Category Archives: Transhuman News

SANTA CLARA, Calif.--(BUSINESS WIRE)--

Affymetrix, Inc. (AFFX) announces the launch of Axiom Strawberry Genotyping Array (also called International Strawberry 90K SNP array or IStraw90), the only solution that successfully enables high-resolution genotyping and fully automated data analysis of the octoploid strawberry genome. This 90,000 SNP array will enable complex trait research and set the stage for multi-trait, marker-assisted breeding of the cultivated garden strawberry (Fragaria ananassa).

The cultivated garden strawberry is an allo-octoploid with a chromosome number of 2n=8x=56. While there are other genotyping technologies available to scan genomes of agricultural species at high resolution, most have been designed for diploids. With Affymetrix advanced bioinformatics and innovative design strategy, Axiom Genotyping Solution provides genome-wide genotyping and accurately calls the genotypes of both diploid and polyploid species. This technology has already been successfully applied to complex genomes such as maize, rose, wheat, trout, and salmon.

Axiom Strawberry Genotyping Array was designed through a public-private partnership between Affymetrix and theInternational RosBREED SNP Consortium (IRSC), an arm of the "RosBREED" project dedicated to the genetic improvement of rosaceous crops. The RosBREED team including Genotyping Team Leader Nahla Bassil (USDA-ARS, Corvallis), Demonstration Breeder Tom Davis (University of New Hampshire geneticist), and Pedigree-Based Analysis Team Leader Eric van de Weg (Wageningen University & Research Center) partnered with the Affymetrix array design and bioinformatics teams to devise SNP selection and data analysis strategies. RosBREED announced the availability of the array through its September 2013 newsletter. Preliminary results from the array were presented at the 2013 annual conference of the American Society for Horticultural Science.

IStraw90 gives us the capability to create high-resolution genetic maps of the strawberry genome and work towards enabling marker-assisted breeding for strawberry breeders worldwide, stated Nahla Bassil. The International RosBREED SNP consortium has been working towards enabling discovery and validation of valuable trait loci. IStraw90 will facilitate many of RosBREEDs goals and expedite marker-assisted breeding in strawberry.

The successful design and analysis of the data from the allo-octoploid strawberry genome was possible only because of the expertise, commitment, and collaborative efforts of the Axiom myDesign custom array, bioinformatics, and product support teams within Affymetrix, stated Eric van de Weg. It is awesome to have the tools to construct such high marker-density maps generated in such a short time. We expect this array to be a valuable resource for genome-wide analysis and marker-assisted breeding in many American, European and other breeding programs.

Genotyping the octoploid strawberry genome demonstrates the power and precision of the Axiom Genotyping platform to type genetic variants within complex genomes, said Andy Last, Executive Vice President of the Genetic Analysis Business Unit at Affymetrix. The array design process and updates to the automated analysis software used with Axiom Strawberry Genotyping Array are significant milestones for our platform because they enable the worldwide plant and animal genotyping community to leverage the Axiom myDesign customization process and analysis software to genotype even more species of interest.

Axiom Strawberry Genotyping Array will complement the catalog of Axiom Agrigenomics Genotyping Arrays that are available for multiple species, including bovine, chicken, and buffalo. These products have been used for genome-wide association studies, quantitative trait locus mapping, genome mapping, and breeding activities that make use of marker-assisted selection and genomic selection. As scientists make progress in decoding genomes of various plants, animals, and fish using next-generation sequencing platforms, they can advance their research and commercial objectives by translating those discoveries to routine applications on the Axiom Genotyping platform.

To learn more about Axiom Genotyping Solutions, please visit http://www.affymetrix.com/axiom for applications in human diseases research and http://www.affymetrix.com/agrigenotyping for applications in agrigenomics.

PLEASE NOTE: Affymetrix, the Affymetrix logo, Axiom, and all other trademarks are the property of Affymetrix, Inc. All other trademarks are the property of their respective owners.

Originally posted here:
Affymetrix Axiom® Strawberry Genotyping Array Delivers Automated Analysis for High-Resolution Genome Scanning of ...

Cosmic Log

Alan Boyle, Science Editor NBC News

Oct. 21, 2013 at 10:16 PM ET

Kolb et al. / PLOS ONE

A world map charts the classification of herpes simplex virus type-1 genomes into different genetic groups, or clades. Patterns of land migration are shown by yellow lines, and potential air/sea migration by a pink line.

To confirm the theory that humans spread out from Africa tens of thousands of years ago, all you have to do is follow the cold sores. Or, to be more precise, follow the mutation patterns encoded in the genome of the virus that causes those cold sores.

That's what researchers at the University of Wisconsin at Madison did: In the journal PLOS ONE, they describe how they sequenced the genomes of 31 samples of herpes simplex virus type-1 to reconstruct how it hitchhiked on humans as they dispersed around the world.

The results match the pattern proposed by the "Out of Africa" theory, which has become the most widely accepted scenario for ancient human migration. The analysis showed that African strains of the virus contained the most genetic diversity suggesting that they had the oldest roots.

The viral strains sort exactly as you would predict based on sequencing of human genomes. We found that all of the African isolates cluster together, all the virus from the Far East, Korea, Japan, China clustered together, all the viruses in Europe and America, with one exception, clustered together, senior author Curtis Brandt, a professor of medical microbiology and opthalmology, said in a UW-Madison news release.

What we found follows exactly what the anthropologists have told us, and the molecular geneticists who have analyzed the human genome have told us, about where humans originated and how they spread across the planet, he said.

Continued here:
Herpes virus genome traces the ancient path of human migration

Oct. 22, 2013 Mantle cell lymphoma is a very aggressive and difficult to treat cancer originated in blood cells and lymph nodes. To identify the molecular alterations responsible for this tumor, and facilitate the development of new treatments, a team of scientists led by Dr. Xose S. Puente and Dr. Carlos Lpez-Otn, at University of Oviedo, and Dr. Slvia Be and Dr. Elias Campo, at IDIBAPS, Hospital Clnic, University of Barcelona, have sequenced the genomes of over 30 of lymphomas. The result of this work, published today in the prestigious U.S. journal Proceedings of the National Academy of Sciences (PNAS), presents the first comprehensive genomic analysis of this disease. "The study provides insight into causes and evolution of this complex neoplasm and has identified targets for new treatments," says Dr. Silvia Be, first author of the study.

The authors analyzed the genome of tumor cells at the onset of the disease and within several years after treatment, when the relapses occur. Thus, it has been possible to evaluate the genomic modifications associated with disease progression. These analyses have discovered the implication of several genes in the progression of these lymphomas and some mechanisms generating resistance to chemotherapy. They also defined a group of patients with very rapid progression of the disease with mutations in NOTCH1 and NOTCH2 genes. These mutations could become therapeutic targets because there are already drugs blocking the activity of these genes which may be useful in complicated cases of mantle cell lymphoma. Researchers also identified a group of patients with a small number of mutations in the tumor whose disease progression was very slow. Thus, knowledge around the genome of these lymphomas might guide the selection of appropriate treatments for each patient.

This work was carried out with funding from the Association for International Cancer Research (United Kingdom), the Lymphoma Research Foundation (USA) and the Instituto de Salud Carlos III (Spain), and illustrates how new genome sequencing technologies are revolutionizing the study of different types of cancer. During the last three years the Spanish Consortium for the Study of the Genome of the Chronic Lymphatic Leukemia, where the researchers of the present study already collaborate, has sequenced the genome of hundreds of patients with the more common leukemia in our society, identifying new mechanisms of tumor progression and new therapeutic targets. These studies should allow the application of genomic studies in clinical practice to improve the diagnosis and treatment of cancer patients.

Share this story on Facebook, Twitter, and Google:

Other social bookmarking and sharing tools:

Story Source:

The above story is based on materials provided by Universidad de Barcelona.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Note: If no author is given, the source is cited instead.

See the original post:
Genome of aggressive lymphoma sequenced