NGS Expert Blog

Everyone is talking about big data. Many IT companies put their focus on analyzing tons of information. Also the pharmaceutical industry collects very large data volume during their drug research, discovery and above all during the clinical phases.

This article from pharmaceutical-technology.com addresses the big data analysis demands of the pharma industry in a very interesting way. Therefore, I encourage everyone to read the article.

Visit “Leveraging big data to solve Pharma’s hard to cure problems”

Great interview with our NGS expert Georg Gradl.  His lab was called on by police in Boston to identify identical twins and finally to find the criminal. Georg said he is also aware of cases in other countries including the United Kingdom, Switzerland and France.

“While traditional DNA tests fail to distinguish monozygotic twins, Eurofins developed a test which can achieve exactly that by finding genetic mutations. For this purpose we apply advanced sequencing and bioinformatics technologies,” says Georg Gradl.

It is an expensive test because there is a lot of just simply consumable costs and labor and so on. Therefore the police have been told by a competitor that the test could run around $160,000, but Eurofins’ lab has found ways to cut the cost.

“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…

To 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.

STAT-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.

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?

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Two days ago a groundbreaking study was published in Nature Genetics: Whole genome sequencing of 2,636 Icelanders and Genotyping of 104,220 Icelanders.

The advantage of using a small population like the Icelanders for this kind of study is that there are fewer rare variants, but sometimes also a higher occurance of some of these variants.

For the study, geenomic DNA was isolated from white blood cells and subsequent sequencing was performed on GAIIx and HiSeq instruments. The resulting reads were aligned to the human reference genome (NCBI Build 36 (hg18).

Gudbjartsson et al. then examined the data from different angles. For example, they looked for geographical dependencies for specific variants or how the data can be used to learn more about phenotypes and their underlying genomic pattern. But they also report an example “how rare variants […] can be used to analyze clinical problems”. (Gudbjartsson et. al)

Since every human being has a unique genomic pattern I think studies like this are of high importance to learn more about disease related genotypes. This will help to gain confidence in the results that we get from molecular diagnostic assays for disease treatment now and in the future.

Read the complete publication here.

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

** 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

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.

Last 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.

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