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.

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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.

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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…

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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 >>

Are you a NGS expert?

Some months ago we asked you for how long you have been involved with next generation sequencing.

blog

Almost 200 people sent their feedback and gave us a very interesting insight in their experience with NGS. To take this into account, we want to further align our posts with the focus topics of our readers.

Feel free to send me your comments and suggestions to make ngs-expert.com even more valuable for you.

The next step after sequencing: Synthesis of a designer chromosome

Next generation sequencing allows deciphering genomes of any kind and size; But, what to do with all this information?

Now a group of scientists from the John Hopkins University in Baltimore around Jef Boeke and 79 other authors published that they have been able to synthesize one of the 16 chromosomes of the baker’s yeast. Instead of the natural 317,000 bases they have reduced the chromosome to 274,000 bases by leaving out what they regarded as redundant or not necessary to grow under cell culture conditions.

Yeast cells already today produce important substances in large fermenters. They are used for bio fuel production but also for the production of Artemisinin, a potent malaria drug.

By reducing the genome of such organisms, the perfect “factory” can be designed in the future that delivers high yield of the desired substance at a minimum cost and a minimum contamination with other undesired metabolic byproducts. The White Biotechnology is certainly a hope for our permanent growing population. A number of companies engaged in this field can be found here.

Why should I buy Illumina stock shares?

What is the impact for a company of winning an award? In case of Illumina you can cleary see it is about brand and market awareness. Only recently we reported about the award for Illumina of beeing the smartest company in 2013. Today we have a short interview for you that answers the question: why to buy stock shares for Illumina.

From my point of view the only risk of being a market leader in a highly dynamic area like next generation sequencing is, that you have a lot to loose. But Illumina is working on this. One example: only this year Illumina launched two new next generation sequencing instruments: the X-Ten for human whole genome sequencing and the Next500 – a mid-size sequencer that fills the gap between the HiSeq and the MiSeq. So let’s see what happens next…