Work where others make holidays !

Prof. Leonid Moroz from the University of Florida has become the first scientist to sequence the genome of fragile marine creatures on board a ship in real-time (see scientific computing world).

copaseticBecause of the difficulties of storing or shipping their genetic material, it has hitherto been difficult to sequence the genomes of marine species. However, researchers at the University of Florida have got round this problem by deploying a fully-equipped genomic laboratory aboard a ship called the Copasetic and sending the initial data via a satellite link to the University’s new HiPerGator supercomputer.

Aboard the Copasetic in early February and later in March-April, Professor Leonid Moroz, from the University of Florida, and his team where able to perform transcriptome sequencing of 22 organisms, among them rare comb jellies.

The first results of the sequencing at sea were presented at the international conference, Advances in Genome Biology and Technology, held at Marco Island, Florida in February.

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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

Is China breaking the dominance of Illumina?

BIGIS-4 is the name of an independently developed next generation sequencer made in China. The sequencer shall challenge the dominance of Illumina. On 18 April, scientists from the Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences and partner company Zixin Pharmaceutical Industrial Co Ltd demonstrated their BIGIS-4 sequencing machine in Changchun, Jilin province.

The Chinese machine has a longer read length than dominant sequencers like those made by Illumina in the US. Its manufacturing cost will be one third cheaper than imported machines, and operation costs about one fifth lower, according to Yu Jun of BIG, chief scientist of the project. Yu was also a co-founder of Shenzhen-based BGI, a spin-off of BIG and now the world’s largest sequencing service provider.

Yu’s sequencer differs from Illumina’s in that the fluorescent tag is cleaved from the newly synthesised DNA as it is incorporated, so that the reading speed is much quicker. This is similar to the pyrosequencing technology employed by Roche Diagnostics’ subsidiary 454 Life Sciences.

A publication about the complete genome sequencing and assembly of a Glaciecola mesophila spec. with BIGIS-4 is published here.

Nanopore MinION to be tested and evaluated in Sweden

There are many researchers and service providers who are talking about the MinION from Nanopore on a regular basis. Great things are expected from this innovative sequencing technology.

As previously mentioned, Oxford Nanopore has shipped some MinIon devices to early access users to receive some more data. As one of the few laboratories in Scandinavia, the Department of Animal Breeding and Genetics at the Swedish University of Agricultural Sciences has been chosen to test one of the latest sequencing technologies from Oxford Nanopore. By the size of the sequencer it is possible to bring the sequencer in the field.

Previously the department has tested leading NGS technologies in research related to the genes involved in the immune system of horses. Now the Nanopore technology will be used, compared and evaluated against the existing well-proven sequencing technologies.

I guess it is just to wait and see what the MinION will bring, if it will come up to expectations or not.

New method: single cell genome sequencing of malaria parasites

Single cell genomics provides new insight into the biology of Malaria parasites (Plasmodium vivax and Plasmodium falciparum), including their virulence and levels of drug resistance to improve treatment and control of the disease. 

mosquitoThe new method for isolating and genome sequencing an individual malaria parasite cell will allow scientists to improve their ability to identify the multiple types of malaria parasites infecting patients and lead to ways to design drugs and vaccines to tackle this major global killer.
Malaria parasite infections are complex and often contain multiple different parasite genotypes and even different parasite species. So when researchers take a blood sample from a malaria infected patient and look at the parasite DNA within they end up with a complex mixture that is difficult to interpret.

“Current sequencing techniques really limit our understanding of malaria parasite biology” says Ian Cheeseman, Ph.D., who led this project. “It’s like trying to understand human genetics by making DNA from everyone in a village at once. The data is all jumbled up – what we really want is information from individuals.”

To achieve a better understanding of malaria parasites – single celled organisms that infect red blood cells – the project team developed a novel method for isolating an individual parasite cell and sequencing its genome. Single cell genomics allows the separation and isolation of cells to extract and sequence individual parasite DNA and determine any differences between the parasites within an infection..

“One of the real challenges was learning how to cope with the tiny amounts of DNA involved. In a single cell we have a thousand million millionth of a gram of DNA. It took a lot of effort before we developed a method where we simply didn’t lose this,” said Nair, the first author on the work.

Their method is set to change how researchers think about infections. “One of the major surprises we found when we started looking at individual parasites instead of whole infections was the level of variation in drug resistance genes. The patterns we saw suggested that different parasites within a single malaria infection would react very differently to drug treatment” said Nair.

Unfortunately the new method is currently too expensive and demanding for routine use in the clinic, as the technology matures the applications for understanding malaria biology are vast.

___________________________

The findings are revealed in a study by researchers at the Texas Biomedical Research Institute and published recently in the journal Genome Research.

The work is funded by the Texas Biomedical Forum, National Institutes of Health, a Cowles Postdoctoral Training Fellowship and the Wellcome Trust and was led by Texas Biomed’s Cheeseman with collaborators at the University of Texas Health Science Center San Antonio, Case Western Reserve University, the Cleveland Clinic Lerner Research Institute, the Shoklo Malaria Research Unit, Thailand, and the Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Malawi.

Get further details here.

New kids on the show – who will be the winner?

Next Generation Sequencing is still a quite young market. Therefore we face the same situation every year: there is a lot of innovation going on in regard to new technologies, new instruments and other inventions. Amongst all these innovations GenomeWeb picked out the new platforms and asked in a survey about the expectancies in the market.

Instruments that were part of this survey are (at least in one of several questions):

  • Oxford Nanopore’s MinIon
  • Illumina’s X-Ten
  • Illuminas NextSeq 500
  • QIAGEN’s GeneReader
  • Life Technologies’ Ion Torrent PGM
  • Illumina HiSeq

Here are some of the results:

  • 35% of the participants say that the MinIon has the greatest impact on the sequencing community
  • 30% of the participtants will purchase most likely the NextSeq 500
  • Illumina HiSeq / MiSeq outperform the Ion Torrent Proton / PGM in data accuracy and throughput, the Ion Torrent instruments are better in respect of run time and instrument price

Read the complete survey here.

NGS Applications – get an insight…

paper_02

You want to know more about projects where your research colleagues used next generation sequencing?

Check out the Nature Reviews overview of interesting publications releated to different applications of next generation sequencing.

Whose genome has been sequenced? Aquila chrysaetos

de-novo-sequencingEvery day an unimaginable number of NGS data is generated. Anyhow the number of avian genomes that have been sequenced so far is still quite small (Doyle et al table 1). Doyle et. al added one more avian genome to this list – the “Golden Eagle” Aquila chrysaetos.

What was sequenced?

A male golden eagle (Aquila chrysaetos canadensis) captured in the southern Sierra Nevada.

Sequencing strategy: Whole genome sequencing

  1. Libraries & Sequencing: 1 channel 2x 100 bp SG paired-end sequencing and 1 channel 2x 100 bp mate-paired sequencing using the Illumina HiSeq platform
  2. Data output: 68.4 Gb of raw data (25.3 Gb from the SG and 43.1 Gb from the mate-pair library). Total genome size (incl mtDNA) ~ 1.28 Gbp. Overall genome coverage ~ 40x. Longest scaffold: 11,517,212 bp
  3. Results: The mtDNA genome is characterised by 13 protein-coding genes, 2 rRNAs and 23 tRNAs. The annotation produced a total of 16,571 predicted nuclear genes.

Besides the nuclear genome Doyle et al could also assemble the complete mitochondrial genome. Furthermore they found ~ 800,000 novel polymorphisms. These polymorphisms can now help to define markers that are involved in carnivory orother biological processes.

Read the complete publication here.

Whose Genome Has Been Sequenced? – Recent posts:

All you need to know about NGS

During my research through the web for news in the area of NGS I found this great practical course:

The EMBL-EBI offers a 15h online course that should help every newby and everyone who needs some refreshing information in NGS. And since we have several users of this blog that are new to NGS I thought it would be worth to share this course.

This course is divided into several subunits so everyone can learn in his own speed and in alignment with other tasks that are on everyone’s desk.

 

The key learnings are:

  • Understand some principles behind NGS
  • Know the challenges created by NGS
  • Know how to submit and retrieve NGS data to and from databases
  • Understand the uses of NGS data in: Whole genome assembly; Gene expression analysis; Genome annotation; Gene regulation analysis; Variation studies

Thank you EMBL-EBI for this great summary!

Analysis of oaks using RAD-Seq

Excellent paper just out that dissects the phylogeny of North American oak trees using RAD-Seq.sequences-per-individual

A phylogenetic study of the American Oak clade based on RAD-seq data has recently be published by PLoS ONE. The study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23-33 million year-old clade.
Associated with the paper is a new R package for downstream analysis of phylogenetic RADseq data, RADami

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data >>