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…

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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.

RAD-Seq for Genome Wide Association Studies

Dear NGS Expert Blog reader,

To kick off the 2014 discussion on RAD Sequencing for the NGS blog, I wanted to share some results from a recently published study describing the use of RAD for high throughput SNP genotyping in Miscanthus.

miscanthusThe tropical grass Miscanthus is an intriguing candidate for bioenergy crop development: It is well adapted to grow in environments worldwide, does not require intensive agricultural efforts to cultivate and is capable of producing large amounts of biomass. To illustrate this point, cultivars of Miscanthus giganteus are capable of growing over 3.5 meters in a single year! With such promise as a bioenergy solution, a number of research groups are working on modernizing breeding efforts in Miscanthus and integrating genomic technologies to help develop superior varieties.

Our group at Floragenex assisted in one recent published study, which illustrates how RAD sequencing was able to facilitate the rapid generation of sizeable molecular resources to aid in a genome wide association study (GWAS). The goal in a GWAS study is to identify a set of genetic variants that tend to be associated with specific traits that are observed in natural, unstructured populations. Some interesting highlights from this paper:

RAD-Seq was able to identify over 100,000 single nucleotide variants (SNVs) across 138 Miscanthus plants. The large number of markers is advantageous for association studies, where understanding the organization of the genome at high resolution is key.

Without an assembled Miscanthus genome, we accomplished variant calling with a two-pronged approach

  • a comparative genomics strategy using the Sorghum bicolor genome as a reference and
  • a de novo clustering approach using the Miscanthus RAD data.

Both were successful methods for high quality SNV discovery and genotyping.

After filtering, approximately 20,000 and 30,000 high quality markers, respectively, were genotyped across the Miscanthus population using the two approaches. After genotyping was complete, the comprehensive genome wide association analysis described in the paper showed statistically significant marker-trait associations for seven key Miscanthus treats, including lignin content, plant moisture and stem diameter. These traits are important for bioprocessing of plant material and the results suggest marker-assisted and genome selection studies could be effective tools in Miscanthus breeding.

The full article, entitled “Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis” can be found at New Phytologist:  http://www.ncbi.nlm.nih.gov/pubmed/24308815

As a co-author on this exciting publication, I would be happy to answer any of your questions on this paper, so do not hesitate to post them. For my next post, I will be comparing many of the new fractional sequencing technologies being utilized for NGS genotyping.

Cheers,
Rick Nipper,
President, Floragenex

Possibility of Ideal Intestinal Remedy

I’m not able to keep intestinal condition without remedy which is prepared by Lactobacillus, Bifidobacterium, Lactococcus, and others. Eating yogurt is also okay for this purpose, ad personam I prefer to take these bacterial tablets and believe more effects. However, many people know these effects of current intestinal remedies are mild not fast-acting properties.

Several reports mentioned that intestinal bacterial flora and its regulation were not simple. It is starting discussion that natural immunity may regulate intestinal flora; e.g. antibacterial peptide α-defensins which is secreted from paneth cells on small-intestinal epithelium could regulate flora distribution (Salzman et al., 2010; Matsuda et al., 2011). By contrary, very simple strategy is reported as following: Clostridium difficile brings bad diarrhea that was resistant to antibiotic. Van Nood and co-workers (2013) injected healthy person’s feces into patient’s guts, and its curative effect was so good surprisingly, but we cannot call it a remedy!

Two NGS platforms, GS FLX/Junior and MiSeq, can perform distributional analysis via deep sequencing of 16S-rRNA amplicons. But it is still difficult for both platforms to do metagenome assembling for getting whole gene information in flora, because their read length is not long enough to make reliable contigs without chimeras between different bacteria one another. Therefore I strongly expect that super long read platforms including PacBio RS series and coming nano-pore technologies will break current limitations and will contribute to develop ideal intestinal remedy for my instable stomach.

Tumor Heterogeneity And The Underlying Genetics

Although this recorded seminar is promoted by Illumina, I still can recommend it as a very good talk about basic concepts on tumor heterogeneity and the underlying genetics. Kenneth Bloom, Chief Medical Officer at Clarient (GE Healthcare) and a pathologist, explains the needs for the application of NGS in clinical lab in a simple and very vivid manner. While watching this video I gained a better idea of the needs of a diagnostics lab and the challenges in developing a diagnostic NGS panel.

CSP for human exome sequencing with Ion Proton

Ion Proton System  - Front FacingEurofins MWG Operon joined the exclusive certified service provider program from Life Technologies. Using the Ion AmpliSeq Solution for human exome sequencing on Ion Proton offers several advantages:

  • Flexible number of samples: starting from 1 exome up to 96
  • Fast turnaround times: 5-10 workding days
  • High data quality: mean coverage ~ 100x;  mean read length ~ 160 bp
  • Low input material: starting from 250 ng / sample

Learn more about human exome sequencing at Eurofins here.Ion Proton