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Note: Affordable prices to distinguish between identical twins

“While traditional DNA tests fail to distinguish monozygotic twins, Eurofins developed a test which can achieve exactly that ,” says Georg Gradl.

“If they ask for $160,000, they should ask us,” Georg continued. “We have a good chance to go significantly under that.” Read the article…

WANTED: NGS Expert to support our team in Germany

NewsTo support our team in Ebersberg near Munich we are looking for a Next Generation Sequencing Specialist.

Your tasks:

  • Sell NGS products
  • Be in charge with projects and customers
  • Represent the company and its products and services at meetings, fairs and events
  • Be responsible for the overall sales cycle
  • Support the field sales team in your role as NGS expert
  • Take care of internal processes

Your skills:

  • Experience in the field of NGS
  • Excellent communication skills
  • Focus on customers
  • Positive and entrepreneurial thinking
  • Proactive attitude

Interested? Just visit our website and send your application to application-eu@eurofins.com.

Breaking the Human Genome Code

On one hand side we are able to sequence anyone’s genome cheaply and quickly due to latest technologies. On the other hand side we are at the beginning to discover the true meaning of individual genomes. This is the reason why the lecture has the subline “Opening Pandora’s Box”.

Professor Winston Hide talks about newly arising questions such as:

  • If you have your genome sequenced, who should see it?
  • How can we safely share a genome without ending up opening a whole new form of cybersnooping?
  • How could the new technologies be used to predict a person’s predisposition for Alzheimer’s, Parkinson’s or motor neurone disease?

Sorry, No Identical Genomes

We asked you about the findings that identical twins do not have identical genomes. Find the results here:

identical_twins

Has the time come for validated NGS panels?

Clinical validation** Challenges of validating next generation sequencing panels ** Advantages and disadvantages of FDA-cleared products **

Most of us endorse that NGS can and should be used as part of clinical molecular diagnostic testing menus. On the other hand side developers of next generation sequencing-based assays agree that there are still significant challenges in developing clinical NGS-based gene panels – from the sequencing technology itself to differences in laboratories’ bioinformatics pipelines, DNA extraction and sample prep protocols, as well as differences in the sample itself.

Please keep apart: assay development and validation

It is important to note that the assay development process should be separated from the validation process:

  • Generation of a protocol for the whole diagnostic test is the main focus of the assay development.
  • The downstream process is important to validate sequencing-based clinical assays. Maybe you are interested in the CAP checklist for NGS in clinical labs.

Researchers should keep in mind that some of the main challenges of assay development and validation have nothing to do with the sequencing itself.

Pros and cons of FDA-cleared products
Pro Contra
  • FDA-cleared in vitro diagnostic tests could resolve some of the issues of developing and validating LDTs
  • No development and validation costs for the lab (Instead, they must verify that the assay performs according to the FDA label)
  • Expensive compared with LTD
  • Dependency on the vendors for trusting their validation and that they will be able to supply reagents
Accounting exercise for cleared products vs. LDTs

Currently, the only FDA-cleared NGS-based tests are Illumina’s 2 cystic fibrosis assays that run on its MiSeqDx system.

A 139-variant assay kit for example has a list price of approx. €6,800 including two runs on the MiSeqDx. Up to 45 patient samples can be multiplexed per run, which could cost €80 per patient.

It is an impressive difference if it is compared with a cystic fibrosis LDT that can be run for less than €45 per patient excluding development and validation costs.

Even more expensive is the full-gene assay by Illumina with a list price of approx. €56,000 including six runs and the ability to multiplex between six to eight patients per run meaning €1,600 per patient. Just keep in mind that costs could soar to €9,500 per patient, compared to an LDT that could sequence the entire CFTR gene for €180.

 

Let’s see what time will bring. There are many aspects that need to be discussed regarding labs’ ability to tweak tests or to combine elements of different technologies and protocols to solve problems.

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What about you? Are you using panels or homebrew protocols for your NGS projects, like exome sequencing or cancer testing? Just participate in our poll.

How to handle variants in a reference genome

When talking about genome sequencing the human genome project is one of the best known projects. “Building” a reference genome that helps to identify disease-causing mutations is only one of many goals for the human reference genome.

But I am sure that all of you already asked the question: how can a reference genome even exists? On earth we have more than 7 billion people and among that many different characteristics. So how can one human reference serve for all mankind?

The Global Alliance, lead by David Haussler, recently won a $1 million grant to create a graphical model of the human genome (BioTechniques). The graph model should help to visualise variants as alternate pathways. Like that a more comprehensive picture of “naturally occuring variants” and disease causing variants might be gained. To support this approach, they got access to 300 complete human genome sequences from the Broad Institute in Cambridge.

From my point of view this is a great idea and I hope it helps to further pave the way how the massive amounts of sequencing data can be handled and interpreted in the near future!

Read the complete article at BioTechniques.com

 

Revealed WGS of Oil Accumulating Diatom

bio-fuelMicroalgae are promising sources for biofuel production through the generation of carbon-neutral sustainable energy.

Biofuel from microalgae receives attention because it reduces CO2 emissions and does not use resources required for food production. A Japanese team revealed the whole genome sequence (WGS) of a marine diatom, Fistulifera solaris JPCC DA0580, which had been screened from their culture collection of microalgae (Tanaka et al., Plant Cell, 2015) as highly capable of oil accumulation. They said de novo assembly of this genome is so tough because it is alloploid, which means it has a very complex genome structure.

Finally, they could annotate about 20,000 genes on 42 chromosome pairs. They also identified a lot of genes which concern oil synthesis and, furthermore, they also analyzed activation patterns of these target genes.

I am sure this study will be a model case to highlight how NGS technologies can accelerate bioengineering!

New Illumina Instruments

HiSeq_picsNew Year – New Innovations. Illumina directly starts off 2015 with a huge announcement: the launch of 4 new systems (GenomeWeb, 12th Jan).

Here a short overview of the new systems:

  • HiSeq X Five – scaled down version of the X Ten; costs: $6 million
  • HiSeq 3000  – uses a single flow cell and offers a lower price per data point than the HiSeq 2500; half the throughput (750G) as the HiSeq 4000; costs: $740,000
  • HiSeq 4000 – uses a dual flow cell and can sequence up to 12 genomes or 180 exomes in 3,5 days or less; costs: $900,000
  • NextSeq 550 – combines microarray scanning with NGS; applications: cytogenetics & prenatal genetic diagnostsis; costs: $275,000

Now I am curious to see if also other providers will have such surprising news as Illumina. We will keep you posted…