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).
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sequence will be placed online in an archive available to historians, scientists and the public, although Ibsen’s will not be published.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.
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?
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.
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.
The 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.
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.
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.
Eurofins 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.
By using novel microfluidic tools, a team of researchers at Indiana University School of Medicine uncovered an unexpected ability of cancer cells to navigate and exit microscopic mazes along the shortest path. To explain this behavior, they propose a novel mechanism that guides cancer cell migration.
Find out how they have harnessed RNA-seq on tumor tissues to reveal efficacious drug targets and implement rational drug combinations in triple-negative breast cancer. Further, ongoing work on how RNA-seq is being used for biomarker discovery in retrospective cancer clinical trials will also be presented.
A multidisciplinary team in the Eurofins flagship Genomics laboratory in Ebersberg, Germany, has successfully completed a research project to genetically discriminate “identical” monozygotic twins.
So far there have been only theoretical considerations against the experimental finding and dogma that monozygotic twins are genetically fully identical. Statistically, around 6 of 1,000 males are identical twins. Up to now, forensic DNA fingerprinting testing could not be used in crime or paternity cases involving identical twins, as there was no possibility of genetically discriminating between them. Such cases are regularly discussed in the World’s press, including murder, child custody and heritage cases. Forensic laboratories around the world had accepted these analytical restrictions, but Eurofins scientists wanted to push these limits of DNA testing. They used the unique combination of leading forensics and genomics labs available at Eurofins to reach this milestone.
Technically, the scientists applied ultra-deep next generation sequencing and associated bioinformatics techniques. They sequenced DNA from sperm samples of two twins and from a blood sample of the child of one twin. Bioinformatics analysis revealed five mutations, so called Single Nucleotide Polymorphisms (SNPs) present in the twin father and the child, but not in the twin uncle. The SNPs were confirmed by classical Sanger sequencing. The results give experimental evidence for the hypothesis that rare mutations will occur early after or before the human blastocyst has split into two, the origin of twins, and that such mutations will be carried on into somatic tissue and the germ line.
The dataset in this project equaled a total of 241 human genomes, resulting from up to 94 fold genomic coverage of the involved three individuals.
The peer-reviewed study “Finding the needle in the haystack: Differentiating “identical” twins in paternity testing and forensics by ultra-deep next generation sequencing” is published in the renowned journal Forensic Science International: Genetics, Available online 8 November 2013, ISSN 1872-4973, http://dx.doi.org/10.1016/j.fsigen.2013.10.015.