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?
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Whole genome sequencing a complete island

http://commons.wikimedia.org/wiki/File:Coat_of_arms_of_Iceland.svg

http://commons.wikimedia.org/wiki/File:Coat_of_arms_of_Iceland.svg

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.

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.

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!

PacBio Forecast 2015

ID-10081802As already predicted, it is not only Illumina who communicates innovations for their NGS portfolio. Here you can read about the implementations Pacific Biosciences plans this this. I think the good news for many users of PacBio machines is, that they do not talk about new instruments, but improvments that affect already installed machines (GenomeWeb):

  • PacBio plans to improve the sequencing chemistry, including the active loading of single polymerase enzymes onto the chip
  • PacBio plans to improve the workflows for an easier and faster handling of samples
  • PacBio plans to improve bioinformatics for faster de novo genome assemblies & better analysis of full-length HLA analysis

With this changes PacBio wants to extend the data output to more than 4 gigabases / SMRT cell and increase the average read lengths to 15-20 kbp.

Read more about it here.

I still wonder if there will be news from PacBio this year about a new system? Maybe a benchtop like everyone has?

I will keep you updated!

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.