NGS Expert Blog

Scientists at GATC Biotech AG and LifeCodexx AG have just begun the clinical validation study of a non-invasive, prenatal diagnostic test based on next generation sequencing with IlluminaHiSeq 2000 technology. The test detects fetal trisomy 21 and is based on the sequencing cell-free fetal DNA from maternal blood.

At least 500 samples are required for the study and the launch of the prenatal diagnostic test onto the market is planned at the end of 2011. It keeps exciting what Sequenom and Verinata are doing in the meanwhile…

The June webinar of the free NimbleGen webinar series is talking about
Genome-wide studies of copy number variation and exome sequencing identify rare variants in BAG3 as a cause of dilated cardiomyopathy >

For further information and registration, please visit the NimbleGen website.

Ten years ago the DNA sequence of the human genome was deciphered – the blueprint of our body. However, listing the single parts of a motor does not explain how it works. The same is true for the letters of all the chromosomes: Reading them does not explain how the genome regulates the necessary steps to develop from a fertilised egg to an autonomous individual.

How is the genome conducting the symphony of all the biological activities in a living organism?

New microscopic techniques allow us to study the organisation of chromosomes in the nucleus, with a big surprise. Different cell types sort their chromosomes differently. Silent genes are more in the periphery of the nucleus, while the active ones are found in the centre together with the transcription machinery. The review from Tom Mistelli in the journal Scientific American inspired me to read more about this fascinating detail of gene regulation.

An interview with Tom Mistelli can be found here and here is additional literature from Cell and Science.

The 4th Congress of European Microbiologists > provides latest information on microbiology. The congress, organized by The Federation of European Microbiological Societies (FEMS),  will be a chance to discuss solutions to future challenges and to provide topical coverage of key disciplines.  Some of them are:

• Clinical microbiology and pathogenesis
• Food microbiology
• Molecular microbiology and genomics

RNA-Seq is replacing more and more the microarray analysis for quantitative comparison of expression levels in different samples. Several studies have compared independently both techniques with respect to accuracy and reproducibility. All of these have reported the superiority of RNA-Seq (Richard et al., 2010 and Sultan et al., 2008).

 Microarray systems rely on hybridization. Background hybridization levels or signal saturation constrict accurate quantification of the expression pattern of low and high abundance transcripts, respectively (e.g. Gautier et al., 2004 and Mortazavi et al., 2008).  Provided that sufficient sequencing depth is applied, RNA-Seq does not show these kinds of limitations. This was demonstrated by e.g. Wang et al., 2008 who compared RNA-Seq read counts to published qRT–PCR measurements for hundreds of genes. They have observed almost linear relationship across five orders of magnitude.

The added value of RNA-Seq is that it enables the identification of new splicing variants and new transcription initiation sites. In addition, the quantification of particular exon and splicing isoform expression at a genome-wide scale is possible. Using RNA-Seq significant differences in gene isoform expression level and transcriptions start sites were found recently between normal and Alzheimer’s disease brain tissue (Twine et al., 2011). This result provided a big step forward in Alzheimer’s disease research.

Given the better accuracy and the add-on values in my opinion RNA-Seq will become an essential technique for researchers analyzing genome-wide gene regulation in any species. This essentially being true where reference sequences are available. Further decrease in costs of next generations sequencing will even facilitate this development.

Have you made first experiences with RNA-Seq in terms of expression profiling that you want to share with other blog visitors?

Find here further features of the Pacific Biosciences serial:

>> New Biology Part II: Cancer

>> New Biology Part III: Infectious Disease

>> New Biology Part IV: Food & Conclusion

Real infotainment by Pacific Biosciences talking about future biology: The serial starts with a smart introduction about cutting-edge technologies that provide the opportunity to create predictive models of living systems, and gain wisdom about the fundamental nature of life itself.

Eurofins MWG Operon is organizing NGS roadshows throughout Germany. After our visits to the Bavarian cities Würzburg and Erlangen the next stops on the tour will be Hamburg (May 24^th), Kiel (May 25^th) and Berlin (May 26^th). On June 20^th, we are inviting to our roadshow in Freising (near Munich). In Baden-Württemberg we are looking forward to welcoming you on June 7^th to Tübingen, on July 11^th to Heidelberg and on July 12^th to Freiburg.

Core of the roadshows are presentations on NGS technologies and examples with a focus on latest developments. Subsequently interested parties have the opportunity to discuss projects in face-to-face conversations with our NGS experts.

For more information please see the official invitations.