore and analysed by David Jaffe from Broad Institute, Cambridge, have finally been presented.  However, the first results were rather disappointing: The average read length was way below the expectations. As reported by In Sequence, Jaffe told that the average read lengths were 5.4 kbp and 4.9 kbp for the two bacterial genomes analysed. The raw error rate of the data was not disclosed. However, Jaffe said that there were “long perfect stretches” and “blocks of errors”.  The data was not suitable for de novo assemblies from MinION data alone. In the end, the researchers used the sequences to create better assemblies from Illumina data.

On a Plant Genomics Meeting in Kuala Lumpur in the end of February, Oxford Nanopore Technologies presented more data. They claim that they could “easily obtain” 50 kbp reads. They had generated reads spanning the entire 48 kbp bacteriophage lambda genome. They also show data to underline that the read length distribution obtained by Nanopore sequencing is determined by the size distribution of the input DNA. Slides of the presentation can be viewed here.

Even if the first results are somewhat disappointing, I think this is still an interesting new technique. Like it was with the PacBio system, the technology may need more time to overcome its childhood diseases. The next few months will show if the technology can hold the high expectations that have been raised.

Illumina – smarter than Google

Technology Review‘s analysed the markets Energy, Biotech, Computing & Communications, Internet & Digital Media, and Transportation in search of the smartest company in 2013. The main criteria is to look for the company with the biggest impact on the industry, mainly driven by innovation. They put together a list of the 50 smartest companies

… and the winner is:  Illumina

Important other companies, everyone knows are well behind… – maybe also because reputation has no influence on the ranking. Here some examples:

  • Google  #3
  • Dropbox #6
  • Amazon #10
  • Siemens #24
  • IBM # 35

By the way: in last year’s ranking Illumina was not even on the list. But Complete Genomics (#11), Life Technologies (#27) and Roche (#34).

erfolg

 

 

Congratulations, Illumina!

Analysis of Richard III’s DNA to Create Complete Genome Sequence

Researchers in England are planning to sequence the entire genome of Richard III by extracting the DNA from his bone material.

Extracting ancient DNA is difficult. Dr. Turi King (Department of Genetics at the University of Leicester) will lead the project. She said it was invariably fragmentary, and it was a question of piecing together and overlaying fragments to complete a jigsaw. King will be working with Professor Michael Hofreiter in the ancient DNA laboratory at Potsdam University. The complete genome sequence will be placed online in an archive available to historians, scientists and the public, although Ibsen’s will not be published.

Richard III will be the first known historical figure to have his genes studied in this way; scientists have previously sequenced the genomes of Oetzi the Iceman, a number of Neanderthals, and most recently a hunter-gatherer from Spain.

The £100,000 ($164,000 / €120,000) cost of the project, which is expected to take at least a year, is being funded by the Wellcome Trust, the Leverhulme Trust and the geneticist Professor Sir Alec Jeffreys.

There is more than one bottleneck in NGS

The blog on NGS perspectives published recently a great survey (sponsered by QIAGEN) about the biggest bottlenecks researchers face by using the NGS technology. 26% of the 924 participants voted for the complexity of the data analysis. And from my point of view the challenge with data analysis has just begun. Because the sequencers out there produce more and more data in a single run. So high-end software solutions are a prerequisite for further usage of these machines.

What is the primary sequencing work done in your lab?

QIAGEN Survey

 

Also interesting: one of the questions from the survey asked about the applications that everyone runs with the NGS-instruments. The answers show that more and more scientists use NGS for dedicated purposes, like to know more about the expressed genes in a sample or about the mutations and existence of specific genes or gene panels.

 

 

Visit NGS Perspectives to view or download the complete survey.