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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.

Rapid Genome Sequencing in NICUs and PICUs

protocolSTAT-Seq to rapidly detect thousands of genetic diseases.

A recently published study in The Lancet Respiratory Medicine reveals the early results of the clinical usefulness of rapid whole genome sequencing in neonatal and pediatric intensive care units (NICUs and PICUs). Children’s Mercy Kansas City’s STAT-Seq test helped diagnose a genetic disease in more than one half of 35 critically ill infants tested, compared to just 9% with standard genetic tests.

Besides the medical impact on treatment strategies I want to share some information about STAT-Seq.

STAT-Seq, which runs on Illumina’s HiSeq 2500, is first of all a research protocol. It is the fastest whole genome test that might take less than 50 hours from test order to delivery of an initial report once it is fully implemented in the lab. STAT-Seq can identify mutations across the genome associated with approximately 5,300 known genetic diseases.

The study showed a significantly improved diagnosis rate for whole genome sequencing versus traditional testing. But it did not show an improvement over what is typically seen in exome sequencing. The latter only examines the parts of DNA that code for proteins, the body’s basic building blocks.

Right now exome sequencing is the more commonly used diagnostic tool because the technology is cheaper and more readily available. Cost effectiveness was not examined in the study, but the costs of genome sequencing are falling rapidly. Currently, the best available cost runs around €3,500 ($4,000), but many genomic researchers say it could drop down to €1,500 ($1,700) until the end of this year.

Whole genome testing could become a more useful tool than exome sequencing in the long run because it provides more complete information. Genes account for less than 25% of the DNA in the genome. The remainder includes areas that control how genes are turned on and off as well as “junk” DNA whose function isn’t fully understood.

Get other aspects of the study in GenomeWeb.

 

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.

Highlights: Advances in Genome Biology and Technology 2015 (AGBT)

NewsLast week the 16th annual Advances in Genome Biology and Technology (AGBT) meeting was held in Florida (USA). The meeting is important to the genomics research community because it provides an dialog forum for the latest advances in DNA sequencing technologies, experimental and analytical approaches for genomic studies and their myriad applications.

The 2015 meeting featured clinical translation of next generation DNA sequencing technologies and pipelines. Find here our best catches:

  • 10X Genomics: GemCode platform lauched. It allows users to obtain long-range genomic information from placing short sequence reads in the context of large DNA fragments. Its applications include haplotype phasing, structural variation analysis and de novo genome assembly. We will see how GemCode will “change the definition of sequencing“.
  • Illumina: New details on newly launched NeoPrep. The system automatically prepares DNA or RNA samples for sequencing on Illumina instruments. In addition to library creation, NeoPrep performs a few quality control checks, quantifying the DNA molecules to be sequenced and normalizing libraries for even coverage during sequencing.
  • PacBio: Whole genome sequencing with high quality assemblies. Get some application cases on GenomeWeb.
  • Kapa Biosystems: Library preparation products for next generation sequencing (NGS) DNA and RNA analysis launched.

Assessment of NGS Tools for Crime Laboratories

protocolUS Researchers has been awarded with $825,000 to evaluate the use of NGS technology for forensic applications.

Pennsylvania State University will work in conjunction with the Battelle Memorial Institute, the lead institution on the grant, and 6 other laboratories. As the sole university partner, Penn State will be performing evaluations of forensic investigative tools that will expand the capabilities of forensic DNA laboratories.

The grant will test the feasibility of new instruments, laboratory materials and software tools in the field of DNA-based forensics. The study’s aim is to vet tools using next generation sequencing technology and implement them into working crime laboratories.

According to the grant abstract, DNA samples are provided by the National Institute of Standards and Technology. They will be sequenced using Illumina’s MiSeq platform or Life Technologies’ Ion PGM Sequencing System.

The laboratories hope to be able to get tools that use NGS into working crime laboratories to replace current less-informative forensic methods. The new technology will increase efficiency in forensic work and could also help generate investigative leads and identify individuals with only traces of genetic evidence.

Visit forensics.psu.edu/research for more information about the Department of Forensic Science at Pennsylvania State University.