Category Archives: Genome

MENLO PARK, Calif.--(BUSINESS WIRE)--

The US Department of Veterans Affairs (VA) has awarded its first contract for whole genome DNA sequencing and data analysis to Personalis, Inc., of Menlo Park, CA. The contract will utilize samples from several VA sources, including from the Million Veteran Program (MVP). Using its secure computing facility and proprietary algorithms, Personalis will QC all raw data, call variants against an advanced human reference sequence, annotate both SNV/indels and SVs, and provide genetic analyses to help confirm sample / data chain of custody. Personalis plans to subcontract the laboratory genetic analysis, including both DNA sequencing and genome-scale genotyping, to Illumina, Inc., of San Diego, CA.

Personalis CEO John West said The VAs MVP has the potential to be the largest and most important medical sequencing effort in the world. We are thrilled that the VA has chosen Personalis for the DNA sequencing and analysis on this project. Our emphasis is on delivering an accurate and comprehensive sequencing solution for the VA.

About the VA Million Veteran Program

Launched in 2011, MVP is a landmark research effort aimed at better understanding how genes affect health. Up to a million Veterans are expected to enroll in the VA study over the next 5-6 years. Data and genetic samples collected through the study are stored securely and made available for studies by authorized researchers, with stringent safeguards in place to protect Veterans private health information. MVP is now enrolling at over 40 VA medical centers nationwide. The VAs central bio-repository is equipped with a state-of-the-art robotic system for DNA extraction and storage and is currently being expanded to support up to 4 million samples. With more than 135,000 enrollees to date, MVP already far exceeds the enrollment numbers of any single VA study or research program in the past.

MVP provides researchers with a rich resource of genetic, health, lifestyle, and military-exposure data collected from questionnaires, medical records, and genetic analyses. By combining this information into a single database, MVP promises to advance knowledge about the complex links between genes and health.

Veterans privacy and confidentiality are top priorities in MVP, as in all VA research. For more information about MVP, visit http://www.research.va.gov/MVP

About Personalis

Personalis provides researchers and clinicians accurate DNA sequencing and interpretation of human genomes. We support researchers engaging in case-control, family-based, or proband-only genome studies of disease, pharmacogenomics, and cancer. Our ACE (Accuracy and Content Enhanced) Technology can supplement a standard exome or genome, substantially increasing its medically-relevant coverage and accuracy. Personalis builds on this foundation with innovative algorithms and proprietary databases for alignment, variant calling, annotation, and analysis. With this combination, we provide genomic data and interpretation of the highest accuracy.

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Personalis Awarded Contract From VA Million Veteran Program – Whole Genome Sequencing and Data Analysis for Over 1,000 ...

When scientists sequenced the human genome in 2000, it revolutionized biomedical research, much like the invention of the Internet forever changed communications.

The Human Genome Project aimed to identify all the genes in the human genome. At first, scientists estimated that humans had less than 100,000 genes. Then improved methods lowered that to 35,000. Now, a new analysis suggests that humans have no more than 21,000 genes. When considering the complexity of a human being, that number does not seem very high.

However, even the highest of those estimates accounted for less than 20 percent of the DNA sequence in the human genome. The rest of the sequence did not appear to encode genes that led to proteins, and was therefore considered nonfunctional or junk DNA.

Now a recent study by more than 400 researchers at 32 institutions challenges that notion, suggesting that more than 80 percent of the human genome is indeed utilized and therefore important in the overall biology of each person. So much for junk DNA! The Encyclopedia of DNA Elements (ENCODE) project concluded that 20,687 genes produce proteins and an additional 18,400 genes produce RNA involved in coordinating the activity of the genes that produce proteins.

This extensive effort originally focused on the genomes of a small number of human cells but later expanded to include almost 150 different cells, including immune, embryonic, liver tissue, umbilical cord and cancer cells. Specific genes produce proteins for different tissues at different stages of human growth, so using this wide array insured that the analysis included all active genomic regions and gave a broader view of the genome.

The analysis also identified genome regions associated with specific human diseases, creating an opportunity for better understanding these diseases and treating them. In addition, the ENCODE project revealed just how different humans are from other mammals like monkeys, dogs, or dolphins. While previous estimates suggested that just 5 percent of the human genome is unique from other animals, ENCODEs research doubled that estimate to almost 10 percent. Another revelation showed just how complex the control mechanisms of the human genome really are. They signal almost 20,000 genes at the exact time and location to allow a fetus to develop normally and instruct the specific workings of tissues, as in the kidneys, lungs, or brain.

So the action of genes is controlled by layer upon layer of interacting and intricate controls that make each person who they are. Homo sapiens is a species of biological wonder and it will require many years of intense study for us to even begin to understand the mysteries of how genes are regulated to make a human being.

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Doctors Column: Revisiting the human genome

AARHUS, Denmark--(BUSINESS WIRE)--

Today CLC bio released CLC Microbial Genome Finishing Module, an add-on module to CLC Genomics Workbench, which has been developed to help finish the assembly of small genomes.

Senior Field Application Specialist, Dr. Marta Matvienko, states, "High-throughput sequencing technologies enable rapid full-genome sequencing, but short read lengths and repetitive sequences often complicate full genome assembly and result in fragmented assemblies. Genome Finishing Module helps produce high quality assemblies for small genomes such as bacterial or fungal species. This suite of tools reduces the extensive workload previously associated with genome finishing, by facilitating as many steps in the procedure as possible."

CLC Microbial Genome Finishing Module is a collection of tools with different functionalities to identify, visualize, and solve problems in genome assemblies. The tools are:

More about CLC Microbial Genome Finishing Module

Click here to get more information:

http://www.clcbio.com/link.php?id=361

Click here to download CLC Microbial Genome Finishing Module:

http://www.clcbio.com/link.php?id=362

About CLC bio

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CLC bio releases module for microbial genome finishing

VANCOUVER, BRITISH COLUMBIA--(Marketwire - March 11, 2013) - Genome British Columbia, the Pacific Salmon Foundation and Fisheries and Oceans Canada are embarking on a remarkable partnership to discover the microbes present in salmon in BC that may be undermining the productivity of BC's Pacific salmon. The project will conduct epidemiological assessments to explore the transmission dynamics and historical presence of detected microbes, with key focus on microbes that are suspected globally to be causing disease in salmon. Researchers will apply genomic technology to identify and verify which microbes are presently carried by BC's wild and cultured fish.

The project is being managed in four sequential Phases with Phase 1 valued at $930,000. The first phase is taking place over 12 months, concluding mid-2013, and comprises the collection phase of both cultured and wild salmon. While later phases are subject to final funding, Phase 2 involves rigorous analysis of the tissue samples collected in Phase 1 and in previous research. Using molecular and genomic tools, the research team will attempt to determine when and where microbes may have been transmitted.The research results will begin to rank microbes by their potential to cause disease in BC salmon based on relationships with microbes associated with disease in other parts of the world and histological evidence from salmon in BC.Phase 3 will focus in on the microbes identified in Phase 2, with an emphasis on microbes that have not been extensively researched and that are thought to be of pathological significance in salmon. Phase 4 will include reporting of research and presentations to management agencies on the potential utility of methods developed and the application of outcomes to future monitoring.

Over 90% of juvenile salmon migrating from freshwater into the ocean will die before returning to freshwater to spawn. The scientific community believes that mortality is highest during the first few months in the marine environment and that disease may be a significant factor in this mortality, but not enough is known about what pathogens or diseases might be involved.

What is already known comes almost exclusively from observations of cultured fish (both in hatcheries and in aquaculture). Consequently, there is a fair understanding of pathogens and diseases that impact salmon in freshwater hatcheries and sea-water net pens, but a much poorer understanding of pathogens affecting Pacific salmon in the ocean.

Uncertainty about pathogens and diseases was highlighted in the final report of the Cohen Commission Inquiry into the Decline of Fraser River Sockeye Salmon. In this report, Justice Bruce Cohen noted that more research is needed to make accurate assessments about the range of possible impacts on wild fish stocks. The research conducted by the Pacific Salmon Foundation and Fisheries and Oceans Canada, and funded in part by Genome BC, will address specific recommendations from the Cohen Commission report and build on the body of research referenced by the Commission.

Phase I is being led by Dr. Brian Riddell of the Pacific Salmon Foundation and co-led by Dr. Kristi Miller of Fisheries and Oceans Canada.

"This project is about developing effective monitoring tools to assess the microbes in BC's salmon, assessing the risk of these microbes to Pacific salmon, and establishing public confidence that people are watching over the health of our wild salmon populations," said Dr. Brian Riddell, president and CEO of the Pacific Salmon Foundation."The uniqueness of the project is its comprehensiveness.We are bringing a strong team of scientists together to assess the risk of disease to all species of wild salmon, including salmon produced in our hatcheries and salmon from aquaculture. We will also engage the full range of stakeholders, including government, industry, communities and conservation groups that have an interest in this research."

From the outset of the project, the development of a stakeholder consultation process that enhances understanding and dialogue about the health of our Pacific salmon is paramount. The stakeholder group will provide input to information needs, public engagement and communications and on ways to integrate research on microbes and disease on BC salmon. This group of stakeholders will encompass a wide cross-section of BC citizens with an interest inBritish Columbia's salmon (including wild, hatchery, and farm raised salmon), including regulators, managers, harvesters, Environmental Non-Governmental Organizations (ENGOs) and farmers.

"This is a unique and collaborative approach to an issue that affects a diverse group of stakeholders," says Dr. Alan Winter, President and CEO of Genome British Columbia. "It is gratifying to see part of Genome BC's $37.5 million investment in salmonid research being used as a foundation for this significant project."

Note to editors: Further details about the SHI project is included in attached background information.

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Genome BC: Salmon Health: Past, Present and Future

The Archon Genome Agenda - TRANSFORMING HUMANS to ROBOTS
This videos formal title is: The Archon Genomics X PRIZE Presented by Express Scripts Published on Aug 29, 2012 http://genomics.xprize.org The Archon Genomic...

By: TheGetjiggy

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The Archon Genome Agenda - TRANSFORMING HUMANS to ROBOTS - Video

By Crux Guest Blogger | March 8, 2013 2:06 pm

By Eliza Strickland

What can you learn from getting your genome sequenced? If youre a relatively healthy person like me, the answer is, not much at least not yet.

I embarked on a mission to get myself sequenced for my recent article The Gene Machine and Me. The article focused on the sequencing technology that will soon enable a full scan of a human genome for $1000, and to make the story come alive, I decided to go through the process myself. I got my DNA run through the hottest new sequencing machine, the Ion Proton, and had it analyzed by some of the top experts on genome sequencing, a team at Houstons Baylor College of Medicine.

The Baylor team has been intimately involved in many of the most important advances of genome sequencing over the last decade. And their accomplishments reveal both the astoundingly rapid progress of the technology, and how far we have yet to go. Heres a synopsis: the story of five genomes.

In April of 2003, the federally funded Human Genome Project finished the first complete human genome. It had taken an army of researchers about 13 years and $3 billion to accomplish the task, but finally the researchers had the sequence of about 3 billion nucleotides, the complete genetic code for a human being.

The genome constructed by the Human Genome Project was a consensus genome made by combining the genetic material of a handful of people. By averaging the variations between these genomes, the researchers came up with their best approximation of what it means to be a healthy, functional person. It was a monumental achievement. Three years earlier, in 2000, President Bill Clinton had announced the completion of the human genomes rough draft, and called it the most important, most wondrous map ever produced by humankind.

Once the Human Genome Project was completed, researchers were eager to start sequencing individual human beings, and to examine the genetic variations that define each individuals traits and quirks. If the cost of sequencing a genome had continued at $3 billion a pop, there would be no way to conduct such experiments. But in 2007, the company 454 Life Sciences invited James Watson, the genetics pioneer who helped discover the double helix structure of DNA back in 1953, to be the first individual to be sequenced on the companys new machine. The machine would bring the cost down to about $1.5 million per genome. Baylors team would do the analysis.

When the sequencing was complete, Watson flew down to Houston. (Another genetics pioneer, Craig Venter, was also sequencing his personal genome at the same time, but the Baylor team says Watsons was completed first.) Watson received his results from Baylor researcher and physician James Lupski, a preeminent geneticist. I had to be the one to say, Well, Jim, we dont know what the hell your DNA means, because youre the first one to be sequenced, Lupski recalled with a laugh. Lupski was exaggerating a bit for comic effect, but the truth was, medical research didnt have much to tell Watson.

The next step in genomic medicine, the Baylor researchers decided, was to sequence someone who wasnt entirely healthy. They chose as their subject their own James Lupski, who has an inherited neurological disease called Chacot-Marie Tooth Disease. A variety of mutations can cause this disorder, and Lupski wondered if a whole-genome scan could identify the particular mutation that caused his familys problems. There still was the question, could we find things that were important for medical management? Lupski told me. Was the signal above the noise? The noise, he explains, is the thousands of genetic variants found in each individual, because everybody truly is unique.

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Should Healthy People Get Their Genomes Sequenced?

SANTA FE, N.M.--(BUSINESS WIRE)--

The National Center for Genome Resources (NCGR) announced today that it will host the ninth annual New Mexico Bioinformatics, Science and Technology (NMBIST) symposium on March 21-22, 2013 on Genome Dynamics. Genome dynamics has been the focus of much recent research even though for some time we have known that genomes are not static. Barbara McClintock's work, beginning in the 1920s, described recombination during meiosis and transposable elements as genes that jumped spontaneously from one site to another, interrupting gene function and genome structures. Genetic material may also get duplicated, combined or modified and effect whole chromosomes and entire genomes. The conference features a diverse line up of speakers who will address the mechanisms and effects of genome dynamics including the variation within the human population, genomic structural rearrangements, mutation rates, epigenetics, and mechanisms of transcriptional regulation. Speakers include:

The NMBIST symposium attracts over a hundred research scientists, university and college faculty and students, as well as high school students from the Southwest and beyond. The purpose of the symposium is to inform, educate and promote the latest developments at the intersection of bioscience, technology, mathematics and software development. In particular, the symposium offers students from research centers in minority-serving institutions a regional opportunity to present their research in a poster session and to compete for a student speaking slot in the plenary session.

The symposium will be held at the Inn and Spa of Loretto in downtown Santa Fe, New Mexico, and is organized by NCGR. Major funding is provided by the National Institute of General Medical Sciences, a division of the National Institutes of Health through the New Mexico IDeA Networks of Biomedical Research Excellence (NM-INBRE) program. Other sponsors include JMP Genomics, Agilent Technologies, Illumina, Pacific Biosciences, Life Technologies, Bioo Scientific, and PerkinElmer. To find out more information and to register, visit http://www.nminbre.org/index.php/nmbist-2013-symposium-march-21-22.

About NCGR: NCGR is a nonprofit research institute whose mission is to improve human health and nutrition through genome sequencing and analysis. To learn more about NCGR, please visit http://www.ncgr.org.

About the New Mexico IDeA Networks of Biomedical Research Excellence: The objective of NM-INBRE is to increase collaborative, multidisciplinary biomedical research at New Mexico's institutions of higher education and expand the pool of biological and biomedical researchers in New Mexico. For more information, please visit http://www.nminbre.org.

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NCGR Hosts Symposium on Genome Dynamics

Vincenzo Costanzo - Novel molecular insights on vertebrate genome stability maintenance
Vincenzo Costanzo - Cancer Research UK The molecular aspect of how cells maintain a stable character shows that cancer cells cannot maintain the structure of their DNA. The cause of this is the failure of a surveillance system in the cells DNA which causes the chromosomes to lose their structure. Dr Costanzo elaborates on how this will factor into his laboratory #39;s focus of DNA metabolism and DNA damage response in vertebrate organisms. Recordered during the IFOM - Kyoto university Joint Symposium, October 2012. For more info visit ifom.eu

By: IFOMeu

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Vincenzo Costanzo - Novel molecular insights on vertebrate genome stability maintenance - Video

Public release date: 6-Mar-2013 [ | E-mail | Share ]

Contact: Winnie Lim limcp2@gis.a-star.edu.sg 656-808-8013 Agency for Science, Technology and Research (A*STAR), Singapore

Scientists at A*STAR's Genome Institute of Singapore (GIS) have developed a novel technique to precisely monitor and study the evolution of micro-organisms such as viruses and bacteria. This is an extremely important capability as it allows scientists to investigate if new drugs designed to kill them are working, and catch the development of resistance early on.

Micro-organisms and cancer cells evolve more quickly than normal human cells as their rapid life-cycles enable faster selection of advantageous mutations. Previously, scientists have had to wait for the selection process to reach maturity before they can observe mutations and assess their impact.

In this new work, led by GIS Principal Investigators Dr Niranjan Nagarajan and Dr Martin Hibberd, the sensitivity of detecting mutations has been significantly increased, thus making it possible to "catch evolution in real time". Being able to do this means that scientists can now observe the process of mutation as it happens, and catch how the organism or cancer cell develops resistance to drugs used.

The novel method, known as LoFreq, was achieved by combining deep sequencing of DNA with computational analysis to detect mutations at extremely "LOw FREQuency" in as few as one in 1000 cells. This approach is currently being used at the GIS to study the dengue virus, characterizing subtle shifts in the viral genome in response to new antiviral drugs.

Dr Niranjan said, "LoFreq has really allowed us to look at viral genome evolution in fine detail and we hope to use it construct better models for transmission of the dengue virus. We can also now identify key functional regions in viral genomes by highlighting spots that never mutate or mutate rapidly. In ongoing work, we are developing extensions to LoFreq that can better characterize mutations in Cancer."

Executive Director of GIS, Prof Ng Huck Hui said, "This innovation in the computational space highlights GIS's effort in developing unique capabilities in analyzing increasingly complex next-generation sequencing datasets. We expect that LoFreq will have wide utility in the analysis of viral, bacterial and cancer genome data."

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Scientists at A*STAR's Genome Institute of Singapore catch evolving germs and cancer cells early

The Cancer Genome Atlas is set to finish up next year after sequencing some 10,000 samples from about 20 different cancer types. TCGA has found, ScienceInsider notes, a number of new cancer genes and confirmed others that were previously identified. But with its price tag reaching over $375 million, some critics say it has been too expensive, though many disagree.

At a National Cancer Institute meeting earlier this week, Louis Staudt and Stephen Chanock discussed what could be a next step by sequencing even more samples, say 10,000 per tumor type, researchers could uncover rare variants contributing to the disease, ScienceInsider adds. Further, it could enable studies examining the interplay of genetics and environmental factors.

However, with the agency facing a 5 percent budget cut, such a grand project might not be realized. ScienceInsider also notes that some skeptics said that the project might reach a level of "diminishing returns." According to ScienceInsider Cold Spring Harbor Laboratory's Bruce Stillman noted that he is a supporter of TCGA, but that taking it to such a new scale "is not very sensible at the moment."

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After the Cancer Genome Atlas