Category Archives: Genome

Technologies like Illumina's sequencing machine are radically cutting the cost of mapping out the human genome.

(CNNMoney)

Afternoon jitters, though, were not the reason Costa, a primary care physician, decided to have his DNA sequenced last year. He wanted to find out if he was predisposed to certain illnesses and see if the test he took -- priced at just $99 -- might be useful for his patients.

Costa, who owns Enhanced Medical Care in Newton, Mass., had his DNA sequenced by 23andMe. The Mountain View, Calif., startup has been a pioneer in low-cost genetic testing aimed at consumers, with a test that currently analyzes around 1 million locations on each client's genome and generates a report on 248 health conditions and traits.

Entrepreneurs and scientists are pursuing an even more dramatic medical breakthrough: The ability to sequence an entire human genome for around that same $100 price tag. That goal remains a few years away, but the obstacles are falling fast.

Sequencing is a way of "reading" DNA molecules -- two strands twisted together to form that famous double helix. The entire human genome contains roughly 3 billion molecular base pairs, which researchers study to find variations that might play a role in the development of diseases. Right now it typically costs $1,000 to $4,000 to map out an individual's genome. (Specialized sequencing -- for, say, a cancer patient -- often costs more.)

That's not cheap, but it's an enormous plunge from where the price tag stood just a few years ago. When one of the first individual genomes was sequenced in 2007 -- that of James Watson, co-discoverer of DNA's double-helix shape -- it cost around $1 million.

"The cost-per-bit of biologic information is coming down faster than Moore's Law," says G. Steven Burrill, the founder of Burrill & Company, a San Francisco financial services firm focused on the life sciences industry. A data set compiled by the National Institutes of Health's genome research lab bears out that comparison: Since 2007, the cost of genome sequencing has been in free-fall, dropping by as much as 90% several years in a row.

Related story: This is what the world will look like in 2045

Dozens of startups are trying to carve off their chunk of a genetic testing market that UnitedHealthcare estimates could reach $25 billion annually by 2021.

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The race to a $100 genome

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Genome Editing with Engineered Zinc Finger Proteins - Philip D. Gregory
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Genome Editing with Engineered Zinc Finger Proteins - Philip D. Gregory - Video

The Innovation Genome ProjectThe 7 Essential Innovation Questions 20130603 1959 1

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Genome Evolution
Gabrielle est une mre de famille calme, aimante et douce. Elle vit dans une socit o tout est valu (du sourire, aux capacits mentales ainsi que physiqu...

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Technology Open Access Human Genome, Environment Trait data
"George Church, PhD, Professor of Genetics, Director of the Center for Computational Genetics, Harvard Medical School" The Project (PersonalGenomes.org) enab...

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Public release date: 23-Jun-2013 [ | E-mail | Share ]

Contact: Alison Heather a.heather@garvan.org.au 61-434-071-326 Garvan Institute of Medical Research

Scientists from Australia and the United States bring new insights to our understanding of the three-dimensional structure of the genome, one of the biggest challenges currently facing the fields of genomics and genetics. Their findings are published in Nature Genetics, online today.

Roughly 3 metres of DNA is tightly folded into the nucleus of every cell in our body. This folding allows some genes to be 'expressed', or activated, while excluding others.

Dr Tim Mercer and Professor John Mattick from Sydney's Garvan Institute of Medical Research and Professor John Stamatoyannopoulos from Seattle's University of Washington analysed the genome's 3D structure, at high resolution.

Genes are made up of 'exons' and 'introns' the former being the sequences that code for protein and are expressed, and the latter being stretches of noncoding DNA in-between. As the genes are copied, or 'transcribed', from DNA into RNA, the intron sequences are cut or 'spliced' out and the remaining exons are strung together to form a sequence that encodes a protein. Depending on which exons are strung together, the same gene can generate different proteins.

Using vast amounts of data from the ENCODE project*, Dr Tim Mercer and colleagues have inferred the folding of the genome, finding that even within a gene, selected exons are easily exposed.

"Imagine a long and immensely convoluted grape vine, its twisted branches presenting some grapes to be plucked easily, while concealing others beyond reach," said Dr Mercer. "At the same time, imagine a lazy fruit picker only picking the grapes within easy reach.

"The same principle applies in the genome. Specific genes and even specific exons, are placed within easy reach by folding."

"Over the last few years, we've been starting to appreciate just how the folding of the genome helps determine how it's expressed and regulated,"

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The genome's 3-D structure shapes how genes are expressed

June 20, 2013 Bacterial DNA may integrate into the human genome more readily in tumors than in normal human tissue, according to a new study from the University of Maryland School of Medicine's Institute for Genome Sciences. Researchers analyzed genomic sequencing data available from the Human Genome Project, the 1,000 Genomes Project and The Cancer Genome Atlas (TCGA). They considered the phenomenon of lateral gene transfer (LGT), the transmission of genetic material between organisms in the absence of sex.

Scientists have already shown that bacteria can transfer DNA to the genome of an animal. The researchers at the University of Maryland Institute for Genome Sciences found evidence that lateral gene transfer is possible from bacteria to the cells of the human body, known as human somatic cells. They found the bacterial DNA was more likely to integrate in the genome in tumor samples than in normal, healthy somatic cells. The phenomenon might play a role in cancer and other diseases associated with DNA damage. The paper was published in PLOS Computational Biology on June 20.

"LGT from bacteria to animals was only described recently, and it is exciting to find that such transfers can be found in the genome of human somatic cells and particularly in cancer genomes," says Julie C. Dunning Hotopp, Ph.D., Assistant Professor of Microbiology and Immunology at the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine and lead author on the paper. Dr. Hotopp also is a research scientist with the University of Maryland Marlene and Stewart Greenebaum Cancer Center. "Studies applying this approach to additional cancer genome projects could be fruitful, leading us to a better understanding of the mechanisms of cancer."

In the research, a team of interdisciplinary scientists and bioinformatics researchers found that while only 63.5% of TCGA samples analyzed were from tumors, the tumor samples contained 99.9% of reads supporting bacterial integration. The data presented a compelling case that LGT occurs in the human somatic genome and that it could have an important role in cancer and other human diseases associated with mutations. It is possible that LGT mutations play a role in carcinogenesis, yet it is also possible that they could simply be passenger mutations.

The investigators suggest several competing ideas to explain the results, though more research is needed for definitive answers. One possibility is that the mutations are part of carcinogenesis, the process by which normal cells turn into cancer cells. Alternatively, tumor cells are so very rapidly proliferating that they may be more permissive to lateral gene transfer. It is also possible that the bacteria are causing these mutations because they benefit the bacteria.

The study was funded by the National Institutes of Health's Director's New Innovator Award Program (1-DP2-OD007372) and the NSF Microbial Sequencing Program (EF-0826732).

"This is the type of basic science research, conducted using the analysis of much publicly available genomic data, that makes us leaders in the cutting edge field of genomic science and personalized medicine," says E. Albert Reece, M.D., Ph.D., M.B.A., Vice President for Medical Affairs at the University of Maryland and the John Z. and Akiko K. Bowers Distinguished Professor and Dean of the University of Maryland School of Medicine. "It is just this type of research that will lead us to a new world of personalized medicine, in which doctors can use each patient's genomic make-up to determine care and preventive measures. We are excited to be a part of this future with the outstanding work of our Institute for Genome Sciences."

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Bacterial DNA may integrate into human genome more readily in tumor tissue

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Say Hello to GMOs - Changing the Human Genome One Meal at a Time

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Say Hello to GMOs - Changing the Human Genome One Meal at a Time - Video