The $1,000 Genome Debate is 'Already ... Irrelevant'

excerpted from GenomeWeb
Matthew Herper and Daniel MacArthur are at odds over the $1,000 genome. Forbes' Herper argues that even though sequencing is becoming cheaper, analyzing a genome still costs much more than $1,000. Over at Genetic Future, MacArthur responds that as sequencing costs continue to fall, "a substantial niche will develop for innovators providing affordable, intuitive, accurate interpretation tools." 

My thoughts on this later.. 

Exome Sequencing hints at sporadic mutations as cause for mental retardation.

1st spotted off Genomeweb
NEW YORK (GenomeWeb News) – De novo mutations that spring up in children but are absent in their parents are likely the culprit in many unexplained cases of mental retardation, according to a Dutch team.
Using exome sequencing in 10 parent-child trios, the researchers found nine non-synonymous mutations in children with mental retardation that were not found in their parents, including half a dozen mutations that appear to be pathogenic. The research, which appeared online yesterday in Nature Genetics, hints at an under-appreciated role for sporadic mutations in mental retardation — and underscores the notion that mental retardation can stem from changes in a wide variety of genes.

 I think it's fascinating to find so many new mutations and changes in DNA that may affect one's quality of life, simply by sequencing the coding regions (and not all of it if I may add). This paper is fascinating as it raises the question if deleterious sporadic mutations are unlikely culprits for a whole variety of diseases that have a genetic risk.
it is certainly more likely that such an event will occur in coding regions but I do not doubt that for some diseases, perhaps the non-coding regions (that play a regulatory role) might have the same effect. If it was a clear cut mutation that results in a dysfunctional protein, and there's no redundancy in the system, it is likely the system will crash. whereas, if it was changes in the expression levels, it might lead to a slightly wobbly system that just doesn't function as well.

While everyone else is waiting for Whole Genome Sequencing to drop in price. There are groups already publishing with exome data. I think in 6 months time, we will see more WGS papers coming up... It's an exciting time for Genomics science!

See the full paper below

A de novo paradigm for mental retardation Nature Genetics | Letter

 

NIH has 4 gene patents!

My voracious reading has led me to a blog post describing the recent events on gene patents
interesting snippets include
NIH holding 4 gene patents (hmmm I wonder what are those.. )

For years, the U.S. Patent Office has taken the position that extracted genes, or “isolated DNA,” can be patented. And, in fact, it has issued thousands of patents on human genes, with perhaps one of every five human genes now under patent.  Patent rights to a gene, of course, give the owner the exclusive right to study, test and experiment on the gene to see how its natural characteristics work.
It has been more than 20 years since the Patnet Office began approving patents for human genes in the form of “isolated” DNA.  Prior to that, the Office had issued patents for synthetic DNA, but then moved on to grant monopoly rights on the natural material when extracted directly from the body and not modified.  The Obama Administration, in the brief it filed late Fridiay in the Federal Circuit, is not challenging patents on synthetic DNA, or on the process of extracting DNA, but only on unmodified genes themselves.
The Patent Office’s long-running approach to genetic patents was challenged in a lawsuit filed in May 2009 by the American Civil Liberties Union and the Public Patent Foundation, contending that locking up genes in the monopoly rights of a patent would inhibit research by other scientists on diseases that might be flagged by the coding or mutations of the genes.   The lawsuit targeted both the Patent Office and Myriad Genetics, specifically because of patents that company was issued on human genes that have been labeled “BRCA1″ and “BRCA2.’  Mutations of those two genes are associted with significantly higher risks of breast cancer and ovarian cancer. .....

"U.S. government is actually the co-owner of four of the seven patents that are involved in the case.  It has granted Myriad an exclusive license under those patents — contrary, it said, to NIH’s usual practice of not granting exclusive licenses under DNA patents for “diagnostic applications.”  In the past, NIH and other government agencies have sought and obtained patents for human genes in the form of “isolated genomic DNA,” according to the brief.

The brief did not say which claims under the four patents co-owned by NIH would be invalid under its theory of patentability."

12 Geneticists unzip their genomes in full public view

A GROUP of 12 genetics experts will expose their DNA to public view today to challenge the common view that such information is so private and sensitive that it should not be widely shared. 

The "DNA dozen" will publish full results of their own genetic tests, including implications for their health, in a controversial initiative to explain the significance of the human genome for medicine and society.
The Genomes Unzipped project aims to demystify the genetic code, showing what it can and cannot reveal about individuals' health and allaying fears about discrimination and privacy.
The participants - 11 British-based scientists and an American genetics lawyer - hope to encourage many more people to share details of their genomes with researchers. This would allow the creation of open-access DNA databases that any scientist could use, enabling a "wisdom of crowds" approach to research that will accelerate discoveries about genetics and health.

What's your BRCA status? Personal Genomics testing.

Do-it-yourself genetic testing
   How to test your BRCA status and why we need to prepare for the personal genomics age.
Genome Biology 2010, 11:404

Interesting read covering issues on personal genomics. Did you know that “the BRCA gene patents, which are held by Myriad Genetics, cover all known cancer-causing mutations in addition to those that might be discovered in the future.” How did that one slip through the patent office?? Not that it really matters “Currently Myriad charges more than $3000 for its tests on the BRCA genes, while sequencing one's entire genome now costs less than $20,000. Furthermore, once an individual's genome has been sequenced, it becomes a resource that can be re-tested as new disease-causing mutations are discovered. “


“Regardless of how easy it might be to test for mutations, the restrictive nature of the BRCA gene patents means that anyone wishing to examine any mutation in BRCA1 or BRCA2 will have to obtain permission from the patent holder Myriad Genetics. This restriction applies even if testing your own genome. If you wanted to look at other genes, you would have to pay license fees for any of them that were protected by patents. In practice, although it may seem absurd, this means that before scanning your own genome sequence, you might be required by law to pay thousands of license fees to multiple patent holders. “


This is complete hogwash! ( the concept that I have to pay genome-squatters (see cybersquatters) in the human genome, I would much rather pay for real estate on the moon! )



related posts
US clinics quietly embrace whole-genome sequencing @ Nature News
Commentary on Personal Genomics testing

Commentary on Personal Genomics testing

I was reading the usual "say no to personal genetics tests" blog post

 The Empty (and Misleading) Promises of Do-It-Yourself Genetic Tests

I shall go out on a limb here and declare up front, I am ambivalent about personal genetic tests. In addition, I am wholly against unscrupulous consumerism that overpromises (which might be genetic tests for factors that can't possibly be done now with our current scientific knowledge e.g. intelligence testing, for a list of good examples you may refer to "Some of the 40 behavioral genes that are tested  here." There are a few of the behavioural genes which I believe are bona fide but 'self detoxification' has to be a joke, I hope)

That being said, I would like to offer the flipside of the story. 

The term 'increased risk' is contentious. If you recall the "Toyota Recall" fiasco, did you manage to get any numbers on the increased risk of driving one of the affected cars? The difference is 0.00028 percent according to this page. 

Would that stop you from not sending your car in?

Of course not, and I am not urging you to stop as well. 

But the point is not wholly about the increased risk, but rather your right to know the risks that you are taking. Knowledge is a double edged sword, I recall a friend being tormented by her positive results for early Down's Syndrome screening for her unborn child. Only the negative results from her amniotic fluid test set her mind at rest. Yet I believe no one would ask that the results of the first test be kept private from a patient to prevent undue worry. And I am sure the doctor explained the test fully. But it is only natural for my friend to be worried. 

I do agree with Taralyn, without a healthcare professional explaining the results of the test, the potential for abuse and fear mongering is there. However, she should expect the average consumer who chooses a genetic test, is not an average consumer. He or she is likely an educated consumer, who has an idea of what the test portends or has a known family history of cancer / genetic disease and wishes to have the knowledge to better manage his/her lifestyle.

And to Taralyn, I would like to answer with a "YES" to your question of "Will I ever be able to air-mail a swab of my saliva for my genetic read-out?" Not because you should but you can if you so choose to. This is because the technology is here.