Category Archives: Genome

Conceptualization of the Human Genome Project Development of Data Release Principles
February 14, 2013 - Human Genome Project (HGP) 10th Anniversary Seminar Series. Speakers: Robert Waterston Sir John Sulston More: http://www.genome.gov

By: GenomeTV

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Conceptualization of the Human Genome Project

1 day ago Feb. 15, 2013 - 11:52 AM PST

Genome sequencing is becoming more affordable than ever before several companies in the industry say the $1,000 personal genome is just around the corner. But, even if you can afford it, is mapping your genes worth it if you dont have a specific medical condition to consider?

Despite the whole knowledge is power argument it could help with early diagnosis and prevention or lead a doctor to better treatment options for an existing condition sequencing skeptics raise valid concerns and questions when it comes to gene sequencing for healthy people. How precise is it? How well will consumers be able to interpret the results? Will it just lead to needless hand-wringing about conditions that people wont be able to do to much to address or that wont surface until much later in life?

For now, those are questions for people with only the deepest pockets. But it wont be long before the conversation becomes more relevant for more of us and, in the Wall Street Journal this week, two doctors weigh in with the pros and cons of the debate over whether healthy people should have their genomes sequenced.

Dr. Atul J. Butte, division chief and associate professor at the Stanford University School of Medicine and director of the Center for Pediatric Bioinformatics at Lucile Packard Childrens Hospital in Palo Alto, Calif., takes the pro position. And Dr. Robert Green, a medical geneticist at Brigham and Womens Hospital and Harvard Medical School in Boston, argues against it.

Even though Dr. Butte acknowledges that gene sequencing isnt perfect, he believes the positives outweigh the negatives. He says:

On the flip side, Dr. Green believes that while affordable genomic analysis opens the door to personalized disease prevention and treatment options, there are still roadblocks. For example:

When it comes to health, I tend to fall on the side of information the more of it we have, the better off we are. And the rise of consumer-ready medical technology that gives us clearer windows into our bodies from Fitbits (see disclosure) to the AliveCor iPhone-compatible heart monitor is setting the stage for an era in which people are armed with even more data about their health. 23andmedoesnt do full gene sequencing but its genotyping services already let people explore their DNA for just $99.

But as we move into this new bioinformation-filled future, its important to keep the skeptics voices in mind because gene sequencing doesnt just have personal implications but public health consequences. One of Dr. Greens most haunting concerns is the rise of patients in waiting who spend their lives in anxiety, undergoing unnecessary tests and potentially doing themselves more harm than good. But asothers have noted, sequencing could take its toll on the health care system with unessential screenings and procedure, tax the patient-doctor relationship and lead to other biotethical questions.

Disclosure: True Ventures is an investor in Fitbit and the parent company of this blog, Giga Omni Media. Om Malik, founder of Giga Omni Media, is also a venture partner at True.

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As genome sequencing becomes more affordable should you do it?

Linda Chin, MD, on Translation of the Cancer Genome
TAMEST 2013 Annual Conference Probing the Depths: under the Sea and into the Brain January 17-18, 2013, Westin Galleria Dallas Hotel, Dallas, Texas http://www.tamest.org

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Linda Chin, MD, on Translation of the Cancer Genome - Video

Coast To Coast AM Archive Jul 05 2010 The Human Genome
Coast To Coast AM Daily - The Coast To Coast AM 2013 Archive - Watch The Best Of Coast To Coast AM Here - The Coast To Coast AM late night talk show hosted by George Noory with Ian Punnett, George Knapp, Richard Hoagland, Rob Simone and John B. Wells are the Coast To Coast AM hosts and will keep you informed late into the night. #9617; #9618; #9619; #9632;Beyond News Forum #9632; #9619; #9618; #9617; articlechase.com

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Coast To Coast AM Archive Jul 05 2010 The Human Genome - Video

Christian Music Genome

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Christian Music Genome - Video

Restriction enzyme display in the UCSC Genome Browser
This tip features a quick look at how to display restriction enzyme cut sites on the UCSC Genome Browser. For more details and references, visit: blog.openhelix.eu .

By: OpenHelixLLC

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Restriction enzyme display in the UCSC Genome Browser - Video

Next-Generation Whole Genome Sequencing Proves Extant Human Relative, Findings Published in Denovo Journal of Science

(PRWEB) February 13, 2013

The team, led by Dr. Melba S. Ketchum, DVM, of DNA Diagnostics in Nacogdoches, TX, sequenced the three whole nuclear genomes using the next-generation Illumina HiSeq 2000 platform at University of Texas, Southwestern from a tissue sample, a saliva sample, and a blood sample. The three genomes all attained Q30 quality scores above 88 on the Illumina platform, significantly higher than the platform average of 85, indicating highly-purified, single-source DNA with no contamination for each sample. The three Sasquatch genomes align well with one-another and show substantial homology to primate sequences.

In addition to the three nuclear genomes, Ketchums team also sequenced 20 whole and 10 partial mitochondrial genomes from the Sasquatch samples. In contrast to the nuDNA results, the Sasquatch mtDNA was fully modern Homo sapiens, indicating that the species is a hybrid cross between modern Homo sapiens in the maternal lineage and an unknown hominin male progenitor.

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Novel North American Hominins, Next Generation Sequencing of Three Whole Genomes and Associated Studies.

Authors: Ketchum MS, Wojtkiewicz PW, Watts AB, Spence DW, Holzenburg AK, Toler DG, Prychitko TM, Zhang F, Bollinger S, Shoulders R, Smith R.

DeNovo. 13 February 2013.

Specimens yielding DNA were obtained, purportedly from elusive hominins in North America called Sasquatch. Sequencing and genotyping were performed in addition to histopathologic and electron microscopic examination of a large tissue sample.

Mitochondrial whole genomes were consistent with modern humans. In contrast, novel data were obtained when nuclear DNA was sequenced. Next generation whole genome sequencing was performed on three samples. Phylogeny trees generated showed homology to human chromosome 11 and to primate sequences. The data indicates that the Sasquatch has human mitochondrial DNA but possesses nuclear DNA that is a structural mosaic consisting of human and novel non-human DNA.

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Researchers Sequence Sasquatch Genome, Novel Hominins Extant in North America

Public release date: 12-Feb-2013 [ | E-mail | Share ]

Contact: Sumrina Yousufzai syousufzai@plos.org 415-568-3164 Public Library of Science

A new form of genetic testing of the bacteria that causes tuberculosis can provide better information on TB transmission and also trace TB outbreaks more accurately than the current standard test, according to a study from Germany published in this week's PLOS Medicine.

A team of researchers led by Stefan Niemann from Forschungszentrum Borstel, Molecular Mycobacteriology, compared the results of the two types of tests on 86 M. tuberculosis isolates from a TB outbreak in the German states of Hamburg and Schleswig-Holstein between 1997 and 2010, in which 2301 people were diseased in the study period.

They found that the new test (whole genome sequencing) provided more accurate information on clustering and longitudinal spread of the pathogen than the standard test (classical genotyping). Importantly, whole genome sequencing revealed that first outbreak isolates were falsely clustered by classical genotyping and do not belong to one recent transmission chain.

By using whole genome sequencing, the authors estimated that the genetic material of M. tuberculosis evolved at a rate at 0.4 mutations per genome per year, suggesting that the bacterium grows in its natural host (infected people) with a doubling time of 22 hours, or 400 generations per year. This finding about the evolution of M. tuberculosis indicates how information from whole genome sequencing can be used to help trace future outbreaks.

Importantly, as the costs of whole genome sequencing are declining, this test could soon become the standard method for identifying transmission patterns and rates of infectious disease outbreaks.

The authors say: "Our study demonstrates that whole genome sequencing-based typing provides epidemiologically relevant resolution of large, longitudinal [Mycobacterium tuberculosis] outbreaks much more efficiently than classical genotyping."

They continue: "We envision that [whole genome sequencing] progressive effective implementation will be accelerated by the continuously decreasing sequencing costs, broader distribution of so-called bench top genome sequencers, and upcoming bioinformatics developments to facilitate quick and relevant interpretation of the resulting data in public health and medical contexts."

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Whole genome sequencing better at tracing TB outbreaks than standard test

BALTIMORE, Feb. 12, 2013 /PRNewswire/ --Exemplar LIMS has been selected as the primary lab management and electronic lab notebook (ELN) solution for NY Genome Center's laboratory operations. Sapio's LIMS system will initially track next generation sequencing workflows from the Illumina family of sequencers from request through analysis. Support for additional next gen sequencers will be added as needed.

Sapio's LIMS software will be deployed on Apple iPads using Exemplar LIMS for Tablets solution. This enables lab technicians to take the LIMS with them as they move around the laboratory, improving LIMS usability and lab technician efficiency. NY Genome Center will also be utilizing Exemplar's Materials Management capabilities for detailed tracking of reagent usage. NYGC will ultimately be processing samples for both research and clinical applications via a CLIA certified laboratory. Sapio's experience with implementing best practices for both research and clinical labs will accelerate the LIMS implementation in support of these NYGC objectives.

"The team at New York Genome Center has been impressed with the flexibility and scalability of Sapio's offerings," commented NYGC President & Scientific Director Robert B. Darnell, MD, PhD. "With Sapio we found an entrepreneurial partner that understands how important customer service and collaboration are to NYGC. We look forward to working with Sapio to design a solution for the genome center of the future."

"The leadership at NYGC has recognized the importance of next generation sequencing technology for both research and clinical applications and has assembled a top-notch team from top to bottom. We are both honored and enthused to be supporting the NYGC objectives with the ultimate goal of curing diseases," said Kevin Cramer, VP at Sapio Sciences. "We look forward to working with the NYGC team towards creating a world-class lab operation as they scale to be one of the largest NGS facilities in the North America."

For more information or to schedule a product demonstration, visit http://www.SapioSciences.com.

About Sapio Sciences Llc

Sapio Sciences is a leading provider of LIMS and Data Management software, enabling scientists to manage samples, protocols, assay data and clinical trials.With extensive expertise in genomics/NGS labs, Exemplar LIMS breaks new ground in its breadth of functionality and ease of configuration. With built-in Sample Management, Electronic Lab Notebook (ELN), scientific data management (SDMS) and integrated analytics, Exemplar LIMS addresses the full life cycle of samples from receipt to processing and analysis. Sapio will continue to lead in ease of use and breadth of functionality across its product line, enablingorganizations toreduce costs while increasing productivity and efficiencyof both laboratories and researchers alike.

About New York Genome Center

Founded in August 2010, the New York Genome Center (NYGC) is an independent, non-profit organization leveraging the collaborative resources of leading academic medical centers, research universities, and commercial organizations. Our vision is to transform medical research and clinical care in New York through the creation of one of the largest genomics research facilities in North America, integrating sequencing, bioinformatics, and data management. For more information, visit http://www.nygenome.org

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New York Genome Institute Selects Exemplar LIMS to Manage Next Gen Sequencing Labs

Quick quick unboxing - Genome
Just a few things I picked up over the past few days. I have been quite busy and not able to open most of the stuff I got but I thought I keep you guys some what updated. I plan on doing a kit overview soon

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Quick quick unboxing - Genome - Video