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Use of SNPs in WTC victim identification
http://www.nydailynews.com/news/local/story/116330p-104915c.html
"City forensic scientists are awaiting approval from state authorities to use an advanced DNA analysis method called single nucleotide polymorphisms, which was adapted from a process used for disease research and requires less genetic material."
Here is yet another new Shriver paper:
http://www.albany.edu/anthro/fac/brutsaert.htm
Brutsaert TD, Parra EJ, Shriver M, Gamboa A, Palacios JA, Rivera M, Rodriguez I, and F León-Velarde. (2003) Effects of birth place and individual genetic admixture on lung volume and exercise phenotypes of Peruvian Quechua. American Journal of Physical Anthropology, In Press
Illustrates the range of phenotypes that are being worked on in addition to obesity, diabetes, skin pigmentation, etc.
OT John, sorry didn't see your private messages until today - and cannot reply to them privately as I am not a subscriber!
Some quotes from the DNA Phenomics website.
From the About DNA Phenomics page:
"The company currently employs five people and anticipates significant growth as it lays out its research agenda and concludes building its contract research facilities."
"DNA Phenomics has a growing list of impressive scientific and corporate alliances and partnerships worldwide."
From the Genetic Diversity page:
Using the latest genotyping technology, super-computing facilities, and sophisticated statistical analysis techniques DNA Phenomics researchers will process more genomic information and in a far more efficient manner than ever thought possible. And most importantly, DNA Phenomics scientists will identify exactly those elemental parts of the human genome which determine an individual's response to a particular drug.
From the Alliances and Customers page:
"DNA Phenomics' list of alliances will grow to include a number of the region's most important and influential business and scientific research organizations. This list will come to include some of the world's leading scientists, as well as pharmaceutical, healthcare, biotechnology, university, and scientific research organizations as both customers and research allies."
On the Scientists, Managemant and Staff page they look to have left room for one more scientific advisor to be added shortly.
On the Locations and Directions page we can see that their address is the CHIME building.
http://www.technopreneurs.net.my/cms/General.asp?whichfile=Press+Room&ProductID=21144&CatID=
CHIME is a centre of excellence in the MSC which will further enhance the telehealth initiative in innovation, research and development (R&D) and enterprise incubation, and in turn deliver improved healthcare, promote people’s health and oversee health issues from "womb to tomb".
Building on the foundation of telehealth concept, CHIME’s key role is to accelerate the telehealth industry to the next stage of development, and to ensure that the developments in the public healthcare sector are mirrored in the private healthcare sector. This will help position Malaysia on the road to an information age health sector as a leading provider of telehealth products and services.
CHIME offers the following benefits to any healthcare enterprise wishing to develop its technologies or ideas at the Centre :
· Professional advice and mentoring programmes by CHIME management and industry professionals;
· Access to infrastructure and common services including telecommunications, office space and services;
· Collaborative networks with universities, medical profession and other organisations;
· Leverage off the MSC brand for local and international marketing; and
· Attractive financial incentives including subsidised rent, joint project financing and MSC-status benefits
From the Products page:
"Currently there are 4 genomic products under development, and another significant set of genomic products in the planning stages by the scientists at DNA Phenomics."
From the Careers page:
"DNA Phenomics employs top scientists and business leaders from around the globe."
Mark Shriver has an updated version of his CV online at the following URL:
http://146.186.95.23/cv/shriver.pdf
There are several interesting items in this document.
Mark is now a reviewer for the National Science Foundation and the National Institute of Health - NIDDK (diabetes). He is also a reviewer for the following journals: Genetics, Nature Genetics, Genome Research, American Journal of Human Genetics, American Journal of Physical Anthropology, Human Biology, Pigment Cell Research, Photochemistry and Photobiology, Analytical Biochemistry, Genomics.
He has two interesting pending National Institute of Health research support applications: "Human Population Genomics using Multilocus SNP Genotypes" and "Quantitative Genetics of Pigmentation and Skin Response".
The first of these is interesting in that it seems similar to the work being undertaken by Jonathan Pritchard and Matthew Stephens:
Falush D, Stephens M, Pritchard JK. Inference of Population Structure Using Multilocus Genotype Data. Linked loci and correlated allele frequencies. Genetics. 2003 Aug;164(4):1567-87.
The full text of this paper is available here:
http://pritch.bsd.uchicago.edu/software/FalushEtAl03.pdf
Also by Jonathan Pritchard:
Wall JD, Pritchard JK. Assessing the performance of the haplotype block model of linkage disequilibrium. Am J Hum Genet. 2003 Sep;73(3):502-15. Epub 2003 Aug 11.
Wall JD, Pritchard JK. Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet. 2003 Aug;4(8):587-97. Review.
Back to Mark Shriver, he is no stranger to NIH funding:
July 1999 – June 2002 National Institute of Health: "Construction and Application of a US Admixture Map" (R01- HG002154, $1,054,912 in direct costs) {Renewal Application Pending}
Dec. 1998 - Nov. 2002 National Institute of Health: "Identifying NIDDM genes using admixed populations" (R01-DK53958, $550,371 in direct costs)
Three of Mark's students have graduated:
Joshua Akey, B.S. in 1999. Josh received his Ph.D. from the University of Texas at Houston with Li Jin and currently holds a postdoctoral position in the lab of Leonid Kruglyak at the University of Washington in Seattle.
(See http://www.hhmi.org/research/investigators/kruglyak.html for Kruglyak)
Carrie Pfaff, Ph.D. in 2001. "Estimating admixture dynamics: implications for mapping genes". Currently in Law School.
Carolina Bonilla, Ph.D. in 2003. "Admixture in three Hispanic populations: ancestry proportions, population structure, and gene mapping" Carolina Currently a postdoctoral fellow in the laboratory of Rick Kittles at Howard University.
(See http://www.genomecenter.howard.edu/units/molecular_gen/default.htm for Kittles)
All of the following are new papers that are currently in review:
Halder, I. and Shriver, M.D. (in review) Measuring and using admixture to study the genetics of complex disease.
N.B. Indrani Halfer is a Genetics PhD student at PSU: http://www.genetics.psu.edu/Grads/detail.asp?pkey=288
Parra, E.J., Hoggart, C.J., Bonilla, C., Dios, S., Pfaff, C.L., Martinez-Marignac, V.L., Norris, J.M., Marshall, J.A., Hamman, R.F., Ferrell, R.E., McKeigue, P.M., and Shriver, M.D. (in review) Association of type 2 diabetes, fasting insulin and body mass index with candidate gene polymorphisms in the Hispanic population of San Luis Valley, Colorado.
Parra, E.J., Kittles, R.A., and Shriver, M.D. (in review) Correlation between constitutive skin pigmentation and individual ancestry in admixed populations: Implications for anthropological and biomedical studies
Shriver, M.D., Kennedy, G.C., Parra, E.J., Lawson, H.A., Huang, J., Makova, K., Akey, J.M., and Jones, K.W. (in review) The Genomic Distribution of Human Population Substructure.
Bonilla, C., Parra, E.J., Pfaff, C.L., Dios, S., Marshall, J.A., Hamman, R.F., Ferrell, R.E., Hoggart, C.L., McKeigue, P.M., and Shriver, M.D. (in review) Admixture in the Hispanics of the San Luis Valley, Colorado and its implications for complex trait gene mapping.
Bonilla, C., Shriver, M.D., Parra, E.J., Jones, A. and Fernández, J.R. (in review) Ancestral proportions and their association with skin pigmentation and bone mineral density in Puerto Rican women from New York City.
Bonilla, C., Parra, E.J., Shriver, M.D. (in review) Admixture analysis of a rural population of the state of Guerrero, Mexico.
Fernández, J.R. and Shiver, M.D. (in review) Using genetic admixture to study the biology of obesity traits and to map genes in admixed populations.
ohiobuckeye, I speculated previously on RB regarding the cost that would be involved with Ancestry testing of subjects going through clinical trials (see below). I think that the additional cost of providing Ancestry testing for all clinical trials is of the order of $6-8 million per year. This figure is obviously a miniscule percentage of the costs involved with running said clinical trials, and (if correct) would presumably not be an impediment to the use of Ancestry.
http://ragingbull.lycos.com/mboard/boards.cgi?board=DNAP&read=236196
Let's hypothesize that the FDA in it's wisdom decided to adopt biogeographical ancestry (BGA) for racial classification in US clinical trials. Given that DNAP has the patent it is safe to assume that they (or their service provider) would be the provider of relevant services. What might that mean in terms of revenue?
You have to make assumptions about number of clinical trials, average trial size (number of patients), average length of trial, cost of each BGA test, number of patients participating in trials per annum, etc. This information is not easy to come by for a number of reasons. One problem is that there seems to be no central statistical resource (I have looked at the FDA, NIH, etc). The best sources of data are sites like:
http://www.clinicaltrials.gov/
http://www.cancer.gov/clinical_trials/doc.aspx?viewid=115667A1-3A71-412C-94D6-82F4DA9234A2
From this type of source you can see that there are some 3,000 trials currently underway (excluding synonyms), of which anywhere between 1,500-1,700 relate to cancer. Some of these trials it may not be appropriate to include but let's say that are 2,000 that are relevant for our purposes.
Average trial size is difficult. I assumed this to be hundreds but one study quotes 75 studies per NDA and 4,850 patients per NDA on average (implied trial size 65). Let's be conservative and say it is 50 patients per trial.
I have seen one estimate for the average length of trials of 26 months, let's say 2 years.
Tony has given us the cost of a BGA bulk test as $160.
One source I found stated that some 25,000 people join cancer trials in the US annually. Let's say that you add on another 50% for non-cancer trials i.e. 37,500 patients.
Method 1:
2,000 trials of 50 patients each at $160 is $16 million, or $8 million per year.
Method 2:
37,500 new patients per year at $160 is $6 million per year.
Looks like a lot of revenue (using conservative assumptions) for just this one service if the FDA would be kind enough to mandate our approach.
W2P, we both know that the use of subjective racial categories as per the initial guidelines will almost certainly be mandated by the FDA. We also both know that this will result in scientific data that is effectively worthless for ascertaining population structure based influences on clinical trial results. It would be nice to see the FDA do the right thing, but I suspect that "political" considerations will militate against this.
OT Lizard spit drug controls diabetes and cuts weight
http://www.forbes.com/home_europe/newswire/2003/08/25/rtr1065259.html
PARIS, Aug 25 (Reuters) - An experimental diabetes drug derived from lizard saliva not only controls patients' blood sugar levels but also cuts their weight, its developers said on Monday.
Amylin Pharmaceuticals Inc (nasdaq: AMLN - news - people) and Eli Lilly and Co (nyse: AMLN - news - people) released new study findings on the efficacy of exenatide at the 18th Congress of the International Diabetes Federation in Paris.
The drug, derived from the saliva of a lizard known as the Gila monster, is the first in a new class of therapies for type 2, or adult-onset, diabetes and is on track to be submitted for approval by regulators in 2004. Analysts forecast annual sales could top $500 million after three years.
The Gila monster lizard lives in the Arizona desert, only eating about four times a year. Its salivary secretions help prevent a sudden surge in blood sugar levels in response to these infrequent but large meals.
The latest Phase III trial results involved 155 patients who had failed to reach target glucose levels on established diabetes drugs metformin and sulfonylurea, or a combination of the two.
When researchers added injections of exenatide, 44 percent of patients who completed 24 weeks of treatment achieved glucose level averages within the target range, the companies said.
Patients also lost on average 3.4 kilograms (7.5 pounds).
Amylin CEO, Dan Bradbury, told Reuters that being able to control the blood sugar levels of so many patients who had previously failed therapy was a "pretty exciting result".
He said that even using the newer glitazone therapies it would be "unusual to get a result of this magnitude". In any case, he said the glitazones were associated with weight gain, a known risk factor in diabetes.
The most frequently reported adverse event in the study was mild to moderate nausea, which decreased with continued treatment.
Copyright 2003, Reuters News Service
Here is a New York Times article about Singapore's biotech initiatives:
http://www.nytimes.com/2003/08/26/business/worldbusiness/26biop.html?ex=1062561600&en=cf8d15cff0....
Singapore Goes for Biotech
By WAYNE ARNOLD
SINGAPORE, Aug. 25 - Like mice to cheese, top biotechnology talent will be drawn to mice - a quarter of a million mice, to be exact. That, at least, is Singapore's hope.
Workers are finishing an underground vivarium to house the rodents beneath Singapore's new, $286 million Biopolis biomedical research and development complex. The expectation is that the mice will prove to be an irresistible to the kind of research Singapore wants to attract.
And if the mice do not do it, there will also be a pub, a fitness center and an electron microscope.
"We call it the Mickey Mouse park," said Philip Su, assistant chief executive of the JTC Corporation, the government industrial park operator that is building Biopolis.
The mice will be surrounded by a sticky mat and what Mr. Su described as a sort of moat, to keep them from running off if they escape their cages. Biopolis's human tenants will eventually be surrounded by a high-technology campus of nearly 500 acres, complete with condominiums, schools and wireless Internet access.
Faced with declining returns in electronics, the industry that helped catapult Singapore into the ranks of the world's wealthiest nations, the government is throwing its administrative might - and at least $2.3 billion in investments, grants and other incentives - behind an effort to become an integrated biotechnology hub. With little home-grown expertise, Singapore has set out to import what it cannot produce.
"Over the last 20 years or so, we've built up manufacturing technology," said Beh Swan Gin, second director for biomedical sciences at Singapore's Economic Development Board. "Biomedical sciences will add an anchor to that."
Singapore needs to find a new niche. Cheap labor in China is drawing jobs away.
The government has warned that unemployment, now at 4.5 percent, is likely to climb to 5.5 percent this year, its highest since 1987, with the economy likely to eke out growth no greater than 1 percent.
The biotechnology initiative has already attracted big-name manufacturers and research talent. But local start-ups are struggling, and economists say the biotechnology investment is unlikely to yield jobs on the scale that electronics once did.
Some critics also question Singapore's timing. Just as the government began pushing "technopreneurship" shortly before the Internet bubble burst, it has turned to biotechnology during an industry crunch. Investors are shying away from an industry in which products take at least a decade to develop. And competition is coming from less developed countries like China, India and Malaysia, which are building biotechnology industries of their own.
Officials are quick to point out that Singapore is not starting from scratch, but that only underscores the challenges. Singapore began promoting biotechnology in the early 1980's, luring Glaxo in 1982. The next decade, Singapore was pushing research and development; it established a Bioprocessing Technology Center Incubator Unit for start-ups, with fully equipped labs in 1997. Yet Singapore spent, and still spends, less as a portion of its gross domestic product on research and development than Japan, South Korea or Taiwan.
To help change that, Singapore in 2000 declared biotechnology the "fourth pillar" of its economy, renamed its National Science and Technology Board as the Agency for Science, Technology and Research, and spent roughly $570 million to establish three biotechnology research institutes.
Close to the Equator, Singapore is considered an ideal location for the study of tropical diseases endemic to the region, like malaria.
Its advanced telecommunications infrastructure and abundant computing resources are another draw. With companies under pressure to produce drugs more quickly from the millions of molecules and billions of genetic combinations on hand, scientists have begun to use powerful arrays of computers to eliminate years of laboratory work, an area of research known as bioinformatics.
"You can do by brute force what before only incredible brain power could accomplish," Philip Fersht, an analyst based in London, said.
For stem-cell researchers, Singapore offers one of the world's most liberal legal atmospheres. It allows stem cells to be taken from aborted fetuses, and human embryos to be cloned and kept for up to 14 days to produce stem cells.
The welcoming climate lured Alan Colman here last year. Dr. Colman helped clone Dolly, the history-making sheep, in Scotland in 1996, but when financing for his diabetes research grew scarce in Europe he moved to ES Cell International, a venture between Australian investors and Singapore's Economic Development Board.
"I was just seduced," Dr. Colman said, "by the enthusiasm for building scientific infrastructure and putting money into biotech.'
Singapore also lured Edison Liu from the National Cancer Institute in Bethesda, Md., to head its Genome Institute. "I couldn't believe the audacity of Singapore," said Dr. Liu, who called Singapore's approach visionary.
As it continues to recruit, the government is also trying to create domestic talent. The Agency for Science, Technology and Research is offering $286 million in scholarships for students to pursue Ph.D.'s in biomedical sciences at home and abroad, in exchange for their promise to work in Singapore for up to eight years.
Singapore has had the most success in attracting drug makers, with tax holidays and other incentives. Among those with factories here are Merck & Company, Pfizer and Schering-Plough.
Pharmaceutical production increased about 50 percent last year, to $5.56 billion, and is well on track to reach the government's goal of $7 billion by 2005. But this industry is less labor-intensive than the electronics industry. "It doesn't translate into job growth," said Song Seng Wun, regional economist at the local brokerage firm G.K. Goh.
Dr. Beh of the development board said the biotechnology push was not about numbers. "It's about providing knowledge-intensive, research-intensive types of jobs," he said.
To encourage companies to do more than make drugs, the board offers to pay up to 30 percent of the cost of building their research and development facilities. Among the companies that have accepted the offer are Eli Lilly and 29 other companies. In addition, Novartis is setting up an Insitute for Tropical Diseases.
But Singapore's own start-ups, feel left out. "Local entrepreneurs still find it hard to get funding," said Gurinder Shahi, chief executive of BioEnterprise Asia, a biotechnology consultancy here.
The Economic Development Board estimates that $5.2 billion in venture capital funds is being managed from Singapore, but little of it seems to be invested in local biotechnology start-ups. The venture capital firm Warburg Pincus, for example, has a regional office in Singapore, but a spokeswoman said that it does most of its financing in North Asia and India.
The board manages a $572 million biotech venture capital fund, which has invested in 80 companies in Singapore and abroad. Dr. Beh said the board makes sure its foreign investments have some link to Singapore. Roughly $14 million of the $572 million is reserved for local start-ups, but so far the board has invested less than $300,000 in two companies.
The board also has a program for local start-ups that provides up to $171,500 in financing if they can find a private investor to match the amount - an approach entrepreneurs say does not help much.
"If I can get private funding, I don't need government funding anymore," said Lee Chee Wee, a local professor who founded Lynk Biotechnologies in 2000. A local politician ultimately gave Lynk start-up money from his own pocket. The company has financed production of its biggest seller, an anti-balding tonic called Biolyn, through an investment from a Hong Kong company.
The board makes no apologies for imposing standards as high as private venture firms on local start-ups. "If they think it's easy money, it isn't," Dr. Beh said. "Ultimately, we are custodians of the taxpayers' money."
Note: Lynk Biotechnologies are one of the companies in the BioEnterprise Asia portfolio.
Sarah Tishkoff is an Assistant Professor, Deptartment of Biology, at the University of Maryland:
http://www.life.umd.edu/biology/tishkofflab/
Her research interests include:
The genetic basis of adaptation in humans
We are interested in characterizing patterns of genetic variation at loci that potentially play a role in the adaptation of humans to environmental change. Such candidate genes likely played an important role in human population differentiation and evolution, and for distinguishing humans from other closely related species such as chimpanzee and gorilla. Additionally, in characterizing genetic variation for candidate genes where variants may be subject to different selection pressures, we may uncover functional variation that had previously been unidentified. This, in turn, may enable us to identify other regions of the human genome that may play a role in human adaptation and human disease. For several of these loci we are collecting phenotype data from geographically diverse populations in order to examine the correlation between genetic and phenotypic variation.
Global patterns of linkage disequilibria (LD) in the human genome
There is an increasing interest in identifying genes involved in complex disease (e.g. hypertension, diabetes, obesity, schizophrenia, and some types of cancer). Gene mapping approaches for complex disease often relies on detection of association between marker and disease alleles within populations. The design and effectiveness of these studies will depend on underlying levels and patterns of LD in the populations of interest. Linkage disequilibria will be influenced both by locus-specific factors (e.g. mutation and recombination rates, selection) as well as by population and demographic history (e.g. substructure, admixture, genetic drift, population expansion, and founder events). Patterns of LD are being examined among ethnically diverse populations in order to better understand how locus-specific effects as well as population and demographic history shape the distribution of LD in the human genome and to identify populations that will be particularly informative for genetic linkage and association studies.
Her Postdoctoral work was done at the Deptartment of Biology, Pennsylvania State University, where her advisor was Andrew Clark:
Tishkoff, S.A., R. Varkonyi, N. Cahinhinan, S. Abbes, G. Argyropolous, G. Destro-Bisol, A. Drousiotou, B. Dangerfield, G. Lefranc, J. Loiselet, A. Piro, M. Stoneking, A. Tagarelli, G. Tagarelli, E. Touma, S. M. Williams, A. G. Clark. 2001. Patterns of haplotype diversity and linkage disequilibrium at the G6PD locus indicate a recent origin of malarial resistance. Science 293:455-462.
Incidentally, Scott Williams, one of the authors of the above paper, is one of the scientific advisors to Genomed.
Tishkoff, S.A. and S.M. Williams, 2002, "Genetic Analysis of African populations: Dissecting human evolutionary history and complex disease", Nature Reviews Genetics, 3(8):611-21.
Connie Mulligan at the University of Florida collaborates with a number of people including Sarah:
http://www.clas.ufl.edu/users/mulligan/Webpage/Research.html
Collaboration with ...Rick Kittles (Howard University)...Sarah Tishkoff (University of Maryland)...Mark Shriver (Anthropology, Penn State)...
Sarah collaborates with Joanna Mountain:
http://www.stanford.edu/group/mountainlab/research/agd/
Joanna is one of the people mentioned here:
http://anthro.psu.edu/biolab/ports/index.html
To be published in the Annual Review of Genomics and Human Genetics, Volume 4, September 2003:
http://www.annualreviews.org/catalog/2003/gg04.asp
Patterns of Human Genetic Diversity: Implications for Human Evolutionary History and Disease, Sarah A. Tishkoff, Brian C. Verrelli
Here is the abstract of this paper from a previous presentation at CMU:
http://www-2.cs.cmu.edu/~durand/Symposium/Symposium03/tishkoff.html
In 2001, a rough draft sequence of the human genome was completed, based on analysis of the genomes of only a handful of individuals. The next major phase of the human genome project will be to characterize levels and patterns of genetic variation among a broad range of globally diverse individuals. Such knowledge will be important both for reconstructing our evolutionary history and for understanding genetic susceptibility towards disease.
The origin of modern humans continues to be a subject of considerable debate. We know little about the population structure, population size, or genetic diversity of archaic humans at the time of emergence of modern human form. Africa has been recognized as a key geographical region for the evolution of modern humans. And yet, Africa has been greatly underrepresented in human genetic studies. My laboratory focuses on characterization of levels and patterns of genetic diversity in African populations. Our studies indicate very high levels of genetic diversity both within and between African populations. These data suggest that non-African populations originated recently in East Africa and that African populations have maintained a large effective population size and a subdivided population structure. The high level of genetic variation observed among African populations also has important implications for medical genetic studies, particularly for the design of linkage disequilibrium studies to identify human disease genes and for the treatment of diseases prevalent among people of recent African descent. The study of genetic diversity in Africa will also play a key role in the identification of genes that provide resistance against infectious agents such as malaria and HIV which are thought to have originated in Africa.
Sarah Tishkoff named one of America's Brilliant 10 scientists in the September 2003 issue of Popular Science:
http://www.popsci.com/popsci/science/article/0,12543,472942-11,00.html
So, what's the connection?
From the Scientist June 30 2003 (The 0.1% Portrait of Human History):
http://www.the-scientist.com/yr2003/jun/research1_030630.html
New tools are being applied. Sarah Tishkoff of the University of Maryland studies multiple types of variation in numerous African populations. In addition to studying microsatellites (short tandem repeat polymorphisms), she's begun to investigate SNPs (single nucleotide polymorphisms), which have some advantages over microsatellites. "They're not as variable or have as high a mutation rate as the microsatellites," says Tishkoff. They also enable more throughput. Tishkoff has been working with Penn State's Mark Shriver to type upwards of 10,000 SNPs per individual. The cost is limiting, she says: They can only hope to type perhaps three populations using this technology.
Article from the August 2003 edition of Family Tree Magazine:
http://www.familytreemagazine.com/articles/aug03/dna.html
Decode Your DNA
By David A. Fryxell
Can't find the records to prove your Native American or East Asian ancestry? Discover what's in your genes with AncestryByDNA.
In an earlier, less-enlightened era, "racial purity" was highly valued (at least among the race that mostly ran things), and ugly phrases such as "half-breed," "mongrelization" and "race mixing" were hurled like curses. Today, though bad, old attitudes still linger in dark corners, golf fans root for Tiger Woods, Cher can boast of her Cherokee blood, and genealogists look for exotic rainbows in their roots.
Even as ideas about race have changed, new tools have evolved for studying the subject. Some geneticists now argue, in fact, that the whole concept of ÒraceÓ isn't really biologically relevant, that the DNA differences underlying our racial divisions are, well, microscopic. Others are using advances in DNA technology to probe the racial mixture of the world's populationÑand discovering, yet again, that we're more similar than we are different. As Tony Frudakis, a molecular biologist and CEO of DNAPrint genomics in Sarasota, Fla., puts it, "In all of us, especially in the US, there is a continuum of ancestries."
A branch of Frudakis' company called AncestryByDNA aims to help genealogists explore the racial mix of their family trees with a simple DNA test. Unlike other DNA-testing kits, AncestryByDNA does not rely on Y-chromosome tests (which only males can use) or mitochondrial DNA. Instead, it looks at a person's Single Nucleotide Polymorphisms (SNPs, or "snips" for short)—think of them as collections of letters among the long sentences of the human genome. Then, AncestryByDNA compares your SNPs to a database of results representing four main human racial groups, based on continent of origin: sub-Saharan African, Indo-European (Europeans, Middle Easterners and South Asians, such as Indians), East Asian (Japanese, Chinese, Koreans, Pacific Islanders) and Native American (ancient migrants to both North and South America). Originally, the test used six groups, distinguishing South Asian from European and Pacific Islander from East Asian, but the current version retreats from that until further refinement in an upcoming version 3.0.
AncestryByDNA simply places your DNA along this racial spectrum, which means the test can't connect you with distant DNA cousins, as some genetic-genealogy offerings promise. But if you've always wondered if you have some African roots, for example, AncestryByDNA offers an easy way to put your theories and family stories to the test. At $158 for an individual, it's cheaper than most DNA tests for genealogy, which typically run $200 to $300. And unlike tests that require Y-chromosomes, you don't have to have the cooperation of a male family member.
The test itself couldn't be simpler. When you order, you get two sterile Gene Guard swabs, which look sort of like small dental instruments. You scrape the inside of each cheek with a serrated swab at least 10 times, using an up-and-down motion and moderate pressure. Then, let the swabs briefly air-dry and pop them in the supplied return envelope.
A few weeks later, you'll receive a CD-ROM that includes a certificate and results table showing your ancestral proportions, a triangular graph charting your results and a map of ancient human-migration patterns. At first, you may be disappointed by the simplicity of the resultsÑit doesn't look like a lot for $158. Basically, you'll learn that your racial mix is X-percent this, X-percent that. But at least you'll know—and you can either pursue your various ethnic ancestors through other genetic and genealogical means, or discount long-held family myths. (Was your great-great-grandmother really an Indian princess?)
For example, I tried AncestryByDNA on behalf of a coworker who'd always suspected that he had Native American ancestry. The circumstances of one grandparent's birth were a bit cloudy, and the grandparent had grown up in an area with many Native AmericansÑin fact, enduring that "half-breed" taunt as a youth. This grandparent even looked more like a Native American than like the Scandinavians who mostly populated the region.
Our coworker got the AncestryByDNA kit and swabbed the inside of both cheeks. The process was no more painful, he reported, than if you scraped with your toothbrush. Then, he tucked the two little swabs in an envelope, sent it off and waited for the results.
Given how sure he was that the evidence pointed to a Native American branch in the family tree, the results were a bit of a surprise: The test found no Native American DNA component whatsoever. So much for those long-held suspicions! Surprisingly, too, the results showed 94 percent Indo-European but also 6 percent East Asian ancestry. (The company says its error rate is 3 percent, too low to explain this figure.)
But, if anything, that 6 percent confirms his pure Scandinavian origins. According to AncestryByDNA's Web site, "DNAPrint has found that many individuals reporting pure Scandinavian ancestry register with detectible East Asian admixture as well. This result may obtain through contribution of the Lapps, indigenous Scandinavians who share physical features, culture and common history with Northern Asian populations."
Even though the answers weren't what he'd expected, our coworker was glad to have tried the test. Whether it's worth $158 depends on how curious you are about your racial roots. For more information, see the Web site or call (941) 366-3400.
Editor-in-chief David A. Fryxell also wrote this issue's guide to the "101 Best Web Sites" for family history.
Good article, and interesting that Gurinder Shahi and Philip Yeo had quotes. I loved this bit from the article: "What's holding Singapore back could be its mindset." Anybody who has ever tried to work with Singapore companies or the Singapore Government will know exactly what this means!
Arch, that's probably why it is the penultimate topic of the day - right before the "discussion". I would like to be a fly on the wall for this one.
Bag8ger, familiar with the website, it is a nice concept but the execution leaves a bit to be desired. The "accesss denied" messages are from the dnaprintasiapacific.com website itself (kartoo is only a meta search engine - a search engine of search engines). Interesting that kartoo finds both dnaprint.com and dnaprintasiapacific.com isn't it? The phonetic equivalent of kartoo in Chinese is to spit.
OT Hwan should appreciate the irony of the Chinese phonetic equivalent of the name that the (French) company have chosen!
Forensic Bioinformatics 2nd Annual Conference (Statistics and DNA Profiling), August 29th - 30th 2003, Wright State University, Dayton, OH.
http://bioforensics.com/conference/conference.html
One topic being presented this afternoon is listed in the schedule as:
Racial identification (Dr. William Shields, SUNY and Dr. William Thompson, UC Irvine)
Here are websites for Drs Shields and Thompson:
http://www.esf.edu/efb/faculty/shields.htm
http://www.seweb.uci.edu/users/wcthomps/Thompson.htm
http://www.seweb.uci.edu/faculty/thompson/
Here is the webpage for the Racial identification topic:
http://bioforensics.com/conference/Racial%20Identification/index.html
Here is what is on this page:
DNAPrint genomics, Inc. has applied the most recent advancements in human genomic technology for the deciphering of an individual's race. We are proud to introduce to the forensic community DNA WITNESS 2.0, a genetic test for the deduction of the heritable component of race, called Biogeographical Ancestry (BGA). This test is the first of its kind, resulting from three (3) years of genomic research, and is the beginning of a revolution in criminal investigations. This test provides not only the majority population affiliation (i.e. Indo European, Sub-Saharan African, East Asian or Native American), but the admixture, as well (i.e. 82% East Asian and 18% Indo-European mix).
This new test provides important Forensic Anthropological information relevant for a wide variety of investigative situations. When biological evidence is gathered, an investigative team can use DNA WITNESS 2.0 to construct a partial physical profile from the DNA and in many cases learn details about the donor's appearance, essentially permitting a partial reconstruction of their driver's license photo. How many times have you wished an unknown suspect left his driver's license at the scene - even if the unique identifiers were smudged?
Recognizing the need for genomics-based physical profiling tools, DNAPrint genomics is the first company to apply human genome power for the precise estimation of Biogeographical percentages from DNA.
Because physical profiling from DNA will effectively offer an objective "eyewitness" for each crime, where biological evidence has been left, the implications for saving investigative dollars and maximizing the efficiency of our criminal justice system are profound. STR identity tests form the cornerstone of forensic DNA analysis, but they are not useful for the assumption of race or any other physical traits, because the STR markers were not selected for the ability to do so. Other non-DNA based investigative work tends to rely on less scientifically robust methodology. For example, "eyewitnesses":
"Are not always reliable, are subjective and sometimes misleading. Most of the felons released from death row, based on DNA testing, were convicted based on faulty eyewitness testimony. " Are not available for each crime.
Until now, no scientific method has been available to help investigators learn what a DNA donor looks like. DNAPrint's DNA WITNESS 2.0 product represents the first wave of a genomics revolution that is afoot in forensics science. We are applying the test to actual casework and we've performed testing for a number of high profile murder/rape cases, where DNA was left at the crime scene.
DNA WITNESS 2.0 could provide additional detail to current cases or cold cases could be re-visited. The results indicating to detectives what population groups to include or exclude in their investigation. The goal of the product is simple, help you focus your investigation and identify from whom a forensic sample was derived. Effectively, what we have done is harness our increasing knowledge of human genomics to help you get the job done. Wouldn't you like to have a DNA eyewitness for your most important cases?
We would be pleased to provide you a CD-ROM of the validation experiments, which was performed for this test on over 2,000 DNA samples.
Please contact us to discuss the possibility of using DNA WITNESS 2.0 on your cold, current, or next case.
Zach Gaskin
Technical Director, Forensic Genomics
941-366-3400
zgaskin@dnaprint.com
Materials
ABC News. (2003). Racial profiling: will a new DNA test shatter serial killer myths?
http://bioforensics.com/conference/Racial%20Identification/Racial%20Profiling.htm
DNA-Defense ListServ. (2003). Cutting edge forensics. Discussion and debate over new DNA technology.
http://bioforensics.com/conference/Racial%20Identification/listserv.html
Frudakis, T. (2003). DNAPrint genomics.
http://www.dnaprint.com/
Pitts Jr., L. (2003). The power of knowing where your family roots begin. Pioneer Press. August 20, 2003.
http://bioforensics.com/conference/Racial%20Identification/roots.pdf
The second item is interesting:
Hello all,
I'm not a member of the forensic community, but a producer with Bill Kurtis Productions, the creators of the program "Cold Case Files" on the A&E network.
I'm currently researching a special documentary program on the very latest in forensic science, and where the state of the art will be in 5, 10, or 20 years.
For example, I've read than in the Baton Rouge rape case, forensic DNA was used to identify the race of the suspect. I'm particularly interested in this use of DNA, not just as a "fingerprint" that's mute on personal characteristics, but rather as a tool that could help give investigators an idea of whether the suspect is likely to be big or small, white or black, thin or fat, prone to various diseases, etc...
I'd like to hear from any listserv members who have information or contacts about this aspect of forensic DNA, or about any other forensic fields that could be considered the wave of the future.
Thank you!
Mike West
Producer
Kurtis Productions
voice: 312-242-6153
fax: 312-951-8251
This is followed by a long rambling discussion about the use of DNA in the legal context. Perhaps somebody would like to contact Mike West (cannot get an email address for him).
So, who are Bioforensics?
http://bioforensics.com
"Forensic Bioinformatics was founded in 2002 by Dr. Dan Krane. Dr. Krane, Associate Professor of Biological Sciences at Wright State University, is recognized as one of the world's foremost authorities on DNA analysis...Joining Dr. Krane as principals are two colleagues who have also gained international recognition for their work in DNA analysis, Drs. William C. Thompson and Simon Ford and two colleagues recognized for their work with computational automation and the use of biological data, Drs. Travis Doom and Michael Raymer."
"Professor Bill Thompson is a Professor in the Department of Criminology, Law & Society at the University of California, Irvine, and editor of an on-line journal about forensic DNA evidence, Scientific Testimony. In addition to a J.D., Bill has earned a Ph.D. in Psychology. Before joining the UIC faculty in 1983, he practiced law in the San Francisco Bay area. Bill argued the first case concerning the admissibility of DNA evidence before the New Mexico Court of Appeals and Supreme Court, and was the first attorney in California to successfully challenge the admissibility of an FBI DNA test. He was been prominently involved in many high-profile criminal trials, including O.J. Simpson, Sammy Marshall, John Cuff, and Dirk Greineder."
Not sure what is being presented during this conference session, who is presenting it, who is attending it, and what connection (if any) there is between DNAP and Forensic Bioinformatics (or Drs Shields and Thompson) - perhaps they just introduce (jointly) the topic or are moderators for a discussion.
Who is working on the genetics of height?
Wu X, Cooper RS, Boerwinkle E, Turner ST, Hunt S, Myers R, Olshen RA, Curb D, Zhu X, Kan D, Luke A. Combined analysis of genomewide scans for adult height: results from the NHLBI Family Blood Pressure Program. Eur J Hum Genet. 2003 Mar;11(3):271-4.
(Apart from anything else, Boerwinkle was Mark Shriver's PhD supervisor).
A Genome-Wide Scan for Loci Affecting Normal Adult Height in the Framingham Heart Study (Nandita Mukhopadhyay et al., Pittsburgh, Pa.) Hum Hered 2003;55.
BTW, in the above journal couldn't help noticing the following:
Population Frequencies of Single Nucleotide Polymorphisms (SNPs) in Immuno-Modulatory Genes (A.-M. Martin et al., Philadelphia, Pa.) Hum Hered 2003;55.
The main guy behind the second paper is Daniel Weeks at the University of Pittsburg:
http://www.hgen.pitt.edu:16080/~dweeks/
Research Interests: Linkage analysis, statistical genetics, parallel computational techniques for linkage analysis, genetic mapping, chiasma interference, simulation studies, genetic mapping of autism, obesity, age-related macular degeneration, inflammatory bowel disease, endometriosis, and Type II diabetes.
Weeks collaborates with other "connected" people:
McGarvey ST, Forrest W, Weeks DE, Sun G, Smelser D, Tufa J, Viali S, Deka R. Human leptin locus (LEP) alleles and BMI in Samoans. Int J Obes Relat Metab Disord. 2002 Jun;26(6):783-8.
Deka is at the University of Cincinnati with Chakraborty and Jin et al:
Sun G, McGarvey ST, Bayoumi R, Mulligan CJ, Barrantes R, Raskin S, Zhong Y, Akey J, Chakraborty R, Deka R. Global genetic variation at nine short tandem repeat loci and implications on forensic genetics. Eur J Hum Genet. 2003 Jan;11(1):39-49.
Weeks also works with people like Robert Ferrell.
Are they all connected? Yes, in many ways. Here is one example of them all together (except Weeks):
Shriver MD, Jin L, Boerwinkle E, Deka R, Ferrell RE, Chakraborty R. 1995. A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol Biol Evol 12:914-920.
The point is that people very closely associated with DNAP (directly or indirectly) are participating in this research. The same is the case with weight (Body Mass Index) as was previously posted (where people like DC Rao are involved). Which should give them some idea of where to start with the development of the relevant components of DNAWitness.
Withdrawn drugs: apart from Baycol, what are the other main drugs that have been recently withdrawn from the market post FDA approval?
The weight-loss (appetite suppressant) drugs Pondimin and Redux (Wyeth-Ayerst/American Home Products), popularly known in combination as Fen-Phen, were withdrawn due to valvular heart disease in some patients. The diabetes drug Rezulin (Warner-Lambert) was withdrawn due to problems with liver failure. The inflammatory bowel disease drug Lotronex (GlaxoSmithKline) was withdrawn due to problems with intestinal inflammation due to lack of blood flow. The high blood pressure drug Posicor (Roche) was withdrawn due to problems with it slowing or stopping the heart rate. The antihistamines Seldane (Marion Merrell Dow) and Hismanal (Janssen), and the heartburn drug Propulsid (Johnson & Johnson), were all withdrawn due to them causing potentially fatal irregular heartbeat. The antibiotic Raxar (Glaxo Wellcome) was withdrawn due to it also causing potentially fatal irregular heartbeat. The analgesic Duract (Wyeth-Ayerst/American Home Products) was withdrawn due to problems with liver failure.
A comment from the DzGenes website (BTW this company has over 11,000 DNA samples with accompanying clinical history in its database):
"Drug companies withdraw drugs two ways, during clinical trials and after they have been approved by the FDA and introduced to the market. While press accounts surrounding withdrawals such as Baycol and Phentermine-Fenfluramine ("Phen-Fen") make the loudest headlines, the majority occur during clinical trials. DzGenes estimates that every withdrawal represents a loss of $2 billion, which assumes annual sales of $150 million for ten years and development costs of $500 million that are written off. The Company estimates potential pharmacogenomics sales to this market segment at $50 million annually initially. The Company believes that resurrecting clinical trials represents an enormous market potential that should be pursued near term."
DNAP were previously quoting $200K per ADMIXMAP study, which is 0.01% of the estimated $2 billion loss per withdrawal. The drugs quoted above were recent cases of post approval withdrawals, i.e. this does not include drugs withdrawn during clinical trials (the majority). IMO I find it hard to believe that DNAP are not working on at least one of these.
Thanks to doug (and Matt) I now have 18 posts per day. So, here is some background material on genomic medicine (all articles published in the New England Journal of Medicine). Not easy reading, but key stuff.
http://nejm.org/earlyrelease/egenmed.asp
The following two articles are the most relevant for drug classifiers:
Drug Therapy: Pharmacogenomics — Drug Disposition, Drug Targets, and Side Effects Evans W.E., McLeod H.L. N Engl J Med 2003; 348:538-49, February 6, 2003
Inheritance and Drug Response Weinshilboum R. N Engl J Med 2003; 348:529-36, February 6, 2003
Chris, you got some good answers. Of course it is not in big pharma's interests, and therefore they will not be proactive unless and until the FDA force them to be. As Tony said in the TWST report: "The FDA is probably going to force them (big pharma) to provide gene sequence data along with their clinical trials in the very near future." This initially will be concerned with adverse drug reaction (ADR), but I personally would think that drug efficacy (and possibly dosage) would not be far behind. After all, why would the FDA NOT require this information if it could be provided?
The sad thing is that it only seems to be bottom line or litigation considerations that would encourage the adoption of such technology in the absence of regulatory oversight. It is also not just big pharma, their lobbyists, or the insurance companies that are to blame for this sorry state of affairs. The medical profession themselves seem to have very little influence and to be quite happy prescribing the "gold standard" treatment, secure in the knowledge that they will not be criticized for doing so, and irrespective of ADR or efficacy considerations. What about the "client" in all of this i.e. the patient (or the administrator of their health scheme). Should they not have a say?
In any case, plenty of opportunity for DNAP to be involved in the rescue of "failed" drugs, provision of drug classifiers, and apparently provision of drugs themselves.
NBC2 News Story
http://www.nbc-2.com/News/stories/082703-DNA_print.shtml
DNA print shows ethnic background
reported by Cara Jones
SARASOTA, August 27, 2003 - It may be the only place in the world where you can scientifically track your ancestry and it is located in Southwest Florida. The Sarasota-based company DNAPrint Genomics pioneered a test that can identify a person’s ethnic background. The technology is also being used to help crack high profile criminal cases.
“I came back with 21percent native American, 79 percent indo-European,” said Carrie Castillo of DNAPrint Genomics.
At the one-of-a-kind DNA laboratory, scientists are pioneering the world's first commercialized test to track your ancestry.
“There are a lot of things that transpire over thousands of years of migration. We find that people are spread across the world in more ways than we can imagine,” said Castillo.
“What this is is a plate that allows us to read the DNA sequence in people's samples,” said Dr. Matt Thomas of DNAPrint Genomics.
It all starts in the lab where the subject’s DNA is scanned by a hi-tech machine. Using computer models, scientists link it to a series of genetic markers and figure out a breakdown.
“This particular person is 98 percent indo European 2 percent Native American,” said Zach Gaskin of DNAPrint Genomics.
The DNA sequence is written and mapped out on a CD along with an explanation of human migration patterns over thousands of years.
“Out of Africa into Europe and the Middle East. Then people branched off here to Europe,” said Gaskin.
DNA samples are collected from a swab of the inside of your mouth. They even allow people to send it in from home.
But not all of their samples are from swabs or even willing subjects. Everything from chewing gum to cigarette butts can be tested to help piece together a criminal profile.
“We're giving a drivers license photo. It might be blurry and not have all the information on it, but it’s still a composite,” said Gaskin.
Earlier this year, the test helped track down a suspected serial killer. For more than a year, Louisiana investigators thought they were looking for a Caucasian male until the lab helped lead them to Derrick Todd Lee.
“He was 85 percent African, 15 percent Native American. At that point we informed them you're looking for someone not Caucasian, but African American,” said Gaskin.
Beyond ethnicity, forensic experts are also working on ways to help identify eye color from their samples.
“If we can tell them that their suspect is Caucasian with blue eyes its more helpful than just Caucasian,” said Gaskin.
The ancestry test results have a 2 to 5 percent variation. Right now they are limited to just four categories European, East Asian, Native American and West African. The test costs $158.
Sarasota Herald business brief
http://www.heraldtribune.com/apps/pbcs.dll/article?AID=/20030826/NEWS/308260603/1024&cachetime=5
SARASOTA - DNAPrint to share its expertise
DNAPrint Genomics Inc. said that it will serve as a subcontractor for a new National Institutes of Justice research grant. DNAPrint will apply its expertise in the measurement of population structure and genome screening to assist the NIJ. DNAPrint would be paid approximately $50,000 to produce approximately 80,000 genotypes.
Tampa Bay Business Journal report (that doesn't add much more information):
http://tampabay.bizjournals.com/tampabay/stories/2003/08/25/daily14.html
DNAPrint joins National Institutes of Justice project
DNAPrint Genomics Inc. in Sarasota announced that it would serve as a subcontractor for a new National Institutes of Justice research grant.
DNAPrint will apply its expertise in the measurement of population structure and genome screening to the project, a release stated.
The project is broken into two phases, the first of which has already been approved. DNAPrint would be paid approximately $50,000 to produce approximately 80,000 genotypes, a release stated.
DNAPrint Genomics trades on the OTC Bulletin Board under the symbol "DNAP." At 11:30 a.m. it traded at 7 cents. Its 52-week range is 1.3 cent to 18 cents.
As I have still not been "verified" by the good folks at IHUB (and hence am limited to three posts daily) I must combine responses to several people.
Joy - hope you found what you were looking for!
Chris, another easy one to answer quickly lol!
The way I look at this is that there are two ways to read the genome to get information about e.g. drug response: a whole genome scan (which is very expensive and takes a long time currently) or by using a "short-cut" such as AIMs to get at the information. Think of it like looking in an index versus having to read the whole book to find out what page you want. So, IF we can patent the AIM approach then this should give us exclusivity until whole genome approaches are economic and can be done in a timely manner. I have seen various estimates about how long this will take in previous articles - I think it is of the order of magnitude of 3-5 years. So perhaps we have this long to get products to market. Another way of looking at this is that we will be 3-5 years ahead of the competition.
Now what if, as DNAP seem to be saying (in the TWST report), analysis of population structure can tell you something fundamental about drug response i.e. that explains the 50% of the response that is not explainable by other analysis. IF they have discovered something fundamental AND this can be patented THEN they MIGHT have a complete stranglehold on pharmacogenomics. Something to think about...
Of course if something REALLY BIG were to happen then the "big boys" would obviously want to get their snouts in the trough as well (assuming they were out of the trough in the first place of course).
What does it mean to stake out market share and shut out competitors anyway? Are we looking at having a monopoly, building a brand of choice, claiming "enough" market share? The economy is going to look very different in the future. I personally have increasingly less idea how all this is going to pan out eventually, but I feel increasingly intuitively comfortable with my investment!
W2P - would tend to agree with you, but interesting that they have two separate projects concerned with SNPs and ethnicity (and that the term "population structure" is used).
Radean, my background is in information technology, but I don't do that anymore!
Have a good day everybody.
Chris, it might be one of these two:
http://www.justnet.org/virlib/InfoDetail.asp?intInfoID=370
Title: Identification and Analysis of Polymorphic Alu Repeats
Topical Area: Investigative and Forensic Sciences
NIJ/OST Portfolio: Investigative and Forensic Sciences
Description: This funding supports the development of a class of DNA markers which may have important application to the use of DNA as an investigative tool for solving crimes.These markers, called ALU repeats or insertions, will expand the investigiatory capabilities of DNA typing. Alu insertions are short, interpersed elements commonly identified throughout human DNA. Because they are variable between lineages, but common within a lineage (such as a subpopulation), and present in high copy number, Alu sequrnces can provide a reliable forensic marker when even small or degraded amounts of biological material are present. Alu sequences identified in an evidence stain can be used to predict the geographic origin of the person who left that stain. From the identification of geographic origin from the Alu repeat, investigators can gain important information about the probable ethnicity or racial background of the source of the sample. This project will identify and characterize new polymorphic Alu insertions and develop corresponding PCR multiplex approapraite for forensic evidence samples. Over the two-year funding period, 20 to 40 new Alu insertion markers will be characterized,their chromosomal location identified, and the gepgraphic distribution of these new markers will be identified for their use as an indication of the ethnicity of the sample.
http://www.justnet.org/virlib/InfoDetail.asp?intInfoID=367
Title: Evolution of Single Nucleotide Polymorphisms (SNPs) for Human Identification Use
Topical Area: Investigative and Forensic Sciences
NIJ/OST Portfolio: Investigative and Forensic Sciences
Description: There are thousands of Single Nucleotide Polymorphisms (SNPs) in human DNA which can be used as genetic markers to identify the biological source of evidence from a crime scene. SNPs are known areas in the nuclear DNA where there can be a single site difference between the DNA of different people. There are 4 different "types" a person could be for each SNP analyzed depending on which combination of the four DNA bases (A,T,G, or C) was contained at that site in their DNA. If sufficient numbers of SNPs are studied they can provide strong identity information in criminal cases. SNPs may be an important addition to the forensic tool-box because, like mitochondrial DNA (mtDNA) markers, they can be used when samples are too small or too old to yield results for other nuclear DNA markers like STRs. However, unlike mtDNA, SNPs are informative about Mendelian traits and thus can use more powerful statistical models to estimate the rarity of the DNA profile than can mtDNA. Moreover, because the analysis seeks to identify only single base pair differences rather than entire numbers of tandem repeats, SNPs are easily amenable to analysis by DNA microchip array, a technology that permits rapid, high throughput, and economical analysis of a sample.
Project Status: In order to assess the efficacy of adding SNPs to the DNA tool-kit available to the forensic community, this project will study the statistical properties of single nucleotide polymorphism (SNPs) by: (1) developing estimators to calculate a DNA profile when the markers used may be genetically linked, 2) estimating the number of SNP loci needed, and their level of independence, to attain the same high discriminatory power as more variable DNA markers reach with 8-10 loci, 3) evaluating the effectiveness of SNP profiles as ethnic indicators for investigative purposes and (4) assessing the impact of SNPS on estimations of biological relationships.
From the PR:
"DNAPrint will apply its expertise in the measurement of population structure and genome screening to assist the NIJ and the grantee map genetic markers of a certain forensics value, considered by the Company to be complementary to its DNAWitness efforts."
The more I look at this the more it looks like it is markers associated with ethnicity (I mean biogeographical ancestry of course), rather than Retinome. We will find out in due course.
Apart from existing DNAWitness components, or extensions to the same, there were two other possiblities that came to mind: that this was a trial parsing of unknown samples in the CODIS database, or the use of DNAP's technology in conjunction with somebody else's infrastructure to demonstrate electronic forensic service delivery. I think both of these are still potential projects in their own right.
Chig/IVRT
Worktoplay has again homed in on the key questions. We do not know yet who the main contractor is, although credit to Phil Abel for posting the list of NIJ projects as at a very recent date (it might not be somebody on that list of course). We also do not know what stage 2 might entail.
The word "complements" was interesting. This could be an extension of current DNAWitness capabilities (perhaps finer interpretation of biogeographical ancestry) or addition of new capabilities.
Despite the uncertainties I agree it is very good news!
mjam, I think that the PR reflects what they (DNAP) can say at the moment about this particular development IMHO. The alternative interpretation would indeed be that it was hastily written and disjointed!
mjam, my take is that the 50K is not important. The first stage is clearly a prototype or proof of concept. The interesting questions are who is the grantee and what does stage 2 involve? As Weizen said on the main board the key thing here is that DNAP is now working for the US Government!
Grateful, that's not too difficult. Philip Yeo is a good one to start with. He is director of a company called Capitaland Limited (Singapore), amongst other things. A guy called Vernon R. Loucks was also a director of this company until 2002. Vernon is chairman of Aethena (not to be confused with Athena Capital who are DNAP's investment bankers), who have acted for, and have lots of links with, people like Affymetrix, Maxygen and Symyx. To cut a long story short, the main people directly connected are George Poste and Ernest Mario; although I maintain that names like Steven Kriegsman, Michael Hayden, and Kyle Chan (once touted as a a DNAP SAB member) are possibly relevant.
Arch, this paper just keeps getting referenced. There are some buzzwords that appeal to editors and/or the paper has some significance!
P.S. The NIH would probably be in the latter camp.
Miss Scarlet
It is a bit complicated. The relevant document is:
http://www.nasdaq.com/about/nasdaq_listing_req_fees.pdf
There are initial listing and continued listing requirments for minimum bid price. For the Nasdaq itself these are $5 and $1 (with a whole host of other criteria) and for the Nasdaq SmallCap market they are $4 and $1. This is where the $4 figure comes from.
Rob
Let me offer you the following information from the US Patent Office for the Phenome and Phenomics trademarks:
Word Mark PHENOME
Goods and Services (ABANDONED) IC 042. US 100 101. G & S: computer services, namely, access to a database containing components of a person's genetic architecture with respect to a complex multigenic phenotype for determining predisposition to certain diseases via a global computer network
Mark Drawing Code (1) TYPED DRAWING
Serial Number 75927822
Filing Date February 25, 2000
Filed ITU FILED AS ITU
Owner (APPLICANT) Pacific Atlantic Corporation CORPORATION FLORIDA 1748 Independence Blvd., Suite D1 Sarasota FLORIDA 34234
Attorney of Record Mary B. Scott
Type of Mark SERVICE MARK
Register PRINCIPAL
Live/Dead Indicator DEAD
Abandonment Date February 26, 2001
Serial Number: 75927822
Registration Number: (NOT AVAILABLE)
Mark (words only): PHENOME
Current Status: Abandoned: Applicant failed to respond to an Office action.
For those that do not know Pacific Atlantic Corporation is George Frudakis's company (indeed they own the DNAPrint trademark).
Word Mark PHENOMICS
Goods and Services (ABANDONED) IC 042. US 100 101. G & S: industrial enzyme research in the chemical and agricultural fields
Mark Drawing Code (1) TYPED DRAWING
Serial Number 75625873
Filing Date January 25, 1999
Filed ITU FILED AS ITU
Owner (APPLICANT) Proteus S.A. JOINT STOCK COMPANY FRANCE 1105 Avenue Pierre Mendes France 30000 Nimes FRANCE
Attorney of Record JOHN A. CLIFFORD, ESQ.
Section 44 Indicator SECT44
Priority Date August 13, 1998
Type of Mark SERVICE MARK
Register PRINCIPAL
Live/Dead Indicator DEAD
Abandonment Date March 25, 2003
Word Mark PHENOMICS
Goods and Services (ABANDONED) IC 009. US 021 023 026 036 038. G & S: electronic apparatus, namely, computer hardware, software, databases, and microprocessors for use in patient monitoring information systems in the fields of clinical research and healthcare management and user manuals and workbooks sold therewith
(ABANDONED) IC 042. US 100 101. G & S: computer software consulting services in the field of computer aided design, development and software integration for use in patient monitoring information systems; and computer services, namely, telephone, on-site and on-line technical support for use in the field of clinical research and healthcare management
(ABANDONED) IC 035. US 100 101 102. G & S: computerized database management in the field of clinical research and healthcare management
(ABANDONED) IC 041. US 100 101 107. G & S: educational and training services, namely, classes, seminars, conferences and workshops in the operation and use of computer hardware and software systems specifically designed for use in the field of clinical research and healthcare management
Mark Drawing Code (1) TYPED DRAWING
Serial Number 75429238
Filing Date February 5, 1998
Filed ITU FILED AS ITU
Owner (APPLICANT) Raya Systems, Inc. CORPORATION CALIFORNIA 2570 West El Camino Real, Suite 520 Mountain View CALIFORNIA 94040
Assignment Recorded ASSIGNMENT RECORDED
Attorney of Record DAVID A LOWE
Type of Mark TRADEMARK. SERVICE MARK
Register PRINCIPAL
Live/Dead Indicator DEAD
Abandonment Date April 24, 2000
Word Mark PHENOMICS
Goods and Services IC 042. US 100 101. G & S: consultation in the fields of medicine and genetics; providing information in the fields of medicine and genetics
Mark Drawing Code (1) TYPED DRAWING
Serial Number 75150978
Filing Date August 14, 1996
Filed ITU FILED AS ITU
Published for Opposition June 9, 1998
Registration Number 2190262
Registration Date September 22, 1998
Owner (REGISTRANT) Gemini International Holdings Limited LIMITED COMPANY BR.VIRGIN ISLANDS P.O. Box 71 Road Town, Tortola BR.VIRGIN ISLANDS
Assignment Recorded ASSIGNMENT RECORDED
Attorney of Record JULIE A PETRUZZELLI
Section 44 Indicator SECT44
Priority Date May 9, 1996
Type of Mark SERVICE MARK
Register PRINCIPAL
Live/Dead Indicator LIVE
There is no WIPO trademark for either Phenome or Phenomic, but there is one for Phenomics on the Madrid database (I've taken the liberty of removing the French text):
(151) 13.01.1999 0709264
(180) 13.01.2009
(171) 10
(732) PROTEUS S.A.
Parc Georges Besse,
Allée Graham Bell
Nimes (FR)
(812) FR
(740) BREESE-MAJEROWICZ
Virginie Barbet
3, avenue de l'Opéra
F-75001 PARIS (FR)
(540) PHENOMICS
(550) Reproduction of the mark where the mark is represented in standard characters
(511) Chemicals and biochemicals for industrial, scientific, agricultural and forestry purposes; fertilizers, chemical and biochemical preparations used for cleaning contaminated earth, sludge and waste water, chemical and biochemical products used for preserving foodstuffs, for improving the nutritional and sanitary quality of foodstuffs; tanning substances, adhesives used in industry; diagnostic reagents, reagents and biochemical products (other than for medical or veterinary use) and chemical and biochemical products for use in research and testing laboratories; chemical and biochemical products for molecular biology.
Scientific apparatus and instruments used in the implementation of biochemical analysis and molecular biology techniques.
Veterinary and agricultural services, legal services; scientific and industrial research; research and perfecting of biochemical analysis, biological analysis and molecular biology techniques for use in industrial, agricultural and agri-food testing, or to be used for human or veterinary diagnosis; research and perfecting of new molecules for industrial use; research and perfecting of new enzymes; research and development of new medicines or new therapeutic methods.
Hope this helps!
DNAP themselves have applied for a number of broad patents on the various constituent components of ADMIXMAP.
Herald Tribune article
http://www.heraldtribune.com/apps/pbcs.dll/article?AID=/20030819/NEWS/308190501/1200&cachetime=5
DNAPrint sees jump in sales
The company's DNA testing products prove profitable in the first six months of the year.
STAFF REPORT
SARASOTA -- Tiny DNA- Print Genomics saw a bump in revenues during the first six months of the year as sales of its geneaology product, Ancestry by DNA, picked up.
The company reported revenues of $330,442, double the $115,159 during the same period in 2002.
DNAPrint spent most of its money during the period on research and development: about $2.1 million during the first six months of 2003, compared with $1.1 million during the 2002 first half.
The company said the increase of about $1 million was primarily the result of the stock-based compensation paid to Tony Frudakis, the DNAPrint's chief scientific officer.
During the six-month period, general and administrative costs were $1.15 million compared with $252,726 during the same 2002 period.
The increase again was largely based on stock compensation paid to the company's three top executives, DNA- Print said.
The company's over-the- counter shares were selling for 7 cents at the close of regular trading on Monday, unchanged.
DNAPrint is expecting its personnel costs to continue increasing through the end of 2003 as it expands its research and sales efforts. The company now has seven full-time employees.
The company's products have a wide range of uses.
The forensics version of its products helped solve the recent serial killing case in Louisiana. The test, marketed as "DNAWitness," analyzes bodily fluids to determine within a few percentage points to what extent a person is of Native American, East Asian, Indo-European, and sub-Saharan African heritage.
The Louisiana case appears to be the first time in U.S. history that DNA was used to cull details of a criminal's physical appearance. Investigators had been looking at white suspects, and, after the test, turned their attention to black suspects.
Meanwhile, genealogy buffs who want to explore ambiguous parts of their family trees can buy the same test under the name "ANCESTRYbyDNA2.0."
spook, the numbers in the 10Q seem to be in line with what Tony Frudakis was saying. Perhaps his projections will bear some relation to reality as well? I agree that having all of these heavy hitters onboard is not necessary if there is not going to be growth. The fact that they are already in place tells me that somebody knows that such growth is going to occur, and I personally would rather the team was in place before the event. I think there is a Whopper waiting for us soon. Can I get fries with that?
Spook
Did Monica do something to offend you in a previous life?
The bean-counting is obviously a key function that grows in importance as the company matures. In the event of e.g. mergers or acquisitions that create a significantly larger entity then the function becomes correspondingly more important, especially if this were to be accompanied by say a listing on the Nasdaq or Amex. Monica is also the Chief Operating Officer, itself a key role.
Monica's compensation will have been decided by the board. Her relationship to Richard Gabriel is a different matter, and frankly none of our concern IMO as long as it has no bearing on how they perform their respective duties. Would you rather that she was paid a regular salary at this stage? What would that do to the operating costs and the net profit and loss?
Despite my previous mail I do not think that Monica (and the others) will be receiving this amount of shares per annnum. I suspect that if events unfold as I anticipate the basis of their renumeration will switch to a more normal mix of salary and (probably) share options. I think that the 20 million shares is to cover the period of their initial employment and to incentivize them by giving them a stake in the company.
BTW, be prepared for the Marketing Director to probably be issued a fistful of shares as well...
Nice article and video featuring Mark Shriver
http://www.sciencentral.com/articles/view.php3?language=english&type=article&article_id=2183...
Here's one I thought would be raised. If the employment contracts are for one year only, and renewable on the same terms (this is the default legally), then does that mean that the three executives will be receiving 75 million shares between them every year?
spook, sorry was busy yesterday. I agree with the 30M shares for Frudakis on the basis that this was a previously negotiated element of his compensation which, due to intervening events, was not going to vest as anticipated. They had to tie up this loose end.
If you look at the share compensation for Gomez, Gabriel, and (the one that most seem to have an issue with) Tamborini (Monica is a girl - deal with it people) in terms of current cash value of shares then you would think that they are being rewarded in a manner which is disproportionate to the "industry norm" (whatever that is and notwithstanding that this is a new industry). However, all of their renumeration is stock (plus the cash to cover the taxes). This is not a usual arrangement for corporate executives, who would typically want to have their cake and eat it too. The executives are sharing the same risk that the shareholders are. In their case they can do something to directly ameliorate that risk! The ball is in their court.
How Richard and Monica do in practice remains to be seen. Their track record is OK. Let's give them a chance. To some extent you either trust people at the company or you don't. Personally I extent them that trust, although do not deny that I would also like to see more frequent shareholder updates on the sort of material events that we are discussing.
spook, quick answers for now as I am about to retire:
Employee numbers - with you on this one, I also would like a rational explanation (as I have previously posted).
Bank account - there is 400K in the bank (or 1.9M if you add in the 1.5M).
Compensation - we have the one-off costs associated with Tony Frudakis's share compensation, and the cash adjustments related to the share compensation of the three other executives. Subtract these from the total and we are more or less on track with what Tony said previously.