Category Archives: Genome

NEW YORK, Sept. 17, 2012 /PRNewswire/ -- Reportlinker.com announces that a new market research report is available in its catalogue:

US Personalized Cancer Genome Sequencing Market

http://www.reportlinker.com/p0968380/US-Personalized-Cancer-Genome-Sequencing-Market.html#utm_source=prnewswire&utm_medium=pr&utm_campaign=Genomics

The US personalized cancer Whole-Genome Sequencing market is primarily classified into targeted genome sequencing and Whole-Genome Sequencing. Our report entitled "US Personalized Cancer Genome Sequencing Market" takes into account the Whole-Genome Sequencing services, i.e. one of the most attractive sectors due to its inherent capability of high revenue generation and efficiency in terms of personalized treatment. The US, which is the frontrunner in the provision of such high-end service, is on the focus by market players because of favorable demographics and rising awareness among the industry participants.

In order to properly analyze the virtues and significance of the US personalized cancer Whole-Genome Sequencing market, our report has effectively studied the current and future status of cancer in the whole country as well as states. In view of the fact that cancer affects some age groups in a significant manner, we have also investigated the age wise statistics of the disease. To get proper insight into the market, an in-depth analysis into the high-income group population is provided so that players can have a clear picture about their potential customer base and market to be tapped.

An in-depth study of the regulatory environment governing the US personalized cancer Whole-Genome Sequencing market has also been provided. It has been found that regulations related to personalized cancer sequencing are primarily governed with the accreditation of the laboratories performing the sequencing services and analysis and also the usage of FDA approved tests for conducting these tests. Further we have also discussed the various constraints faced by the industry players with suitable suggestions for overcoming them.

The report analyzes the competitive landscape in the market through properly analyzing the business, services and activities of the companies. It also provides the competitive benchmarking taking into account the strengths and weaknesses of each player. Overall, the report is a complete source of knowledge and statistics for the clients who want to get an in-depth understanding of the market.

1. Analyst View

2. Research Methodology

3. Cancer Statistics by Demographics

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US Personalized Cancer Genome Sequencing Market

Non-coding regions of the human genome play a larger role in cell function than previously thought, scientists from Yale and other schools have shown.

Scientists from Yale and an international research consortium recently published the discovery of information identifying functional regions of the human genome.

Whereas the human genome, sequenced under the worldwide Human Genome Project in 2003, defines the overall structure of human DNA, the new project, titled Encode (ENCyclopedia Of DNA Elements), investigated how many of the elements of DNA work to control activity within the body. The results of Encode, published in over two dozen scientific journals, annotated the human genome by identifying regions previously considered junk as essential for determining cell function. Knowledge gained by the project will help scientists better understand the role of genes in human development and disease, said Sherman Weissman, professor of genetics at the Yale School of Medicine and a member of the project.

The Yale division of Encode was led by Michael Snyder, former chairman of the Yale Department of Molecular, Cellular and Developmental Biology, and launched worldwide in 2003 with a grant from the National Human Genome Research Institute.

John Rinn GRD 04, an assistant professor of stem cell and regenerative biology at Harvard University who was not part of Encode, said that the Human Genome Project left scientists with enormous quantities of unanalyzed information. The purpose of Encode, he said, was to decode those uncharted territor[ies].

Like Magellan navigating the ocean, [Encode] set out to make maps of the genome, Rinn said.

Every cell contains the entire genome, but only reads certain parts for example, a liver cell reads only the section describing the liver, and disposes of the remainder of the genome, Rinn said.

Encode mapped the presence of certain regions containing noncoding RNA, which organizes and determines the activities of various cells by deciding which section of the genome is read for each cell. Scientists were surprised to discover that noncoding RNA exists in equal quantities as messenger RNA (mRNA) that plays a role in protein building.

Weissman said that the results will facilitate other genetic research.

If you want to study an unknown gene, now you can look at [Encode] and see what kind of proteins bind to the DNA near it, or the control sites of nearby DNA, Weissman said. It saves individual laboratories from doing studies on single genes.

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Yale maps “uncharted” genome regions

PBR Staff Writer Published 12 September 2012

Illumina has introduced its rapid Individual Genome Sequencing (IGS) service with a turnaround time in as little as two weeks.

The IGS service uses Illumina's HiSeq 2500 sequencing system, which is capable of completing a sequencing run on a whole human genome in one day.

The service, which is available only through a physician's order, is designed to assist clinicians with diagnosis and treatment decisions, according to Illumina.

The services have also been implemented in Illumina's CLIA-certified laboratory to enable the same fast turnaround for the IGS service.

Illumina President and CEO Jay Flatley said Illumina has long believed that sequencing will become a mainstream practice in the clinical setting.

"Whole genome sequencing is quickly gaining recognition for its potential in diagnostics and treatment decisions, particularly in cases where physicians are challenged with identifying a disorder based on symptoms that don't quite fit with a known disease,'' Flatley added.

"When this happens, rapid whole-genome sequencing can provide big-picture information about genetic makeup, enabling physicians to make more informed decisions and patients to obtain answers more quickly."

Illumina is also working on a suite of analytic tools and professional services in collaboration with physicians and medical geneticists to improve clinical interpretation.

CHOC Hyundai Cancer Institute medical director Leonard Sender said,"Illumina has delivered on the promise of personalized healthcare by notonly enabling clinical interrogation of the whole genome, but also providing theresults in a turnaround time consistent with the demands of patient care."

Link:

Illumina unveils upgraded genome sequence service

By Joe Dermody

Tuesday, September 11, 2012

Irish genome research has been given a welcome boost with the opening of a Teagasc Animal Bioscience Facility at Grange, Co Meath.

The facility will optimise research into animal breeding. It will also be used to assist in the commercial development of new meat and milk products.

Officially opened by Agriculture Minister Simon Coveney, the Animal Bioscience Facility was developed as part of the Teagasc vision programme initiated in 2006, with the objective of establishing centres of excellence in the sciences that underpin agriculture. The tech-nologies being developed have the potential to accelerate the rate of gain in efficiency and quality.

Teagasc director Professor Gerry Boyle said: "The publication of the genome sequence for cattle in 2009 has opened up the possibility to use DNA-based approaches to study commercially important traits. These include milk and meat production, immunity and disease, nutrition, and reproduction."

The facilities include molecular biology laboratories, and labs for DNA/RNA preparation, immunology, biochemistry, microbiology, cell culture, and flow cytometry.

Head of the Teagasc Animal and Bioscience Department, Dr Richard Dewhurst, said: "We are developing the optimal breeding programmes to maximise genetic gain in the long term. Our main research activities include the development of multi-breed genetic and genomic evaluations, breeding objectives, and breeding programmes for dairy cattle, beef cattle, and sheep.

"We also aim to identify genes, pathways, and biological processes mediating resistance to infectious diseases in cattle and sheep and how these genes interact with pathogens and the environment."

The Teagasc Animal and Bioscience Department carries out research in the areas of animal breeding and genomics, animal health and welfare, infection and disease, computational and systems biology, fertility and reproduction, feed efficiency, and product quality.

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Genome research given a boost with opening of bioscience facility

Thirty-one papers simultaneously published by the ENCODE (Encyclopedia of DNA Elements) project indelibly repaint the picture of the human genome, throwing its information-processing characteristics into even sharper relief. (The whole collectionsix papers in Nature, 18 in Genome Research, four in Genome Biology, and one in BioMed Central Geneticsis posted with open access at Nature Encode. The lead article, Architecture of the human regulatory network derived from ENCODE data, is must reading for information-systems designers.)

Just a few years ago, the prevailing wisdom said that the genome comprises 3 percent or so genes and 97 percent junk (with 2 or 3 percent of that junk consisting of the fossilized remains of retroviruses that infected our ancestors somewhere along the line). After a decade of painstaking analysis by more than 200 scientists, the new ENCODE data show that indeed 2.94 percent ofthe genome isprotein-coding genes, while 80.4 percent of sequences regulate how those genes get turned on, turned off, expressed, processed, and modified.

This fundamentally changes how most biologists understand the master instruction set of life: we are, in short, 3 percent input/output and 80 percent logic. (Though perhaps a surprise to biologists, the finding will hardly astound anyone who has designed a complex interactive system.)

And though only 3 percent of the genomes three-billion-odd base pairs of DNA code for proteins directly, 62 percent of your DNA is, at some time or another, transcribed into RNA, which has relatively recently been revealed to have myriad functions beyond directing the assembly of amino acids into proteins.

It will take years to analyze the healthcare implications of the ENCODE vision of the genome.Stanford University biologist Michael Snyder told theNew York Times that,Most of the changes that affect disease dont lie in the genes themselves; they lie in the switches.

The Times also quoted Massachusetts General Hospital researcher Bradley Bernstein, who said: I dont think anyone predicted that would be the case. I cant resist pointing out that some folks did predict exactly this. In 1991, for example, the editor of Nature Biotechnologythen called Bio/Technologypointed out that even simple communications programs available then were 75 percent logic and 25 percent input/output. He added that, [R]esearchers are announcing new disciplines whose names are redolent of bits and bytesgenomics, bio-informatics. Maybe they will see past the junk epithet to discover whether the logic lies within the genome, but beyond the gene.

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Re-Imagining Our Genes: ENCODE Project Reveals Genome as an Information Processing System

SAN DIEGO--(BUSINESS WIRE)--

Illumina, Inc. (ILMN) today announced the introduction of its rapid Individual Genome Sequencing (IGS) service with a turnaround time in as little as two weeks. Rapid turnaround whole genome sequencing services were announced by Illumina in June 2012, enabled by technology innovations to the HiSeq platform. Now these advancements have been implemented in Illuminas CLIA-certified laboratory to enable the same fast turnaround for the IGS service.

The IGS service is only available through a physicians order and is designed to assist clinicians with diagnosis and treatment decisions. As the only CLIA-certified, CAP-accredited whole genome sequencing service laboratory in the world, Illumina continues to increase access and lay the foundation for routine clinical use of whole-genome sequencing.

Illumina has long believed that sequencing will become a mainstream practice in the clinical setting. By delivering a whole human genome in as little as two weeks, we have taken significant strides towards that goal, said Illumina President and CEO Jay Flatley. Whole genome sequencing is quickly gaining recognition for its potential in diagnostics and treatment decisions, particularly in cases where physicians are challenged with identifying a disorder based on symptoms that don't quite fit with a known disease. When this happens, rapid whole-genome sequencing can provide big-picture information about genetic makeup, enabling physicians to make more informed decisions and patients to obtain answers more quickly.

Validated for laboratory use in accordance with CLIA and CAP regulations and guidelines, Illuminas fast IGS service uses Illuminas HiSeq 2500 sequencing system, which is capable of completing a sequencing run on a whole human genome in one day. The service will continue to deliver the highest quality, most comprehensive data with the broadest coverage of exomic, promoter, and regulatory regions, as well as fully annotated variants to facilitate clinical interpretation, now available faster. Illumina is also working on a suite of analytic tools and professional services in collaboration with physicians and medical geneticists to improve clinical interpretation.

Illumina has delivered on the promise of personalized healthcare by notonly enabling clinical interrogation of the whole genome, but also providing theresults in a turnaround time consistent with the demands of patient care. This is a game-changer that will revolutionize our field, saidDr. Leonard Sender, Medical Director, CHOC Hyundai Cancer Institute and Director of the Young Adult Cancer Program at the Universityof California, Irvine Chao Family Comprehensive Cancer Center.

Initially, the rapid turnaround option is available with limited capacity, and cases will be prioritized by severity in consultation with ordering physicians. Later this year, Illumina will begin offering focused clinical interpretation for CLIA services, working closely with ordering physicians and leveraging bioinformatics tools and internal medical genetics expertise.

About Illumina

Illumina (www.illumina.com) is a leading developer, manufacturer, and marketer of life science tools and integrated systems for the analysis of genetic variation and function. We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA, and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its application, paving the way for molecular medicine and ultimately transforming healthcare.

Forward-Looking Statements

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Illumina Announces Expedited Individual Genome Sequencing Service (IGS)

Public release date: 9-Sep-2012 [ | E-mail | Share ]

Contact: Dianne G. Shaw dgs@med.unc.edu 919-966-7834 University of North Carolina Health Care

In the September 9, 2012 early online edition of Nature, scientists with The Cancer Genome Atlas (TCGA) report that they have characterized the lung squamous cell carcinoma genome.

Squamous cell carcinoma is the second most common form of lung cancer, a disease that kills more Americans than any other type of cancer.

The national team of scientists examined tumor samples from 178 patients with untreated lung squamous cell carcinoma and completed genetic analysis of the tumors, work that paves the way for developing better, more targeted therapies to treat the cancer.

Neil Hayes, MD, MPH, a UNC investigator with TCGA, explains, "The work confirms the prevalence of commonly known cancer genes such as p53 and p16 in LSCC: alteration of p53 in patients is approaching 100 percent while 70-80 percent of patients have clear alterations of p16. Our report documents a long list of mutations that could be targeted therapeutically, some even now with drugs currently available or in clinical trials."

Dr. Hayes served as co-chair of the manuscript writing committee for the paper. With Matthew Wilkerson, PhD, he served as genomic analysis leader and mRNA sequence analysis. Dr. Hayes is an associate professor of medicine.

He says, "UNC scientists generated all of the microarray and sequencing data on RNA and provided technical expertise in analyzing it. Analyzing gene expression data is very challenging, and UNC brought a large number of collaborators in computer science, statistics, and genetics to help.

"We and all TCGA scientists worked closely together on all aspects of this work," he explains. "Participating institutions provided high-quality tumor samples for the analysis. The study required a wide range of technical expertise to perform all the assays, and no one center could have done it all. "

Putting the study in a scientific context, he explains, "This is like a lot of great science advances. Think back to the late 1700s before it was widely known that many diseases were caused by infections. It's very hard to consider the idea of an antibiotic until you've thought of a germ. We have a disease that's caused by alterations in DNA. It's hard to think about therapies until you know what's wrong with the DNA. In the case of lung cancer, we've made a huge step forward in understanding what's wrong with the DNA of lung cancer."

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UNC Lineberger scientists lead definition of key lung cancer genome

In the decade since the human genome was published, scientists have been frustrated by their inability to figure out exactly how variations in genes promote disease.

But the information assembled by ENCODE research -- which shows that regions of the genome once thought to be junk are actually stuffed with DNA switches that help direct genes in their work -- may help change that, scientists involved with the collaboration said Wednesday.

Now that we have the switches, we can start to understand why a combination of DNA variants might increase the chances of a particular disease -- we can see which switch is malfunctioning and why, said Harvard Medical School and Broad Institute pathologist Dr. Bradley Bernstein.

Past efforts to figure out the puzzle of how DNA in the genome caused disease had focused on hundreds of genome-wide association studies, which screened genomes of people with particular medical conditions to determine DNA variants linked to those diseases, said University of Washington genome scientist Dr. John Stamatoyannopoulos, lead author of a study examining the connection between gene regulation and disease published Wednesday in the journal Science.

But the data coming from those studies has been less clear than most people would have hoped, failing to identify key genes driving most disorders, he said.

There turned out to be hundreds or thousands of variants involved in common diseases, and it was unclear what each one did. Only about 5% of the shared variants were in sections of DNA forming the template for genes.

We were missing too much information to put the story together, said Eric Schadt, a computational biologist at the Mount Sinai School of Medicine in New York.

Scientists working on the ENCODE project, which sought to delve deeper into DNA function, were able to show that there are millions of DNA segments in the genome that are involved in turning the 20,000 genes in the human genome on and off, Stamatoyannopoulos said. The 100,000 to 200,000 of these gene regulators that are activated in a cell determine what kind of cell it is and what function it performs.

Stamatoyannopoulos and his coauthors compared the gene regulation data from ENCODE and other projects with the associations uncovered in genome-wide association studies, looking to see when common variants were located in regulatory regions of the genome.

In many cases, it made sense that the identified regulatory regions were linked to certain diseases. For instance, the team discovered that one variant that had been associated in genome-wide studies with platelet count was actually part of the regulatory DNA that helps control a distant gene involved in platelet production.

Link:

New human genome research aids understanding of disease

15-03-2012 14:58 March 14, 2012 - Current Topics in Genome Analysis 2012 More:

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Genome-Wide Association Studies - Karen Mohlke (2012) - Video

04-04-2012 13:48 Google Tech Talk March 27, 2012 ABSTRACT It is often said that genomics science is on a Moore's law, growing exponentially in data throughput, number of assembled genomes, lowered cost, etc.; and yet, it has not delivered the biomedical promises made a decade ago: personalized medicine; genomic characterization of diseases like cancer, schizophrenia, and autism; bio-markers for common complex diseases; prenatal genomic assays, etc. What share of blame for this failure ought to be allocated to computer science (or computational biology, bioinformatics, statistical genetics, etc.)? How can the computational biology community lead genomics science to rescue it from the current impasse? What are the computational solutions to these problems? What should be our vision of computational biology in the coming decade? We will discuss three systems: TotalReCaller, SUTTA-Assembler and Feature-Response-Curves, in this context. For more info: About the speaker Professor Bud Mishra is a professor of computer science and mathematics at NYU's Courant Institute of Mathematical Sciences, professor of human genetics at Mt. Sinai School of Medicine, and a professor of cell biology at NYU School of Medicine. He founded the NYU/Courant Bioinformatics Group, a multi-disciplinary group working on research at the interface of computer science, applied mathematics, biology, biomedicine and bio/nano-technologies. Prof. Mishra has a degree in Physics from Utkal University, in ...

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The Genome Question: Moore vs. Jevons with Bud Mishra - Video