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.


Resource: Brief Guide to SNPs

Applied Biosystems has published a brief guide to genetic markers.  This 10-page document provides a quick introduction to such things as restriction fragment length polymorphisms (RFLPs), short tandem repeats (STRs), single nucleotide polymorphisms (SNPs), and haplotypes.  Linkage and association studies are also briefly introduced.

Applied Biosystems. "SNPs — Powerful Tools for Association Studies" August 2003.

454 wins gold in WSJ Tech Innovation Awards

454’s sequencing technology was awarded the gold prize in this years WSJ Innovation Awards.  The money quote:

"Judges saw the [sequencing] technology as ‘potentially’ or ‘clearly’ revolutionary"

Michael Totty. "Innovation Awards: A Better Idea" WSJ October 24, 2005.  (Or listen to a podcast)

Roche AmpliChip Video

Roche has posted a video describing their Amplichip CYP450 test, a DNA microarray that can identify 2D6 and 2C19 gene variants.

Venter Ups the Ante for the $1000 Genome

In October 2003, the inaugural post of this blog pointed to the announcement by Craig Venter of a $500,000 prize aimed at stimulating the development of sequencing technology that enables the drastic reduction of the costs of sequencing human genomes.  Today Venter announced plans to up the ante to as much as $10 million to speed the "race to the bottom" even more:

Noting that Solexa believes it can deliver a $10,000 genome by 2008, Venter said, “Our goal is really to have a $1,000 genome, but instead of having accountants tell us what it is, we’re going to require people to sequence maybe 100 genomes and really demonstrate the technology. So we’re trying to finalize the rules for this…
We’re thinking of a timeline that this has to be done sometime between 2008 and 2010. We’re trying to raise the prize value to reward the scientists that actually come up with these breakthroughs, not by calculation but by actual demonstration.”

Kevin Davies.  Venter Raises Stakes for “$1,000 Genome” Prize. Bio-IT World, Oct 19, 2005.

Visionaries Need Only Apply

Harriet Pearson Interview about Genetic Privacy

Harriet Pearson, Chief Privacy Officer at IBM discusses genetics and privacy in an interview with Scott Berinato of CSO.  Listen to the podcast.

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.

History of Patenting Life and Its Parts

Daniel Kevles reviews the history of patenting "life and its parts" in a recent talk at Duke Law School.  The talk provides an overview of the major events that have shaped our current intellectual property regime, including Ananda Chakrabarty and the oil-slick eating bacteria, Philip Leder and the Oncomouse, Stan Allen and the triploid Pacific Oyster, Craig Venter and Expressed Sequence Tags (EST), Myriad’s patent claims on the BRCA genes, and lots of interesting minutiae.   He ends the talk with this comment:

"We all have a stake in human genes, just as for example, down-river residents have a stake in up-river holders of riparian rights.  We limit the rights of the up-river holders to do with their property whatever they wish, the time may well be coming, in fact I think its already here, when we will limit the IP rights in human genes too…"

Watch the streaming webcast

Daniel Kevles "Patenting Life and Its Parts: Ethics and Rights in the Political Economy of Intellectual Property" Duke Law School’s Center for the Study of the Public Domain, April 7, 2005. (streaming webcast)

Daniel Kevles faculty profile at Yale.

: Personal genome sequencing presents some interesting challenges to intellectual property — or perhaps it is the reverse, intellectual property claims present some interesting challenges for personal genome sequencing.  Jay Shendure framed the issue in an excellent paper on the cost of sequencing:

[Ultra low cost sequencing] technologies will probably not be able to avoid the resequencing of patented genes.  Interesting legal issues arise around the question of patients’ rights to have analysed (or to self-analyse) their own DNA sequence versus corporate interests that presumably own the rights to that analysis.

If personal genome sequencing were available cheaply today, this issue might be problematic, to give an example, with the way in which Myriad Genetics exercises their patent claims on BRCA1 and BRCA2.  Daniel Kevles points out they they require that all sequencing of these genes be done at Myriad’s labs.  If other companies adopt similar models to enforce intellectual property rights, the $1000 genome would appear to be dead in the water.  If a person had to send blood or buccal samples to hundreds of labs in order to get a full genome sequence, the shipping costs alone might be more than $1000.

John A. Robertson. "The $1000 Genome: Ethical and Legal Issues in Whole Genome Sequencing of Individuals" The American Journal of Bioethics 3(3):W35-W42

Shendure J, Mitra R, Varma C, Church GM (2004) Advanced Sequencing Technologies: Methods and Goals. Nature Reviews of Genetics May;5(5):335-44.

Genetic Ancestry of IBMers

Around 9000 employees of IBM have contributed to the Genographic Project and to showcase this effort, they have built a website describing the ancestral diversity of a several employees with different haplotypes.  Their podcast "IBM and the Future of…" has a an episode on the Genographic Project featuring anthropologist Spencer Wells and computational biologist Ajay Royyuru. 

How many DNA kits have they sold?  According to Spencer Wells, they have sold 67,000 kits as of the podcast (which was published October 7, 2005).

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