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The future of miRNA analysis

We asked you in which technology you see the future of miRNA analysis.
Find here the voting of the 102 participants:

miRNA

 

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

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.

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.

Analysis of Richard III’s DNA to Create Complete Genome Sequence

Researchers in England are planning to sequence the entire genome of Richard III by extracting the DNA from his bone material.

Extracting ancient DNA is difficult. Dr. Turi King (Department of Genetics at the University of Leicester) will lead the project. She said it was invariably fragmentary, and it was a question of piecing together and overlaying fragments to complete a jigsaw. King will be working with Professor Michael Hofreiter in the ancient DNA laboratory at Potsdam University. The complete genome sequence will be placed online in an archive available to historians, scientists and the public, although Ibsen’s will not be published.

Richard III will be the first known historical figure to have his genes studied in this way; scientists have previously sequenced the genomes of Oetzi the Iceman, a number of Neanderthals, and most recently a hunter-gatherer from Spain.

The £100,000 ($164,000 / €120,000) cost of the project, which is expected to take at least a year, is being funded by the Wellcome Trust, the Leverhulme Trust and the geneticist Professor Sir Alec Jeffreys.

Transcriptome Sequencing In Translational Oncology Research

By using novel microfluidic tools, a team of researchers at Indiana University School of Medicine uncovered an unexpected ability of cancer cells to navigate and exit microscopic mazes along the shortest path. To explain this behavior, they propose a novel mechanism that guides cancer cell migration.

Find out how they have harnessed RNA-seq on tumor tissues to reveal efficacious drug targets and implement rational drug combinations in triple-negative breast cancer. Further, ongoing work on how RNA-seq is being used for biomarker discovery in retrospective cancer clinical trials will also be presented.

Genetic Differences Between “Identical” Twins Discovered

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A multidisciplinary team in the Eurofins flagship Genomics laboratory in Ebersberg, Germany, has successfully completed a research project to genetically discriminate “identical” monozygotic twins.

So far there have been only theoretical considerations against the experimental finding and dogma that monozygotic twins are genetically fully identical. Statistically, around 6 of 1,000 males are identical twins. Up to now, forensic DNA fingerprinting testing could not be used in crime or paternity cases involving identical twins, as there was no possibility of genetically discriminating between them. Such cases are regularly discussed in the World’s press, including murder, child custody and heritage cases. Forensic laboratories around the world had accepted these analytical restrictions, but Eurofins scientists wanted to push these limits of DNA testing. They used the unique combination of leading forensics and genomics labs available at Eurofins to reach this milestone.

Technically, the scientists applied ultra-deep next generation sequencing and associated bioinformatics techniques. They sequenced DNA from sperm samples of two twins and from a blood sample of the child of one twin. Bioinformatics analysis revealed five mutations, so called Single Nucleotide Polymorphisms (SNPs) present in the twin father and the child, but not in the twin uncle. The SNPs were confirmed by classical Sanger sequencing. The results give experimental evidence for the hypothesis that rare mutations will occur early after or before the human blastocyst has split into two, the origin of twins, and that such mutations will be carried on into somatic tissue and the germ line.

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The dataset in this project equaled a total of 241 human genomes, resulting from up to 94 fold genomic coverage of the involved three individuals.

The peer-reviewed study “Finding the needle in the haystack: Differentiating “identical” twins in paternity testing and forensics by ultra-deep next generation sequencing” is published in the renowned journal Forensic Science International: Genetics, Available online 8 November 2013, ISSN 1872-4973, http://dx.doi.org/10.1016/j.fsigen.2013.10.015.