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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.

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.

Prepare NGS for clinical use

Molecular diagnostics (MDx) is to my opinion the most sensitive application for all kinds of molecular biology techniques like PCR, Sanger Sequencing or Next Generation Sequencing. Today, NGS is still a niche application and needs further improvement to be a common tool for MDx. One thing that is lacking is the standardisation of NGS for clinical use.

The NGS Working Group, established by the Friends of Cancer Research worked out a master plan (The ASCO Post), with critical points that need to be addressed to use NGS more commonly:

1. Define a regulatory pathway for cancer panels (a selection of multimarker gene assays) intended to identify actionable oncogenic alterations (those with supporting data to create risk-benefit assessment of treatment choice) that allow flexibility in the appropriate FDA medical device pathway—for instance, one based on risk classification of different panel components depending on the specific marker.

2. Approaches to validation studies should be based on the types of alterations measured by the assay rather than on every alteration individually.

3. Determine the contents of a cancer panel by classifying potential markers based on current utility in clinical care and clinical trials and peer-reviewed publications, as well as recognized clinical guidelines. Draw upon various sources to determine the recommended marker set for an actionable cancer panel.

4. Promote standardization of cancer panels through development and use of a common set of samples to ensure reproducibility on each platform.

5. Establish a framework for determining an appropriate reference method rather than relying on any single method for all studies.

Get more information to each proposal here.

More Updates: Illumina & IonTorrent

Quarter 4 of 2014 seems to be another exciting one for Next Generation Sequencing. Beside the chemistry update for PacBio RSII also Illumina and IonTorrent / ThermoFisher announced two major improvements / achievements:

  • Chemistry update for the Illumina HiSeq X Ten and the HiSeq 2500 Rapid Run
    The new v2 reagent kit for the HiSeq X Ten supports a PCR-free sample preparation kit, which eliminates amplification during the library preparation. So far only sample preparation kits with PCR were possible, which sometimes results in a lower quality of challeging genomic regions.
    The new v2 reagent kit for the HiSeq 2500 enables users to sequence 2x 250 bp and the new chemistry therefore delivers up to 300 Gbp of data in only 60 hours. (Press Release)
    To my opinion Illumina proves once more that NGS is highly dynamic and that their continous update for existing systems is the key for their success (the latest financial report confirms that Q3 of 2014 with a growth of 10% is the strongest since 2011 for Illumina (Fierce Medical Devices)).
  • IonTorrent goes diagnostic
    The Ion PGM Dx System is now also CE-Marked for in vitro diagnostic (IVD) use in Europe. Thermo Fisher Scientific believes that the CE-mark “will enable European clinical laboratories to more easily […] implement new […] diagnostic assays” (Press Release).
    In September they announced already that the PGM is now listed with the U.S. FDA as a Class II Medical Device.
    To my opinion the clearance for diagnostic use in Europe as well as in the U.S. will further strengthen the position of the Ion PGM in clinical laboratories.

PacBio launches new chemistry and software

In a press release Pacific Biosciences announced the latest enhancement for the PacBio RS II single molecule DNA sequencer. The latest release of the polymerase 6 and chemistry 4 (P6 – C4) version in combination with improved software enhances the performance and output of the platform by 45%. The average read length is now 10,000 – 15,000 bases and up to 40,000 bases for the longest reads. Depending on the nature of the DNA a single SMRT cell will deliver 500 million to 1 billion bases.

The new chemistry will replace the current P5 – C3 chemistry and is recommended for all SMRT sequencing applications.

This new release also includes improvements to the SMRT Analysis software suite for long amplicon analysis and the Iso-Seq™ method. Together with chemistry enhancements, these advances boost accuracy, speed up analysis, and support sequencing of multiplexed amplicons of different sizes.

Quality Before Quantity?

The  “$1.000 genome” is to my knowledge the buzzword everyone knows when thinking about Next Generation Sequencing.

And quite often I ask myself: What will be the future of NGS? Whole genome sequencing of everyone and everything?

I am confident that this is part of Illumina’s  strategy for their new HiSeq X Ten instruments – at least for humans.

Contrary there is still all the data that needs to be analysed. And an interview with Lex Nederbragt highlights that data analysis is still a bottleneck. Also the latest report from Markets&Markets for whole exome sequencing predicts a strong growth in targetd sequencing. They estimate a growth for whole exome sequencing  from $326.6 M in 2013 up to $884.1 Million by 2018.

So will quality, like sequencing distinct regions outcompete the $1,000 genome? What are your thoughts about that?

Large genome sequencing studies in the USA

senior-asian-woman-100226669The launch of the Illumina HiSeq X Ten enabled them to put in practice their plans and great visions. I’m speaking of two persons of great influence in the United States. This year, Dr. J. Craig Venter, known for being one of the first to sequence the human genome and Patrick Soon-Shiong, considered as the world’s richest doctor, both revealed some details about their large scale sequencing projects:

  • J. Craig Venter founded the company Human Longevity that aims to develop treatments for cancer and age-related conditions. To unveil the mechanisms how people can live long and healthy lifes, the company will become one of the largest DNA sequencing facilities in the world. The plan is to set up a sequencing center that is capable of sequencing 40,000 human genomes a year.
  • Patrick Soon-Shiong recently announced that his company NantHealth is purchasing sequencers being able to sequence 22,000 genomes annually. The samples will derive from the 22,000 patients diagnosed with cancer annually at the 34 hospitals owned by Providence Health & Services. Consequently, the company from Soon-Shiong probably will become the first one using their sequencing capacity for clinical sequencing on a large scale.

Such huge collections of sequencing data make it possible to uncover the molecular causes of an complex process as aging or such a diverse and complex disease as cancer in a general approach. Big and very valuable databases will be created, that may contribute to develop new pharmaceuticals or develop personalized therapies.

Unexpected Heroes

Image courtesy of FreeDigitalPhotos.netThere are several mutations known which are linked to childhood diseases. This knowledge is already being used e.g. to analyze genomes of sick newborns for any known diseases, or for prenatal diagnostics. However: A person carrying such a mutation must not necessarily get ill.

Some individuals carry a mutation that should have caused a severe disease in their childhood. However, some yet unknown factors have protected them from getting ill. Even though they may be very rare, studying such persons may help to understand more about the diseases, or even find new treatments.

Researchers of the “Resilience Project” are now looking for such individuals who they call “unexpected heroes”: Adults who are “resilient to a certain rare disease despite carrying genetic mutations that would indicate onset of the disease in childhood.” In order to find those rare individuals, they are asking for volunteers to donate DNA samples for the project. Since they expect only 1 of 20,000 individuals to be such an “unexpected hero”, they need to analyze the genomes of more than 100,000 individuals. Participants can register online and will receive a test kit by mail. In return, the volunteers get a report indicating whether any of the analyzed mutations have been found in his or her genome.

The researchers hope to identify genes that can “buffer” the effects of the mutations, as well as environmental factors which help people carrying the mutations to stay healthy. The goal is to find new treatments, or even prevent people from getting ill at all.

Next Generation Sequencing Market Trends

paper_02The GEN report by Enal Razvi, Ph.D. provides an overview of the current NGS field in terms of application areas and utilization patterns.

Some findings of the report:

    • The exponential growth of NGS-focused publications illustrates the expansion of NGS and its penetration info research.
    • 49% of next generation sequencing methods are used for basic research.
    • 29% of researchers are using NGS for comparative genome sequencing
    • 38% of research efforts are studying somatic mutation
      33% are studying mRNA expression via RNA-Seq