50 million personal genome sequences by 2015?

Just how quickly will the market for personal genome sequences grow? My back-of-the-napkin calculation pegs it at 50 million sequences obtained by 2015, give or take. While this is far from a scientifically derived calculation, my rationale is simply to assume that the trend line for the personal genome sequencing market might look a lot like the one experienced in the personal computer market.

Welcome to 1980
The personal computer industry grew from several thousand units sold in 1975 to 50 million units in 1995. If the personal genome sequencing market follows suit, we might say that 2007 for personal genome sequences was like 1979 for personal computers, and we’ve just turned the corner into 1980 where units sold remains sub 1 million, but growth is noticeable. If growth continues apace, we’ll hit 50 million sequences obtained somewhere around 2015-2020.

PCs 1980-1995: sparkline
pDNA 2007-2015: sparkline


Deus ex machina
A difficulty with predicting the future is human agency, or choice. How quickly will people warm to the idea of surfing their personal genome sequence? Although we’re in the early days, personal genome sequencing evangelists are starting to appear in unexpected places. Enter Christopher Hitchens. In a recent interview about his newest book on the Hoover Institute’s show Uncommon Knowledge, he paused and said: “As it happens, I’ve had my DNA sequenced recently. You can get yours done too. And you should, by the way…”. Here is the clip (you can skip the 8 min point):


History, on repeat
How else might the personal genome sequencing market resemble the personal computing industry? For some ideas, witness this absolutely brilliant piece of video from Britain in 1969 — a year when computers were not yet “personal” computers, but they were clearly heading that direction:

Part 2, and Part 3

The interviews with people on the street are amazing. When asked, “So what do you think of computers?”, responses range from the aloof “What are computers?” to the utopian “a revolution like we’ve never seen” to the dismissive “yeah, they’re great, but I don’t know what all the fuss is about” to the completely dystopian “the government will use them to control us”.

At the close of the video, renowned professor Donald Michie (University of Edinburgh) had this to say:

“[Computers are] bringing about the greatest revolution the human race has ever known…This revolution could lead to terrible consequences, or it could lead to the greatest advances ever for the human race. Which of these things are to happen, is up to us.”

Fools Game
Attaching a number to a 10 year forecast is a fools game. The timescale may be off-base in either direction. The point of writing this post though is to help set expectations about a near-term future where many millions of people have obtained personal genome sequences (including partial sequences). This point still escapes many people who work in and around the genetics field.

Can I see some ID?

Should there be a minimum age requirement for personal genome sequencing? If so, what age?

Or maybe that question is irrelevant — or only relevant for the next decade or two. Future generations might get sequenced at birth (or maybe even prior to birth via PGD). That might leave no individual choice about personal sequencing, in which case, maybe there will be regulations about the minimum age for disclosure of personal genomic data to individuals. 13? 18? 21? 30? What age?

Read more

Best Sentence I Read Today

Who knows how long it will take for personal genomes to become useful, but one thing is for certain, someday it will be said that it all started with the genomes of ten volunteers.

From a very thoughtful comment by Willy Lensch on this blog post about last Wednesday’s meeting with the first 8 volunteers and the staff of the Personal Genome Project (including me).

More notes on the meeting to follow soon…

Genomic Counseling

Tired: Genetic Counseling
Wired: Genomic Counseling

Who came up with the phrase "genomic counseling"?  The earliest data point I can find is from a June 2004 SACGHS Meeting, where Dr. Muin J. Khoury is quoted as saying:

"So how is NSGC [editor: The National Society of Genetic Counselors] going to or has begun to address this range of genomic information, from somatic cell to polymorphisms, and is there a role for something that we might call genomic counseling, and where does genomic counseling end and health education start, and the practice of medicine? So there is that tension between having more specialists versus integrating the genomics knowledge into the practice of daily medicine."

(If anyone knows a different provenance to this phrase, let me know in the comments or drop me a line.)

The question of where the hand-off is from the education (or counseling) of consumers about genomic data to the integration of this information into medical/clinical care is a good one.  In my mind, the answer to that question depends on the type of information genomic data can provide, i.e. whether the information is clinician-centric or consumer-centric. 

Some types of information will be actionable only by the clinician,
e.g. genetic testing to determine warfarin dosing. 

While other types of information will be more
relevant to the actions of the consumer, e.g. CF carrier screening by couples planning a pregnancy. 

There are also types of genomic data that create actionability somewhere in-between, i.e. where a clinicians actions should take into consideration a patient’s preferences.  A good example is genetic testing for irinotecan dosing, where this genomic data should inform the dosing, in light of the patient’s preference for aggressive treatment versus toxicity risk (see the excellent interview with Howard McLeod about this issue). 

Even when genomic information is clinician-centric, there will remain (for the foreseeable future) a role for the patient in creating physician awareness about how this information may influence patient care.  Nobody is more interested a therapeutic outcome than the patient who is at risk.  For this reason patients will continue to be — and increasily will become even more — informed about their care.  In terms of recent genetic testing history, there have been more than one study (or this one) showing that the number one predictor of whether a physician orders a genetic test is patient demand. 

Another question for genomic counseling: What is the likely format?  Face-to-face?  Probably not.

An Interview with Howard Mcleod. To Test or Not Test: An Update on UGTA1T1 Testing.  Oncology Issues, Nov/Dec 2006. (PDF)

Wideroff L et al. Physician use of genetic testing for cancer susceptibility: results of a national survey. Cancer Epidemiol Biomarkers Prev. 2003 Apr;12(4):295-303.

Sifri R. et al. Use of cancer susceptibility testing among primary care physicians. Clin Genet. 2003 Oct; 64(4):355-60.

The Incidentalome

A very important paper was published last week in JAMA.  The punch line is this: Once the new high throughput diagnostic testing technologies — like massive SNP panels — are widely deployed there will be a significant spike in both true-positive and false-positive results.  The implications of this fact are deep and wide.

If you’ve got access to JAMA, check it out.  Otherwise, I’ll summarize the important parts the paper later this week. 

Isaac Kohane, Daniel Masys, and Russ Altman. "The Incidentalome: A Threat to Genomic Medicine" JAMA 296(2): 212-215. July 12, 2006. (sorry subscribers only)


Back in 2004, Life Science Insights surveyed a group of genome experts for opinions on the date when cheap human genome sequencing would be available.  Here is a summary of what they said:

Forty percent of the genome experts interviewed by LSI believe that the $1000 genome will not be reached within ten years.  This compares to a mere 17% who believe it will be here in five years. Ten percent of respondents said that scientists would not even reach the $100,000 genome within ten years. Clearly, there is disagreement over how fast these technologies are developing.

Predictions are fun to watch play out over time, particularly when expert opinions vary wildly.  Remember GeneSweep?  The experts in this contest made predictions about the number of genes in the human genome.  They ranged from 25,000 - 300,000.  Here is a snapshot of the distribution of bets, dating from March 2003:


With such wildly different opinions about the future of personal genomics, perhaps a Long Bet is in order.  GenomeSweep anyone?

Zachary Zimmerman, The Promise of the $1000 Human Genome (PDF). Life Science Insights, October 2004.

GeneSweep History from Cold Spring Harbor.

Internet Archive snapshot of GeneSweep page from March 2003.

In case you’re wondering, the winner of GeneSweep was Lee Rowen from the Institute for Systems Biology in Seattle.  Her prediction was 25,947 genes.

Flockhart on the ascent of PGx

MIT Technology Review interviewed David Flockhart of IUPUI recently.  Here is a snip about the adoption of PGx testing:

TR: But the FDA has already approved a number of genetic tests to guide prescriptions. Aren’t doctors using them?

No…A major problem is
going to be educating physicians who are, as yet, relatively uneducated
about the availa­bility of genetic tests to guide some of their
prescribing decisions.

TR: How long will that take?

…The movement of these tests into the clinic will happen
gradually with fits and starts….Demand will kick in within a year or
two, as patients realize the power of these tests. That will be the
biggest driver…

Erika Jonietz. Getting Personal about Drugs. Genetic tests are poised to revolutionize prescription writing. MIT Technology Review. March/April 2006.

David Flockhart’s website at IUPUI.

Mexican HapMap Project

Mexico has launched its own genome project:

Mexico has launched a racebased genome project to determine if a genetic basis exists for its growing health crisis. The goal is to glean insights into genetic differences, believed to be unique to its population, that may play a key role in chronic diseases like asthma, diabetes and hypertension.

…The Instituto Nacional de Medicina Genomica (National Genomic Medicine Institute of Mexico, or INMEGEN) will manage the resulting ‘Mexican HapMap’…According to Gerardo Jimenez, director of INMEGEN and the new collaboration, INMEGEN will begin by sampling individuals in six remote regions of Mexico to construct a consensus genetic map that fits the entire Mexican mestizo population, a mixture of Europeans (mainly Spaniards) and Indians. The first objective is to determine if every block of nucleic acid sequence will be alike for all the Mexican groups. “My own prediction,” says Jimenez, “is that we are not going to find huge differences.”

INMEGEN will release newly mined genomic data into the public domain as fast as technology allows, but Jimenez is quick to point out that the measure of the project’s success is not the science, but rather the medicines that come out of it. He also envisions the initiative—the largest genotyping study ever launched in Latin America—having value beyond his country’s borders, informing public health research and drug discovery throughout mestizo countries. To that end, INMEGEN will seek alliances with other Latin American regions in the near future.

Stephen Herrera, Mexico launches bold genome project, Nature Biotechnology. September 2005. (sorry subscribers only) BUT see here!

INMEGEN homepage.

In a Home Near You Soon: DIY Tests for Nearly Everything?

More and more do-it-yourself (DIY) medical tests are coming down the pike.  This week A DIY home HIV test will be reviewed by the FDA’s Blood Products Advisory Committee, they are expected to give guidance on potential OTC status for the OraQuick Advance test on November 3.  The manufacturer, Orasure Technology, currently sells the kits to clinics and doctors for less than $20 each.

This past week, scientists from the Morgagni-Pierantoni Hospital in Forli, Italy published a paper in JAMA demonstrating efficacy of a urine test for bladder cancer.

Maria Aurora Sanchini et al. "Relevance of Urine Telomerase in the Diagnosis of Bladder Cancer" JAMA Vol. 294 No. 16, October 26, 2005.

Bernard M. Branson, MD. "Home Sample Collection Tests for HIV Infection" JAMA. 1998; 280:1699-1701.


Solexa: On track for $100K human genome

Solexa released a progress report on their genome sequencing platform.  They also claim to have the expectation of being "the first to deliver whole human genome
sequencing at $100,000 per genome."  They have memorialized this expectation in their about us section as follows:

"Solexa expects its first-generation technology to generate over a billion bases of DNA sequence per run and to enable whole genome resequencing below $100,000 per sample, making it the first platform to reach this important milestone. Solexa’s longer-term goal is to reduce the cost of human re-sequencing to a few thousand dollars"

As George Church has remarked, in the realm of genome sequencing technology, its a "race to the bottom."

Update: See also,
Kevin Davies. Solexa Sets Sights on “$100,000 Genome” Threshold. Bio-IT World. October 25, 2005.

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