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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.

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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sequence will be placed online in an archive available to historians, scientists and the public, although Ibsen’s will not be published.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

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.

1,000 Fish Transcriptome Project

The China National Genebank (CNGB) announces the official launch of the 1,000 Fish Transcriptome Project (Fish T1K). It marks the beginning of an amazing transcriptome study designed to unveil the mysteries of the origin, evolution, and diversification of the largest group of vertebrates.

The findings could enable scientists to pursue innovative approaches and strategies to address challenges in fish breeding, disease control and prevention, seafood safety and biodiversity conservation.

Read more at BGI news

Next Generation Sequencing in Lung Cancer

Dr. Benjamin Levy (Head of Thoracic Medical Oncology, Division of Hematology-Oncology, Beth Israel Medical Center, Continuum Cancer Centers of New York and Assistant Professor of Medicine, Albert Einstein College of Medicine) is talking with Selma Schimmel about next generation sequencing in lung cancer.

The interview was filmed at the American Society of Clinical Oncology Annual Meeting in Chicago 2013.

Do You Use RAD-Seq?

The last months we asked you if you are familiar with RAD-Seq, a new approach combining restriction site associated DNA marker genotyping (RAD) with next generation sequencing technology.

73 people did answer the questions. Nearly the half never heard of it.
For this reason we recommend some basic information about RAD-Seq.

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