MetaFilter posts tagged with genomics

Breast cancer rules rewritten in 'landmark' study

Blasdelb — Mon, 05 Nov 2012 00:58:09 -0800

What we currently call breast cancer should be thought of as 10 completely separate diseases, according to an international study which has been described as a "landmark". The categories could improve treatment by tailoring drugs for a patient's exact type of breast cancer and help predict survival more accurately. The study in Nature analysed breast cancers from 2,000 women [Abstract] . It will take at least three years for the findings to be used in hospitals. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups [Abstract] The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in ~40% of genes, with the landscape dominated by cis- and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP and MAP2K4. Unsupervised analysis of paired DNA–RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, oestrogen-receptor-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the ‘CNA-devoid’ subgroup and a basal-specific chromosome 5 deletion-associated mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome.

ENCODE: the Encyclopedia of DNA Elements

Westringia F. — Thu, 06 Sep 2012 07:52:35 -0800

In 2001, we learned the sequence of our genome; now, we have amassed a vast amount of knowledge about what those sequences actually do. Yesterday, the data from the ENCODE project went live. ENCODE, the Encyclopedia of DNA Elements, is a project to identify and annotate all functional elements of the human genome, including transcription, transcription factor association, chromatin structure, and histone modification. It is a major achievement that was announced in a fanfare of publications. An elegant and accessible description of the project was posted by science writer Ed Yong on his Discover blog Not Exactly Rocket Science. The data is publicly explorable through a very nice interface, including an iPad app and a virtual machine. ENCODE constitutes a vast amount of data that will have a significant impact on research in genetics, bioinformatics, and medicine. Ewan Birney, the lead data analysis coordinator, discusses in Nature how the vast amount of data was wrangled, and has posted additional thoughts on his blog.

Buzzing about network graphs

Blazecock Pileon — Sun, 04 Dec 2011 02:07:51 -0800

A hive plot (slides) is a beautiful and compelling way to visualize multiple, complex networks, without resorting to "hairball" graphs that are often difficult to qualitatively compare and contrast. Hive plots were conceived by Martin Krzywinski, the primary author of the Circos software package, used to represent genomic and other data that render well in circular form. To make your own hive plots, take a look at Krzywinski's linnet library, or if you like R, there's HiveR.

master of information

kliuless — Sat, 09 Apr 2011 11:00:18 -0800

The New Biology - Eric Schadt's quest to upend molecular biology and open source it. (via)

Possible pre-Columbian Native American gene found in modern Icelanders

knile — Fri, 19 Nov 2010 07:23:20 -0800

An Icelandic company called deCODE genetics (previously) has found evidence, though not conclusive, that an unknown American woman traveled to Iceland, possibly against her will, as early the year 1000 but not later than 1700. She had offspring in Iceland with natives. 80 of her descendants are still extant in that country. This finding has been announced in a pre-print online publication of the American Journal of Physical Anthropology. The work involved explorations of mitochondrial DNA, which are frequently employed to examine humans' centuries-old lineages. One surprising result is that this lineage does not seem to line up with previously known Native American genetic markers, but the authors believe that the explanation above is "[more] likely" than this common ancestor being European or Asian. (Via Daily Mail.) deCODE has also recently made the news by publishing a new, higher-resolution map of the human genome (Nature subscription required to view full article).

Venter creates spiraling coils of self-replicating DNA.

BoatMeme — Thu, 20 May 2010 10:50:37 -0800

"The ability to design and create new forms of life marks a turning-point in the history of our species and our planet." - Freeman Dyson, on the J.C. Venter Institute's creation of a cell controlled by a synthetic genome. We are now in the business of engineering life.

"You Can't Patent Nature"

zarq — Wed, 31 Mar 2010 12:53:09 -0800

Followup to this post: A US District Court has ruled that Myriad Genetic's patents on breast cancer genes BRCA1 and BRCA2, which allow them to hold exclusive rights to a widely used genetic test for inherited breast and ovarian cancer susceptibility, are invalid. Genomics Law Report analyzes the ruling in two posts. The decision is likely to be challenged in a legal appeal — but if upheld, it could have huge implications for the biotechnology industry. Biotech stocks tumbled after the announcement. Fortune's Daily Brainstorm blog asks, "Is the DNA Patent Dead? GenomeBoy: After the Gold Rush Discover: Tuesday’s decision, if upheld, could have wide repercussions for the multi-billion dollar biotech industry, which is built on more than 40,000 gene patents. Already, about 20 percent of the human genes have been patented. The decision, however, is not binding on other federal courts and other judges may or may not abide by it. But it does the set the stage for years of litigation over other gene patents. Myriad Genetics plans to appeal the judgment.
AOL Daily Finance: "After a U.S. District Court ruling yesterday, women in America may soon be able to get the same access to inexpensive, verifiable gene-testing for breast cancer that women in Europe currently enjoy."

I'm sure this'll end well....

zarq — Mon, 22 Feb 2010 09:48:15 -0800

We may soon be able to clone Neanderthals. But should we? An essay from Archaeology Magazine examines the ethical, scientific and legal ramifications. (Via Heather Pringle's Time Machine blog, where essay author Zach Zorich posted a reply and elicited a response.) Background: Last year, a team of researchers led by geneticist Svante Pääbo at the Max Planck Institute announced that they had completed a draft sequence of the Neanderthal genome. The project was begun in 2006. William Saletan covered some of the same ground in Slate in 2008, as did Reason.com last year: One science fiction trope says that it is impossible for two intelligent species to evolve simultaneously on the same planet since one would inevitably out-compete the other. This may have happened on our planet. Neanderthals disappeared around the same time that modern humans began to move into their territory. New research suggests that our ancestors killed them off. Perhaps we should use modern science to resurrect Neanderthals in order to right an ancestral wrong.

Cracking the Cancer Code

zarq — Thu, 17 Dec 2009 09:59:24 -0800

Cracking the Cancer Code: We already know that all cancers are caused by DNA mutations acquired during a person's lifetime. But what mutations actually cause cancer? We may be one step closer to finding out. International research teams led by the Cancer Genome Project at the Wellcome Trust Sanger Institute have now mapped the entire genetic code of two of the most common human cancers: lung and skin (malignant melanoma). Their findings have the potential to revolutionize preventative and treatment therapies as well as pave the way for new early detection tests. More. Additional research is now underway to map the mutations of cancerous breast, hepatic, oral, stomach, ovarian, pancreatic and brain cells.

Gene Genie

storybored — Mon, 19 Oct 2009 10:53:58 -0800

I.B.M. Joins Pursuit of $1,000 Personal Genome The target is remarkable given that the original Human Genome Project successfully sequenced the first genome less than ten years ago and cost roughly $500 million to $1 billion. Advances in sequencing technology puts Moore's Law to shame: "In the last four to five years, the cost of sequencing has been falling at a rate of tenfold annually, according to George M. Church, a Harvard geneticist. In a recent presentation in Los Angeles, Dr. Church said he expected the industry to stay on that curve, or some fraction of that improvement rate, for the foreseeable future." The old way of doing things was laborious. The new way involves "a 'DNA transistor,' which it hopes will be capable of reading individual nucleotides in a single strand of DNA as it is pulled through an atomic-size hole known as a nanopore. A complete system would consist of two fluid reservoirs separated by a silicon membrane containing an array of up to a million nanopores, making it possible to sequence vast quantities of DNA at once...[the goal is to build a machine that could sequence] an individual genome of up to three billion bases, or nucleotides, 'in several hours.' "

Do they preserve scientific transparency, protect profits or both?

zarq — Wed, 13 May 2009 10:16:38 -0800

On behalf of medical organizations, universities, & individual patients, pathologists and genetics researchers, the ACLU has filed a lawsuit against Utah-based Myriad Genetics and the US Patent and Trademark Office. Myriad holds the US patents to the BRCA1 and BRCA2 genes, associated with hereditary causes of breast and ovarian cancers. Their patents guarantee the company the right to prevent anyone else from testing or studying those genes, which the ACLU says is unconstitutional and inhibits researchers from finding treatments and cures. The ACLU has posted a FAQ explaining the suit. It might be news to some that genes, gene fragments and the tools used to assess them can be patented. Here's some general info on patent eligibility and qualifications. Some question whether such patents spur or stifle research Myriad's BRCA test to measure the likelihood that someone would develop ovarian or breast cancer was in the news a couple of years ago, when a study revealed that it produces false negatives. Concerns were also raised in the EU over the patents when they were initially filed. Previously on MeFi

The Genomic Self

homunculus — Sat, 10 Jan 2009 17:48:16 -0800

My Genome, My Self: Steven Pinker considers what we can expect from personal genomics. Searching for Intelligence in Our Genes: Carl Zimmer looks at the hunt to learn about the role of genes in intelligence.

Metafilter of the brain

Gyan — Mon, 02 Oct 2006 16:27:22 -0800

Neuroscience Gateway - "a comprehensive source for the latest research, news and events in neuroscience and genomics research"

OMG hypoallergenic kitten!!!

ikkyu2 — Mon, 12 Jun 2006 18:21:50 -0800

The all-new sneeze-free cat this week joins a distinguished roster of altered organisms, such as glowing green pigs and bunnies, ampicillin-resistant maize and tomato, and even a potato with a bacterial pesticide spliced in. And don't forget OraGenics, the company that wants to infect your teeth with bacteria that won't cause decay - and will crowd out the ones that do. Brave New World, indeed. What's next?

so what's in that 0.1%?

shoos — Thu, 05 Jun 2003 00:30:14 -0800

DNA used to ascertain race of unidentified serial killer. Florida company DNAPrint Genomics claims their test can identify the race (ie, African, Caucasian, East Asian or American Indian) of a person from their DNA. CEO Tony Frudakis says that "of over 2,200 blind samples tested, the test is yet to get one wrong."