Whole Genome Sequencing Costs Continue to Drop

by Dr. Hsien-Hsien Lei
Posted February 11, 2008 in DNA Inventions and Gadgets, DNA Testing, DNA in General

One of the cheapest going prices for whole human genome sequencing has been set by Illumina at $100,000 with completion time of less than four weeks. Last year, 454 Life Sciences claimed a complete sequence in two months at around $1 million.

While Illumina and 454 Life Sciences (Roche) are considered by some to be leaders of the pack, Dr. Jonathan Eisen of The Tree of Life says competitors are emerging, including ABI and Helicos. Helicos BioSciences has received its first order for the Helicos Genetic Analysis System that includes HeliScope Single Molecule Sequencer, the HeliScope Analysis Engine, and the HeliScope Sample Loader.

Even as sequencing becomes cheaper and more efficient, Dr. Eisen reminds us of two considerations: data management and analysis as well as linking gene sequence to function. Writing from the Advances in Genome Biology and Technology conference in Marco Island, FL, Dr. Eisen:

Function and process have been replaced by terms like “systems biology” and “SNPs” and “networks” and “massively parallel.” We have in a way regressed in terms of treating organisms (or communities) as a black box. Fine scale detail has been lost in a sea of data.

Regardless, the big race now is towards the $1,000 genome and the Archon X PRIZE for Genomics. The first team to sequence 100 human genomes in 10 days for $10,000 or less per genome will win $10 million.

To aid in the sequencing of genomes, Pacific Biosciences aka PacBio is developing a “transformative DNA sequencing platform.” Their machines can read more bases at one go than others.

• PacBio – 1,000+ bases
• Human Genome Project – 800+ bases
• Illumina – 30-50 bases
• 454 Life Sciences – 200 to 450 bases

PacBio expects to begin selling machines in 2010 with second-generation machines that can perform $1,000 whole genome sequencing available in 2013. The New York Times has a profile of the company and their technology (Dr. Eisen has more). Other companies mentioned were Intelligent Bio-Systems, NABsys, VisiGen Biotechnologies, and Complete Genomics.

VentureBeat’s David Hamilton :

Although the “$1,000 genome” is a purely arbitrary goal, it’s become a Holy Grail of sorts for the genomics field. (The startup Knome, which we covered here, currently offers full-genome sequencing for $350,000.) Cheap, fast sequencing of all six billion DNA “letters,” or bases, in humans could make it possible, for instance, for doctors to better tailor treatments to a patient’s own genetic quirks or to identify the specific weaknesses of tumor cells. More broadly, it would also vastly increase our understanding of the genome, which has turned out to be a much more mysterious realm than just about anyone expected only a decade ago, and illuminate the ways DNA varies between individuals, groups and even among cells and tissues within a single individual.

There’s obviously a lot of DNA sequencing going on and it’s not limited to the US. Medical Solutions has become the UK’s first commercial provider of Illumina’s DNA sequencing and genotyping platforms – Genome Analyzer and Infinium on the BeadStation platform, respectively.

For those preparing themselves to have their whole genome sequenced, I recommend following Misha Angrist’s lead – So You Want To Know Your Genome .

NB: Jonathan Eisen, David Hamilton, Misha Angrist, and I are all members of The DNA Network .

(6 comments)

What’s in your DNA? #25

by Dr. Hsien-Hsien Lei
Posted February 10, 2008 in In Your DNA

Metrodad Pierre Kim at Karen Cheng’s Snippets of Life on buying handbags for his wife:

My overall track record of buying clothes for my wife is pretty good. However, I apparently lack the gene that gives one the ability to choose handbags. For her past birthday, I spent over a month researching Vogue magazines and scouring all the handbag sites. I was absolutely 100% convinced that she would love the bag I selected for her. Totally backfired. She hated it. Thank god for generous return policies.

Now, I’m in full training mode. My wife will show me a handbag and ask me whether she’d like it or not and I have to answer right away. It’s futile. I’m a lost cause. What is it with you women and your handbags?

India Knight of The Sunday Times (UK) thinks our genes are innocent of causing childhood obesity:

The fat kids you see waddling around aren’t fat because their genes just made them that way – they’re fat because they take very little exercise and are fed a great deal of fattening food which, to add insult to injury, contains very little that’s of any nutritional value. It’s not rocket science. Give your child sugar-laden “juice” and batter-covered chicken, chuck in industrial quantities of “food-product” stodge, dole out sweets as “treats” and raise them to be suspicious of vegetables, and voilà: you can start your own obesity epidemic. Especially if you blame their chafing thighs on their genes.

Sting at Magical Milestone reflects on her vision:

Both my parents were short sighted so I guess it’s written in my DNA. I suppose the fact that I was reading comics and story books at night under the blanket with a torchlight also contributed to it!

(1 comment)

DNA Video: 23andMe Genetics 101 Part 4

by Dr. Hsien-Hsien Lei
Posted February 9, 2008 in DNA Podcasts and Videos

New personal genomics company, 23andMe, created a series of videos introducing basic genetics concepts. Have a look at part 4 – What is phenotype? (Watch part 1, part 2, and part 3.)

Tags: genetics, genes, dna, personal genomics, genomics, 23andme, science, video

(1 comment)

DNA Quote: Kevin Kelly

by Dr. Hsien-Hsien Lei
Posted February 8, 2008 in DNA Quotes and Excerpts

From Kevin Kelly’s essay, Better Than Free:

Right now getting your copy of your DNA is very expensive, but soon it won’t be. In fact, soon pharmaceutical companies will PAY you to get your genes sequence. So the copy of your sequence will be free, but the interpretation of what it means, what you can do about it, and how to use it — the manual for your genes so to speak — will be expensive.

Kind of what I said – Drug Companies Should Offer Free DNA Tests.

(HT: Ryan)

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Genetic Testing for Psychiatric Diseases

by Dr. Hsien-Hsien Lei
Posted February 6, 2008 in DNA Testing, DNA and Disease

Three companies–Neuromark, Psynomics, and SureGene–are joining the genetic testing fray. Each is offering genetic tests for variants associated with mental illness.

• Neuromark’s Mark-C test is undergoing confirmatory studies (according to the website). The test will examine two genetic markers, GRIK2 and GRIA3, that appear to increase the risk of suicidal thoughts in people taking antidepressant drug Celexa.
• Psynomics claims to be the “first and only” company in the world to offer DNA tests for mental illness. Psynome tests for two mutations in the GRK3 gene associated with bipolar disorder. Psynome2 tests for mutations in the Promoter L allele gene that are associated with response to serotonin-based drugs.
• SureGene has developed the AssureGene test that examines a panel of (unspecified) genes and markers that is being marketed to aid in the diagnosis of patients at risk of developing psychosis. The test may also be used to predict drug response to antipsychotic medications.

Not surprisingly, the genetic tests have met with skepticism. Dr Cathryn Lewis at the Institute of Psychiatry, London was quoted in Guardian:

The general risk of developing bipolar depression is around one per cent. If you possess the worst set of gene variants, then your risk rises to three per cent. That means you are three times more likely than average to get bipolar depression. That may seem worrying but it is still a very low risk. It is still 97 per cent likely that you won’t get depression. People are not likely to realise that, however.

Without seeing the reports issued by these companies and not knowing whether genetic counselors are available by phone or email, I can’t say for sure that these companies are not providing proper customer service and information. At this early stage of genetic testing, however, potential consumers who have done their homework and studied their family medical history may find that these tests provide a tip-off towards more careful follow-up.

Family practice physician Tim Janzen wrote the following in a GENEALOGY-DNA list discussion (reprinted with permission):

I think that those in the medical profession are going to have positions all over the map on this topic. Some will be afraid that the results of genetic tests will cause unnecessary anxiety among those who are tested and shown to be predisposed to certain diseases. I fully admit that it may do that for at least some people. Others will welcome the information in that it will hopefully allow the doctors to be better informed as to which of their patients are at higher risk for mental illness.

I wouldn’t be surprised if the results of genetic tests are eventually integrated into treatment algorithms for people with mental illness. For instance, if a patient presents with depression and the genetic tests indicate a strong predisposition to depression, the doctor may be more inclined to treat that patient for many years with an antidepressant rather than just the 6 month minimum that is generally recommended for patients who present with depression for the first time.

The medical profession will simply need to keep in mind that these genetic tests will show predispositions to certain diseases, but a predisposition is frequently not equivalent to being destined to have the disease. We already welcome information such as cholesterol levels and blood pressure readings that tell us which patients are predisposed to heart disease and stroke. We act on those results accordingly.

Patients who have a family history of mental illness or other conditions already know that they have a predisposition (unless they are adopted). Thus the genetic results will either reinforce the fact that specific patients are at increased personal risk or they will show that they are at lower risk than they might otherwise be. We shouldn’t forget that environment also plays a role in mental health. Drug abuse is one environmental factor that also predisposes to mental illness.

For more about mental health, visit Alicia Spark’s Mental Health Notes.

NB: Andro Hsu of 23andMe has made a similar point in the past about presenting risk information.

(HT: UCL Institute of Human Genetics and Health)

(3 comments)

Geeky DNA T-shirt: CSI

by Dr. Hsien-Hsien Lei
Posted February 5, 2008 in Geeky DNA T-shirts

I haven’t watched CSI in a while but this t-shirt is still pretty cool looking. Available from the CBS Store.

CSI: Crime Scene Investigation

Every crime scene tells a story

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10 Reasons NOT To Take a DNA Test

by Dr. Hsien-Hsien Lei
Posted February 4, 2008 in DNA Testing

Some thoughts on why a person might NOT want to take a DNA test.

1. You have no idea what DNA is and where it is found in your body. (Although you can easily bring yourself up to speed by reading 100 Facts About DNA.)
2. You are on a tight budget and your health insurance won’t cover the cost of DNA testing. (On the other hand, you could raise money publicly like Andrew Meyer at Buzzyeah.)
3. You believe that ignorance is bliss.
4. You think genetic test results are no better than what you’d get going to your local psychic.
5. You’re not convinced that genetic discrimination can be totally banned.
6. You are not at high risk of an inherited disease because you live a healthy lifestyle and do not have a positive family medical history. (Of course, there are other more fun reasons to get genetic testing, such as genetic genealogy.)
7. You are not prepared to share your DNA test results with family members yet will feel guilty if your results have implications for their health or family relationships, e.g., BRCA breast cancer and ovarian cancer gene or non-paternity event.
8. You are not ready to accept any results from a genetic test that do not confirm your pre-existing beliefs. For example, a person with a family history of Huntington’s disease may be shocked to find that they do not carry the HD gene mutation.
9. You are not prepared to change your lifestyle even if you are found to have a mutation that increases your risk of a specific disease that involves both genes and environment, e.g., coronary heart disease and obesity.
10. You are a fatalistic person and will let genetic information control your life.

What other reasons can you think of to convince someone NOT to take a DNA test?

(27 comments)

Craig Venter on the Sinfest Forum

by Dr. Hsien-Hsien Lei
Posted February 3, 2008 in DNA Fun, Personalities with DNA

A fun conversation I saw on the Sinfest forums about Craig Venter’s genome:

Dro: My father was reading Craig Venter’s autobiography. I flipped it open to see if there was anything interesting about sequencing the genome. I read, “My Ph.D. committee was amazed by the length and rigor of my thesis”. Put down book.

mouse: a little thesis envy there, dro?

wish i could remember where i saw it – back when venter was sequencing the human genome, someone put up a poll on “who is the unidentified individual whose dna is being sequenced?” – and the choices were a) craig venter; b) craig venter or c) craig venter.

man doesn’t seem to have any self-esteem problems.

FYI, Sinfest is a webcomic by Tatsuya Ishida.

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DNA Video: 23andMe Genetics 101 Part 3

by Dr. Hsien-Hsien Lei
Posted February 2, 2008 in DNA Podcasts and Videos

New personal genomics company, 23andMe, created a series of videos introducing basic genetics concepts. Have a look at part 3 – Where do your genes come from? (Watch part 1 and part 2.)

Tags: genetics, genes, dna, science, video, 23andme, genomics

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The Journal of Genetic Rationalization

by Dr. Hsien-Hsien Lei
Posted February 1, 2008 in DNA Fun

The Journal of Genetic Rationalization by Mike S. Adams is horribly un-PC but may get a chuckle out of you this Friday. Here’s a tidbit about the “overspending gene.”

The Overspending Gene.

Overspending is a compulsion that brings many unwanted consequences. Among those consequences are debts, which, when incurred in college, cause a person to be less desirable to members of the opposite sex who are seeking marriage partners. This study shows that debt also varies positively with a woman’s likelihood of seeking an abortion. Furthermore, the present study shows that, today, more and more people are getting into deeper debt. The Darwinian implications of these findings are ignored altogether. It is concluded that debt is a condition no one would choose freely. Hence, the present study argues for the existence of an overspending gene. Future research is encouraged in order to find some actual evidence for such a gene.

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