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Was our amphibian friend looking for this?
http://www.clerk.co.sarasota.fl.us/srqapp/cache/45795179.pdf
It is concerned with the download of information from the impounded computer and other related matters.
Not a nonsensical premise in sight...
OT: bab8ger, they are examining one woman who just returned sick from Vietnam. Do I know anyone who could get Dr Moskowitz's treatment protocol to be considered should it occur? Yes, the same people we corresponded with last year over SARS. They have all the information.
bag8ger, the dates were there for the WIPO patents, which were filed after DNAP. I cannot see GNSC's US patent equivalents for the WIPO ones and therefore do not know what date they filed these. In any case, given that the two companies have taken different approaches and DNAP seem to have the nap hand (as opposed to the nap head), I don't think it really matters when GNSC filed their patent applications.
80spitfire, I don't follow Genaissance that closely as I do not personally own the stock or view them as a significant competitor. They seem to be buying a lot of pieces with no clear picture of how it all fits together long term. I get the impression that they are desperate to acquire revenue streams to try to buy time until something comes of the pharmacogenomic research or one of the existing pharma collaborations. JMHO though.
Statin patent applications
Details of the various applications with some observations by me in italics. You really get a good feel for the relative strength of the applications by the length and content of them, and I have to say that DNAP's looks to me to be in a different ballpark to the others.
IHC Health Services, Inc.
US Patent Application: 20020164598
Title: Method for evaluating and applying an individual's genetic characteristics to determine response to cardiovascular medication therapy
Filed: May 3, 2001
Last Update: November 7, 2002
A process for evaluating the genetic sensitivity of individual patients to medications and to appropriately prescribing or not prescribing medication according to established correlations between the genetic sensitivity and the specific medication is described. In the present preferred embodiment/example, this invention provides a process for determining whether a person, having either cardiovascular disease or cardiovascular risk factors, has a genetic characteristic which would indicate whether the ordinarily prescribed statin medication is likely to be effective or even detrimental.
It is desirable to provide a method for predicting the performance and applicability of drug and other medication treatment for patients with specific medical conditions. It is particularly desirable that such a method be based on the application of a genetic test, which provides for the detection of one or more genotypes, the presence of which can be used as a predictor of therapeutic response. In its present preferred embodiment, this invention makes use of the CETP Taq 1B Genotype as a predictor of therapeutic response to statin therapy in patients with severe coronary artery disease.
Note: single gene only (one of the ones Genaissance is working on).
Cedars-Sinai's Medical Genetics-Birth Defects Center
US Patent Application: 20020106657
Title: Genetic test to determine non-responsiveness to statin drug treatment
Filed: July 3, 2001
Last Update: August 8, 2002
The present invention relates to a method of detecting a genetic predisposition in a human subject for non-responsiveness to statin drug treatment for coronary artery disease. This genetic testing method involves analyzing amplification products of the nucleic acids in a human tissue sample that includes a non-coding or untranslated region within the 3' end of the human LPL gene. Homozygosity for a variant allele in a non-coding or untranslated region within the 3' end of the human LPL gene indicates a genetic predisposition for non-responsiveness to treatment with statin-class drugs, such as lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, and cerivastatin, which are typically prescribed to treat atherosclerotic stenosis in subjects with coronary artery disease, or to prevent graft worsening (stenosis) in CABG patients.
Note: single gene only testing for non-responsiveness
DNAPrint Genomics
US Patent Application: 20030215819
Title: Compositions and methods for inferring a response to statin
Filed: July 1, 2002
Last Update: November 20, 2003
The present invention relates to compositions and methods useful for inferring a statin response of a subject from a nucleic acid sample of the subject. The invention is based, in part, on a determination that single nucleotide polymorphisms (SNPs), including haploid or diploid SNPs, and haplotype alleles (i.e., combinations of two or more SNPs in a single gene, e.g., a cytochrome P450 gene and/or a 3-hydroxy-3-methylglutaryl-coenzymeA reductase (HMGCR) gene), including haploid or diploid haplotype alleles, allows an inference to be drawn as to whether a subject, particularly a human subject, will have a positive response to treatment with a statin, for example, by exhibiting a decrease in total cholesterol or in low density lipoprotein levels, or will have an adverse response, for example, liver damage. The statin can be any statin, including, for example, Atorvastatin or Simvastatin.
The results of this SNP screen are shown in Table 9-13. From Table 9-13 it is evident that many different genes impact variable Statin response. For most of the outcomes, there were SNPs from at least four different genes associated. It is also clear that the gene compliments are highly unique for each end point and each gene. The GSTs (GSTM1, GSTT2, GSTA2) were quite strongly associated with LIPITOR response, linked with LDL, TC and SGOT outcome, but not ZOCOR response. The NAT2 gene was only found to be relevant for ZOCOR response, and only had impact on the TC lowering effect of the drug, not the LDL lowering effect. CYP2C8 was an important determinant for both LIPITOR and ZOCOR, for the former, impacting both TC and SGOT outcome. Of significant interest, no SNPs, or only weakly associated SNPs in the HMGCS1, MVK or HMGCR gene were identified, though we previously described HMGCR haplotypes associated with response. Usually, the ability to identify associations at the level of the SNP indicates the gene contribution towards response is relatively strong compared to genes with associations only apparent at the level of the haplotype. The HMGCS 1, MVK and HMGCR genes are part of the cholesterol synthesis pathway inhibited by Statins, yet our results suggest that most of Statin variable response is attributed by xenobiotic metabolism gene sequences, not target pathway sequences. The associations we have described earlier in this application therefore are a function of haplotype, not SNP sequences. With these haplotypes, and SNPs from genes below, a linear or quadratic discriminate classifier (as we have described elsewhere, (T. Frudakis, U.S. patent application Ser. No. 10/156,995, filed May 28, 2002), Frudakis et al., J. Forensic Science, (2002); Frudakis 2002a) is possible to predict each outcome.
Note: Multiple genes testing for whether there will be a positive response or an adverse response for any of the statin class of drugs (different methods are included for each statin).
Genaissance
Poster presented at the 52nd Annual American College of Cardiology Scientific Session, March 30 - April 2, 2003
We discovered 179 SNPs including 30 novel, non-synomymous SNPs in ABCA1. We found a significant association between an ABCA1 haplotype marker and LDL-C reduction by statin treatment (P<0.0001). The association is also seen in the individual statin groups with p-values ranging from 0.04 to 0.003. The marker includes GLU(1192) ASP plus 4 other SNPs. Patients with >1 copy of the marker respond with 10% less LDL-C reduction than those without the marker. There were no differences in baseline lipids or HDL-C response between individuals based on this marker.
The fact that variability in drug response is determined by a disease pathway gene, and not by the drug target, is also significant. This finding suggests that a candidate gene approach to pharmacogenetics is dependent upon the
inclusion of genes in the disease pathway, as well as those in the target pathway. Indeed, this approach is essential even when mechanism of action is poorly understood, as is the case with statins.
Note: single gene, and different conclusion to that highlighted in the DNAP patent applicaiton.
Genaissance Pharmaceuticals Describes Link Between Genetic Markers and Drug Response in Cardiovascular Disease
— Clinical Data Support DNA-Based Diagnostic Tests to Enhance Treatment and Dosing Decisions for Cardiovascular Indications —
Orlando, FL, November 11, 2003 – Genaissance Pharmaceuticals, Inc. (Nasdaq: GNSC) today presented, at the American Heart Association's Scientific Sessions 2003, clinical data describing associations between genetic markers (HAP™ Markers) and response to treatment with the statin class of drugs. The two presentations provided additional results from Genaissance's Statin Response Examined by Genetic Haplotype Markers (STRENGTH) clinical study.
In one presentation, Genaissance confirmed an association between HAP™ Markers in the gene apolipoprotein E (ApoE) and levels of C-reactive protein (CRP), which has been associated with inflammation and linked to risk for arteriosclerosis. Genaissance also extended the association by identifying ApoE HAP™ Markers that are present in those patients who showed the greatest reduction in the level of CRP when treated with a statin.
"We believe that this finding could help predict which patients will experience the greatest anti-inflammation effect of statins, further reducing their risk for arteriosclerosis," said Richard S. Judson, Ph.D., Senior Vice President and Chief Scientific Officer of Genaissance Pharmaceuticals. "Our new findings, combined with our previously released data, provide the basis for new DNA-based diagnostic tests for the cardiovascular market that could be used to help physicians make dosing and other treatment decisions."
In the second presentation, Genaissance described an association between HAP™ Markers in the gene P-Selectin, which has been associated with diabetes and cardiovascular conditions, and changes in the level of HDL-Cholesterol (HDL-C) in response to statin therapy. The association was observed with all of the statins studied (atorvastatin, pravastatin and simvastatin) and represents an effect of the statin class of drugs. The HAP™ Markers also identified patients most likely to experience a reduction in HDL-C if switched to a higher dose of a statin.
"Having a high level of HDL-C is considered to be beneficial to one's health," said Dr. Judson. "We believe that genetic markers, such as those for P-Selectin, could aid a physician in treating a patient with the statin class of drugs so as to maximize the lowering of LDL-C, the bad cholesterol, while maintaining as high a level as possible of the good cholesterol, HDL-C."
WIPO Patent Application: WO 04/003167
Title: GUCY1B2 GENETIC MARKERS FOR LDL CHOLESTEROL RESPONSE TO STATIN THERAPY
Filed: June 28, 2002
Last Update: January 8, 2004
Genetic markers in the GUCY1B2 gene associated with LDL cholesterol response to treatment with atorvastatin calcium are disclosed. Compositions and methods for detecting and using these GUCY1B2 genetic markers in a variety of clinical applications are disclosed. Such applications include articles of manufacture comprising a statin composition approved for treating patients having one of these GUCY1B2 haplotypes, methods and kits for predicting the response of an individual to a given statin treatment based on their haplotype profile, and methods for treating individuals with hyperlipidemia based on their haplotype profile.
Note: single gene for atorvastatin only.
WIPO Patent Application: WO 03/091698
Title: CETP GENETIC MARKERS FOR STATIN-SPECIFIC CHANGES IN HDL CHOLESTEROL
Filed: April 28, 2003
Last Update: November 6, 2003
Genetic markers in the CETP gene associated with statin-specific changes in HDL cholesterol after statin treatment are disclosed. Compositions and methods for detecting and using these CETP genetic markers in a variety of clinical applications are disclosed. Such applications include articles of manufacture comprising a statin composition approved for treating patients having one of these CETP haplotypes, methods and kits for predicting the response of an individual to a given statin treatment based on their haplotype profile, and methods for treating individuals with hyperlipidemia based on their haplotype profile.
Note: single gene only.
Bayer
WIPO Patent Application: WO 03/072813
Title: SINGLE NUCLEOTIDE POLYMORPHISMS PREDICTING ADVERSE DRUG REACTIONS AND MEDICATION EFFICACY
Filed: February 14, 2003
Last Update: September 4, 2003
The invention provides diagnostic methods and kits including oligo and/or polynucleotides or derivatives, including as well antibodies determining whether a human subject is at risk of getting adverse drug reaction after statin therapy or whether the human subject is a high or low responder or a good a or bad metabolizer of statins. The invention provides further diagnostic methods and kits including antibodies determining whether a human subject is at risk for a cardiovascular disease. Still further the invention provides polymorphic sequences and other genes. The present invention further relates to isolated polynucleotides encoding a phenotype associated (PA) gene polypeptide useful in methods to identify therapeutic agents and useful for preparation of a medicament to treat cardiovascular disease or influence drug response, the polynucleotide is selected from the group comprising:SEQ ID 1-80 with allelic variation as indicated in the sequences section contained in a functional surrounding like full length cDNA for PA gene polypeptide and with or without the PA gene promoter sequence.
Note: single gene only.
So why did Bayer and AstraZeneca partner with Genaissance in 2003 in relation to STRENGTH? I agree with the deficiency of the program but it is not dead in the water yet, and Genaissance are still updating their patents. I have spent a lot of time reviewing all the statin response patents (not just DNAP and GNSC) and will post something about the relative merits of each when I get a chance.
I liked this bit:
"I know if it were my daughter or son that had been murdered or raped, I would want this test run," said Zach Gaskin, Technical Director of Forensics. "I frequently give lectures on how our test works and how to use it. DNAWitness(TM) is becoming known as a reliable test for law enforcement across the country and abroad, allowing them to narrow their field of suspects rapidly.
I wonder whether the previously quoted total of DNA Witness being used in 20 to 30 criminal investigations nationwide is set to increase dramatically...
What are the most popular hobbies in the US?
http://www.courierpress.com/ecp/community/article/0,1626,ECP_737_2590933,00.html
"The study of genealogy and family history is now the second most popular hobby (after gardening) in the United States..."
http://www.senate.gov/~hatch/index.cfm?Fuseaction=Services.Genealogy&IsTextOnly=True
"Experts say that in the United States, genealogy is now the second most popular hobby next to gardening. It is believed that more that 80 million Americans are currently actively searching for more information about their ancestors."
That's a big number. You can now roughly estimate the total size of the Ancestry market (excluding DNA Witness) by making some simplistic assumptions. The size (over time) will be the number of tests completed multiplied by the price per test (ignoring subsequent generations). I give my estimates below. If you disagree use your own numbers and/or your own methodology.
The number of tests can be arrived at by taking a percentage of the 80 million, as not everybody will want to use it. However. some people will order the test for multiple family members as we have seen in practice. Assuming that the latter is a relatively small percentage of the total and that only 1% of people interested in genealogy order the test. That's still 800,000 tests.
The price per test for Ancestry 2.5 is $219. Ancestry 2.0 was cheaper but the original price plus the upgrade is more expensive. Let's say for the sake of argument that the average price for all the tests over a period of time is $180.
So the total market over time is 800,000 x 180 = $144 million.
Over what period of time is this money received? Let's ignore discounted cash flows and the like and suppose that we will incur this revenue over a 70 year period. That's still just over $2 million per year.
We made $565,000 from Ancestry during the first nine months of 2003. How much would be make in the full year? If we pro-rata the nine month earnings you would say $734,000. However, we reasonably expect that there will be higher volume of orders in the last three months so it could be more than this. It looks like a minimum of some 4,600 tests will be included in 2003 figures ($734,000 divided by $158 per test). What would the typical gross revenue be in a typical year? How many tests are implied in a typical year? To achieve the revenues postulated above we would need sales volume of some 11,400 tests per year.
Don't forget this is assuming only 1% of the market and includes the US only. It seems to me that on a reasonable guess basis Ancestry on its own could make a significant contribution towards operating costs.
Bradenton Herald business section
http://www.bradenton.com/mld/bradenton/business/7812227.htm
FLORIDA: Sarasota - DNAPrint genomics Inc. in Sarasota introduced a new version of its popular ANCESTRYbyDNA 2.0 test, which can determine an individual's ancestral makeup.
The new test, ANCESTRYbyDNA 2.5, provides a customer's proportional Native American, East Asian, Indo-European, and West Sub-Saharan African biogeographical ancestry. An increased number of genetic markers used in the new test allows for more sensitive and accurate determinations of low levels of "admixture" (such as that which may have been contributed by a single great-grandparent). The test is marketed to those interested in genealogy and has been used in criminal investigations to help describe suspects.
The new test sells for $219. Customers who purchased the 2.0 version will receive an upgrade to 2.5 at a reduced rate of $158. Information: www.ancestrybydna.com.
As Doug says the same scientific peer names keep popping up - apart from O'Brien and Kidd, David Goldstein (UCL) is the other main critic. This begs the question of why some of the other peers are not quoted? Chakraborty was quoted once with some spin. Apart from people like Parra (Toronto) who work with Shriver, there are only a handful of others who are qualified to comment including e.g. Rosenberg (USC), Smith (NCI), Altschuler (Harvard), McKeigue (LSHTM), Pritchard (Chicago), and Seldin (UCD). Maybe you could add Mike Hammer (Arizona) to the list as he is a forensics specialist. Perhaps the reason that some of these people are not quoted is that they are collaborators? Just a thought.
Criticism by academics
There has been some criticism recently by (leading) academics about Ancestry/DNA Witness. One such academic is Stephen J O'Brien:
O'Brien initially voiced criticism in the New York Times article "For Sale: A DNA Test to Measure Racial Mix" from October 1, 2002:
"It's possible in principle to estimate the extent of admixture, but the number is not going to be very accurate," said Dr. Stephen J. O'Brien, a population geneticist at the National Cancer Institute, referring to the proportion of different ancestry in people of mixed race.
O'Brien had another rant in the recent Native Times article:
"The company will be able to provide you with an estimate, but it won't be much better than looking at the guy," Stephen J. O'Brien, chief of the Maryland-based Laboratory of Genomic Diversity at the National Cancer Institute told the St. Petersburg Times. "I'm sure it won't have much use to the recipient."
Well, at least we have gone from "it's possible in principle" to "The company will be able to". I agree with Tony's comment from the same article in reference to O'Brien:
"That same guy that said it wouldn’t work knows the test is do-able, and do-able with quantifiable precision. He’s lying."
What makes Tony sure that O'Brien is lying? Perhaps it has something to do with this:
Smith MW, Lautenberger JA, Shin HD, Chretien JP, Shrestha S, Gilbert DA, O'Brien SJ. Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. Am J Hum Genet. 2001 Nov; 69(5): 1080-94.
Michael Smith, one of the co-authors of the above paper, is of course familiar with this area from previous research:
Shriver MD, Smith MW, Jin L, Marcini A, Akey JM, Deka R, Ferrell RE. Ethnic-affiliation estimation by use of population-specific DNA markers. Am J Hum Genet. 1997 Apr; 60(4): 957-64.
A relevant quote from Stephen O'Brien's research summary:
http://home.ncifcrf.gov/ccr/lgd/about/staff/obriens_rn.asp
The specific objective of this project is to discover and characterize human genetic loci operative in differential host responses to two pathological viruses, HIV and hepatitis B virus, using the combined methods of human molecular genetics, population genetic theory, and epidemiology. Towards this goal, we have developed a new approach to mapping disease loci in populations when family studies are not feasible (as in the case of infectious disease susceptibility). The method, termed Mapping by Admixture Linkage Disequilibrium (MALD), takes advantage of linkage disequilibrium that occurs temporarily in admixed racial groups, such as African Americans and Hispanics.
Leaving the developer of MALD, and turning to the article by Cindy Rodriguez in the Denver Post yesterday:
We see some comments by Kenneth K Kidd of Yale who was "incredulous":
Kidd said it's not possible to determine, from DNA, if someone is Latino.
Further, Kidd said he doesn't support the work of DNAPrint Genomics because it has yet to publish a detailed paper about the DNA markers it is using.
It's customary for researchers to publish findings so that other scientists can test them. But the two papers that Kidd has read from the company had scant information, he said. Furthermore, he said the population samples that they referred to, which are used as a benchmark, were not large or diverse enough for that use.
That's this Kidd by the way:
Love the moustache.
Kidd is of course familiar with this whole area as well:
Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. Genetic structure of human populations. Science. 2002 Dec 20; 298(5602): 2381-5.
Chakraborty R, Kidd KK. The utility of DNA typing in forensic work. Science. 1991 Dec 20; 254(5039): 1735-9.
If "the population samples that they referred to, which are used as a benchmark, were not large or diverse enough for that use" then how come they have been successfully used? Never mind, that's not important right now. There is a difference between publication of findings for peer review by academics and non-disclosure of proprietary intellectual property. I am sure that O'Brien, Kidd and countless others would dearly love DNAP to publish a "detailed paper about the DNA markers it is using" but I think they had better not hold their breath waiting.
Perhaps there is an agenda here on the part of O'Brien and Kidd? Me thinks they doth protest too much...
You could always ask TonyTox for his considered opinion...
Don't think we'll have to wait long Jim!
bag8ger, it says something when you have to have an undergraduate level grasp of the science in order to undertand what is going on. We're a long way from normal fundamental analysis...
Jim, these are typically either previous versions of the same patent, and/or of related patents, which have been extended by addition, and/or themselves superceded, and which can thus be abandoned in their own right.
Here's an interesting article.
Hinds DA, Stokowski RP, Patil N, Konvicka K, Kershenobich D, Cox DR, Ballinger DG. Matching strategies for genetic association studies in structured populations. Am J Hum Genet. 2004 Feb; 74(2): 317-25.
Perlegen Sciences, Mountain View, CA, 94043, USA. David_Hinds@perlegen.com
Association studies in populations that are genetically heterogeneous can yield large numbers of spurious associations if population subgroups are unequally represented among cases and controls. This problem is particularly acute for studies involving pooled genotyping of very large numbers of single-nucleotide-polymorphism (SNP) markers, because most methods for analysis of association in structured populations require individual genotyping data. In this study, we present several strategies for matching case and control pools to have similar genetic compositions, based on ancestry information inferred from genotype data for approximately 300 SNPs tiled on an oligonucleotide-based genotyping array. We also discuss methods for measuring the impact of population stratification on an association study. Results for an admixed population and a phenotype strongly confounded with ancestry show that these simple matching strategies can effectively mitigate the impact of population stratification.
Nah! Couldn't be...
Robert, yes when you put text from the DNAP/PSU press release:
http://www.dnaprint.com/pr_7_10.htm
"Researchers from both institutions will team to complete admixture mapping and candidate genome screens to identify the complex genetic determinants of variable human skin pigmentation, tanning/burn response and melanoma risk."
Next to the text you posted:
"Our work on human pigmentation genetics has provided a framework to understand normal variation in this physical trait and the associated genotypic risk for skin cancer development. The genes that determine an individual's skin phototype and the cellular mechanisms that result in the tanning response of melanocytes after UV-exposure of the skin are actively being investigated."
The synergies are readily apparent. The number of areas of overlap that there are with forensic and medical initiatives in Australia is, as others have noted before, quite intriguing.
Ming
Leglessinseattle
Homer Wolfe
For those that have not seen this particular young man, some sample websites:
http://ijmms.hindawi.com/volume-2003/S0161171203201046.html
International Journal of Mathematics and Mathematical Sciences. 2003:38 (2003) 2447-2453. TOTAL CHARACTERS AND CHEBYSHEV POLYNOMIALS. EIRINI POIMENIDOU and HOMER WOLFE.
http://sa.rochester.edu/jur/currentissue/f03/johnson.pdf
The Riemannian Metric and Curvature Tensor on a Manifold
Niles G. Johnson, David T. Guarrera, Northwestern University, Homer F. Wolfe, New College of Florida.
Advisors: DaGang Yang and Morris Kalka (Tulane University)
Department of Mathematics
This young man also takes part in community activities:
http://catalyst.ncf.edu/pdf/S03_04.pdf
Thesis-student Homer Wolfe volunteers his time with the children in the Keys to the Future Program. "The kids are really uplifting to be around. They require a lot of energy from me, but they also inspire me to produce it. Really, all they want is attention; for someone to show them that they are worthy of the same degree of attention that many adults give only to cars, televisions, and other dead objects," he said.
http://studentweb.ncf.edu/ncsa/Clubs.htm
Math Clinic Tutoring math to Students in the Sarasota Community Homer Wolfe
The Annual Lorne Genome 2004 Conference, Brisbane, Australia program has now been finalized. Here is the relevant bit:
http://www.genome-conf.net.au/lorne/program.asp#
SYMPOSIUM 6 08:45-10:35
SNPs AND GENETIC ANALYSIS
Chair: Rick Sturm
Session sponsored by Sequenom
SYM-6-1
08:45 Admixture mapping for molecular photofitting and pharmacogenetics
Frudakis, T.N., Ponnuswamy, V., Thomas, M., Gaskin, Z., Gunjipulli, S. (U.S.A.)
SYM-6-2
09:15 Searching for SNPs associated with breast and ovarian cancer
Chenevix-Trench, G. (Australia)
SYM-6-3
09:45 Genetic polymorphism(val66met) in brain derived growth factor gene associated with deficits in episodic and working memory in humans
Schofield, P.R., Luty, A., Williams, L., Gordon, E. (Australia)
SYM-6-4
10:05 Association of body fat distribution and obesity with uncoupling proteins variants in Anglo-Celtic caucasians in Australia
Lin, R.C.Y., Dalziel, B., Speirs, H., Morris, B.J., Brand-Miller, J., Robertson, B., Dawes, I.W. (Australia)
SYM-6-5
10:15 Perfomance effects and evolutionary history of a common polymorphism in the ACTN3 gene
MacArthur, D.G., Yang, N., Gulbin, J., Easteal, S., North, K. (Australia)
The term "molecular photofitting" is used above - previously the term "DNA photofitting" was used to describe the forensic applications that DNAP are working on e.g. in this article:
http://www.usnews.com/usnews/issue/030623/misc/23dna.htm
Incidentally, the date shown on the DNAP website for this conference is wrong. The speech referred to above is actually on 17 February.
The speech after Tony's is interesting. Georgia Chenevix-Trench has recently got a lot of funding from both Australia and the US for her group's research.
BTW, have a look at what the session Chair does:
http://www.imb.uq.edu.au/index.html?id=11690
OT: No confusion here frog, but you seem to have got your parties confused (or perhaps it is just you that is confused). You might recall that I declined to participate in the activities of the trading clique. I hope that all this trading is profitable and fulfilling for you (emotionally, spiritually, or otherwise). Now, don't forget that I rank pretty low on your priority list so don't feel obliged to waste too much time here. There is always the entry price to worry about, apart from the aforementioned design and development of course...
OT: Frog, glad I can be of assistance. Yes the stress on the part of you and your team is obvious. Try buying and holding the shares for a change, it might help...
OT: frog, it was rhetorical, but such wit on your part! I just hope that all this banter and repartee is not detracting from your efforts to "design and develop lifesaving medical devices that intervene in life threatening situations". Time far better spent than on these boards I suspect.
OT: ifida, perhaps it is Biophan? Or maybe one of their competitors...
An interesting information resource
I cam across the following today, which is a student resource page for the Medical Genetics course at the University of British Columbia:
http://obiweb.bcgsc.ca/medgen/medgen520/
The first sample answer to question 2 on this page is particularly relevant:
http://obiweb.bcgsc.ca/medgen/medgen520/midterm.htm
I've posted this link before, it shows a collection of "typical" features for different "races", and gives some idea what Tony was talking about in the article.
http://www.angeltowns.com/members/racialreal/
Put it together with something like this and...
http://www.efitforwindows.com/
Here's the text of the Denver Post article:
DNA test suggests race of woman's killer in '97
By Marcos Mocine-McQueen
Denver Post Staff Writer
BOULDER - Boulder police have turned to an unconventional DNA test to create a racial profile of the suspect in a high-profile 1997 murder, but some experts wonder if the test is worth the high price tag.
Susannah Chase, 23, died several days after she was found beaten in a Boulder alley on Dec. 21, 1997. Police found several clues and received a "slew" of tips, but nothing ever came of them.
"Essentially everything had been exhausted up to this point," said Kurt Weiler, commander of detectives.
In an effort to reignite interest in the case, Boulder police announced Wednesday that a test by a Florida company found that DNA at the Chase crime scene was "indicative of someone exhibiting features that are common to Hispanics or Native Americans."
A representative of the company, DNAPrint Genomics, said the test has been used only in 20 to 30 criminal investigations nationwide. The test determines what ancestries are present in a person's DNA. The company calls this blend of ancestries "admixture."
Using information from the Human Genome Project, the company can place people into four basic groups - Indo-European, Sub-Saharan African, East Asian and American Indian (which includes all of the Americas), or mixes of those four.
Some scientists have questioned the reliability of the test the company uses, but Greggory LaBerge, who heads the Denver Police Department's DNA lab, said he doesn't doubt the science. Instead, he questions whether the results are helpful.
"There's nothing it's going to glean for us that's useful in an investigation," LaBerge said.
Knowing the range of a suspect's race doesn't mean much by itself, he said.
"How's that going to tell you anything about how that guy's going to look?" LaBerge said. "Nothing."
Tony Frudakis, founder of DNAPrint Genomics, said the company is working on a remedy for that problem. It plans to develop a database of thousands of pictures so that investigators could see a variety of appearances a particular admixture can take on.
The company began in 1999 and aimed its research at medical breakthroughs.
"But with the recession, we ran low on money," Frudakis said. "We figured out that this would be valuable to law enforcement, and it gave us more revenue."
The forensic version of the test cost the Boulder police $1,100. Another version of the test aimed at citizens curious about their racial makeup is available for $158.
LaBerge said that while he likes the idea of the test on an intellectual level, its cost outweighs its value.
"We're on a really tight budget," LaBerge said. "We're not going to drop that type of money on a test that doesn't tell you as much as what we're doing here (in the Denver police lab)."
Additionally, the test requires DNA from a crime scene, and if there is a limited sample of that available, it should be saved for other, more specific comparison tests once a suspect is identified, LaBerge said.
Weiler said there is more than enough DNA to go around in this case, and the Police Department checked with the Colorado Bureau of Investigation to make sure. He also said the department is treating the test results with healthy skepticism and won't be making any blanket requests for Hispanic or American Indian men to provide DNA samples.
And the Herald Tribune
http://www.heraldtribune.com/apps/pbcs.dll/article?AID=/20040121/APN/401210657
AP article again
And the Florida Ledger
http://www.theledger.com/apps/pbcs.dll/article?AID=/20040121/APN/401210657
It's the same Associated Press article
And the Bradenton Herald
http://www.bradenton.com/mld/bradenton/7760526.htm
Colorado police turn to Florida DNA lab for clues in 1997 slaying
Associated Press
BOULDER, Colo. - With the trail growing cold, police investigating a six-year-old beating death turned to an unusual source for clues: a Florida DNA lab that normally helps people determine their own ethnic makeup.
The test results showed DNA found on the body of Susannah Chase might be that of a Hispanic or Indian man, police said.
Chase, 23, was beaten and left to die in a downtown alley on Dec. 21, 1997. Investigators submitted the sample to DNAPrint Genomics of Sarasota, Fla.
"Essentially everything had been exhausted up to this point," Kurt Weiler, commander of detectives, said Tuesday.
The DNA doesn't necessarily belong to the killer, police Sgt. Kerry Yamaguchi said.
"I think it just gives us some guidance. In the past, we've had to work in theories and guesses. Now we have something a little more concrete ... to take another look at things," he said.
Yamaguchi said investigators hope the new information may jog someone's memory and generate a new lead.
The investigative-quality DNA test cost police $1,100. DNAPrint Genomics charges $158 for a test to satisfy someone's curiosity about his or her racial makeup.
DNAPrint Genomics tested DNA in a Louisiana serial slaying case, said Tony Frudakis, the company's scientific director. The tests showed the killer was likely black, not white as police suspected, he said.
Police eventually arrested Derrick Todd Lee, who is black. He has pleaded innocent and faces a March 1 trial.
Louisiana investigators said they worked with DNAPrint Genomics but declined to comment further.
Yamaguchi said the DNA results will be used as a tool, not the determining clue in finding Chase's killer.
"This is new technology, a new theory," he said. "We want to be a little careful on the weight we give results of the testing."
Then there's the Rocky Mountain News
http://rockymountainnews.com/drmn/local/article/0,1299,DRMN_15_2591842,00.html
Boulder murder revisited
DNA test may reveal clues in 1997 case
By Berny Morson, Rocky Mountain News
January 21, 2004
BOULDER - Police are re-examining the 1997 Susannah Chase murder with the help of a DNA test that reveals a suspect's ethnicity.
The method, available for less than a year, points to a Hispanic or American Indian as the suspect in a case that shocked the city, Sgt. Kerry Yamaguchi said Tuesday.
Police will go back and talk to some people interviewed previously and reconsider old tips, Yamaguchi said.
The 23-year-old University of Colorado student was beaten in downtown Boulder early on Dec. 21, 1997, possibly with a baseball bat found nearby.
She died the next day without regaining consciousness.
The new tests were performed on DNA taken from sperm found during the initial investigation. Police received the test results last week.
The test is more than 90 percent accurate, said Richard Gabriel, the president of DNAPrint Genomics, of Sarasota, Fla., the company that did the lab work. It is based on 172 genetic markers, he said.
The test has been on the market since February 2003.
Gabriel said the test provides a "fuzzy photograph." But it's enough to point police toward certain leads.
Baton Rouge, La., police used the test in an investigation that led to the arrest of a suspected serial killer last May, according to that city's daily newspaper, The Advocate.
Boulder police have never established a motive in the Chase murder, although sexual assault is a "strong possibility," Yamaguchi said. The semen that was recovered did not belong to Chase's boyfriend or anyone else police have identified, Yamaguchi said.
Police are not close to identifying a suspect, but they have not given up, Yamaguchi said.
"We've never stopped (investigating)," Yamaguchi said. Tips are still coming in, with the latest coming in last month."
And one from the Casper Star Tribune
http://www.trib.com/AP/wire_detail.php?wire_num=69828
Police turn to unusual DNA lab for clues in 1997 slaying
coboudenpvsde
BOULDER, Colo. (AP) - With the trail growing cold, police investigating a six-year-old beating death turned to an unusual source for clues: a DNA lab that normally helps people determine their own ethnic makeup.
The test results, made public Tuesday, showed DNA found on the body of Susannah Chase might be that of a Hispanic or Indian man, police said.
Chase, 23, was beaten and left to die in a downtown alley on Dec. 21, 1997. Investigators submitted the sample to DNAPrint Genomics of Sarasota, Fla.
"Essentially everything had been exhausted up to this point," Kurt Weiler, commander of detectives, said Tuesday.
The DNA doesn't necessarily belong to the killer, police Sgt. Kerry Yamaguchi said.
"I think it just gives us some guidance. In the past, we've had to work in theories and guesses. Now we have something a little more concrete ... to take another look at things," he said.
Yamaguchi said investigators hope the new information may jog someone's memory and generate a new lead.
The investigative-quality DNA test cost police $1,100. DNAPrint Genomics charges $158 for a test to satisfy someone's curiosity about his or her racial makeup.
DNAPrint Genomics tested DNA in a Louisiana serial slaying case, said Tony Frudakis, the company's scientific director. The tests showed the killer was likely black, not white as police suspected, he said.
Police eventually arrested Derrick Todd Lee, who is black. He has pleaded innocent and faces a March 1 trial.
Louisiana investigators said they worked with DNAPrint Genomics but declined to comment further.
Yamaguchi said the DNA results will be used as a tool, not the determining clue in finding Chase's killer.
"This is new technology, a new theory," he said. "We want to be a little careful on the weight we give results of the testing."
And here's an article from the Boulder Daily Camera
http://www.bouldernews.com/bdc/city_news/article/0,1713,BDC_2422_2592511,00.html
DNA offers clue in Chase killing
Analysis shows woman's killer may have been Hispanic or Native American
By Christine Reid, Camera Staff Writer
January 21, 2004
A new DNA analysis shows that Susannah Chase's killer may have been a Hispanic or Native American man, giving police their first solid clue of a suspect that has eluded authorities since 1997.
The 23-year-old University of Colorado student was brutally beaten Dec. 21, 1997, and left to die in a downtown Boulder alley between Spruce and Pearl streets.
DNA from seminal fluid found on Chase's body was submitted last month to DNA Print Genomics in Florida, which specializes in defining ethnic makeup from genetic material. Police released the company's ancestral profile of that sample Tuesday.
"I think it just gives us some guidance," said Boulder Sgt. Kerry Yamaguchi. "In the past, we've had to work in theories and guesses. Now we have something a little more concrete ... to take another look at things."
Yamaguchi said investigators are also hoping the new information will jog someone's memory and possibly generate "the quality lead we need."
The DNA doesn't necessarily belong to the killer, Yamaguchi said.
DNA Print Genomics reported that its technology helped lead to the arrest last year of a suspect in the murders of six women in Louisiana. That was the company's first test in crime solving, said Zach Gaskin, technical director of forensics for the company.
Previously, the company only solicited DNA samples from people looking to determine their own ethnic makeup.
Scientists at the firm determine ethnic makeups by studying 175 genetic markers on the spiral staircase of DNA samples.
Gaskin, a former police officer, said the technology can help investigators edge closer to solving old cases and should be used for the national database that holds DNA profiles of thousands of suspects.
"If it were my family that was the victim, I would want samples in that database to give any lead to a stalled investigation," Gaskin said. "It may be helpful or it may not be, but it's another piece of information they didn't have."
Yamaguchi said the results will be used as a tool, not the determining clue in finding Chase's killer.
"This is new technology, a new theory," he said. "We want to be a little careful on the weight we give results of the testing."
The test, costing a couple of thousand dollars, could be used for other unsolved cases, Yamaguchi said.
There's an article in the Denver Post today "DNA test suggests race of woman's killer in '97". However, the article is not accessible at the moment. Here's the link:
http://www.denverpost.com/Stories/0,1413,36~53~1903981,00.html
Ann, speakers also include Gary Stormo. You can find him here (together with some other people we know):
http://www.biostat.wustl.edu/gems/faculty.shtml
Gu CC, Rao DC, Stormo G, Hicks C, Province MA. Role of gene expression microarray analysis in finding complex disease genes. Genet Epidemiol. 2002 Jun; 23(1): 37-56.
...you must be getting old! lol
Then Mr SBJ ...
OT: Step Hen, QILV?
Synergy in practice
http://www.primepharmaceutical.com/overview.htm
Prime has ensured a long-term source of scientific technology through a strategic alliance with Utek Corporation, a Florida based, technology transfer company. Utek (UTK) is a public company listed on the American Stock Exchange, which has entered into an agreement whereby they will source and introduce appropriate technology acquisition opportunities for Prime. Utek, with its advisory board of 18 scientists, of which 3 are Nobel prizewinners, has recognized the huge potential of Prime Pharmaceutical Corporation and made a substantial equity investment in the company.
http://philadelphia.bizjournals.com/tampabay/stories/2003/05/19/focus2.html
"Our preference is to help local companies," said Dr. Douglas Weiland, managing director and principal at Athena Capital Partners Inc. in Tampa.
Athena also works to relocate life sciences businesses to the Bay area. The firm focuses on investments between $1 million and $20 million, about 70 percent to 80 percent of which are in the life sciences industry.
Weiland, a former orthopedic surgeon, works with local companies such as DNAPrint genomics Inc. in Sarasota and Apollo Pharmaceuticals LLC in Tampa. He also is working on bringing CBD Technologies Inc., an Israeli company, to the Bay area.
http://www.primepharmaceutical.com/26Aug2003.htm
August 26, 2003
Press Release
Prime Pharmaceutical Corporation
TORONTO – Prime Pharmaceutical Corporation (Prime) is pleased to announce the receipt of all upfront fees and confirm the final closing of a Licensing Agreement with Apollo Pharmaceutical LLC (Apollo), pursuant to the Private Placement/Licensing Agreement with Athena Capital Partners Inc. (Athena), dated May 6th, 2003 as set forth in a prior news release.
License Agreement
Prime has agreed to license to a US joint venture company organized by Athena Capitals Partners Inc., Apollo Pharmaceuticals LLC., for an upfront fee and ongoing royalties, the exclusive rights to market and sell all of the current and future dermatology products of Prime worldwide except for Canada. These license agreements for various territories require performance standards as well as ongoing royalties. Prime has agreed to manage Apollo Pharmaceuticals, subject to the terms and conditions of a Management Contract. Upon the successful closing of a minimum placement $835,000 USD, Prime shall obtain a 20% equity ownership of Apollo Pharmaceuticals, in exchange for 970,000 Series A 5% preferred shares as per the offering. Prime will be guaranteed that no dilution will occur for a period of 24 months from the date the shares of Apollo Pharmaceuticals are issued to Prime. Prime shall also have the right of first refusal to the Canadian license to any products that Apollo Pharmaceuticals may develop or acquire outside the scope of the license agreements noted above.
http://www.sunbiz.org/scripts/corevt.exe?a1=DETNAM&n1=L03000016462&n2=FLAL
WCW ENTERPRISES, LLC
NAME CHANGE AMENDMENT 10/20/2003 OLD NAME WAS : APOLLO PHARMACEUTICALS, LLC
Registered Agent: WEISS, LISA R
http://www.athena-capital.com/
Athena Capital Partners, Inc. was formed in December of 2000 and received NASD approval in April of 2002. Our goal is to provide capital markets expertise for both emerging companies and alternative investment funds, including venture capital and hedge funds.
Principals
Lisa R. Weiss, CFA - Managing Director and Founder
Ms. Weiss has over 25 years of institutional investment experience as both a portfolio manager and sell-side analyst.
(Apart from DNAPrint Genomics, Athena "Clients" include Apollo Pharmaceuticals and Prime Pharmaceutical Corporation.)
http://biz.yahoo.com/bw/031120/205377_1.html
UTEK Corporation Appoints Hector Gomez, M.D., Ph.D., to Scientific Advisory Council
Thursday November 20, 10:29 am ET
PLANT CITY, Fla.--(BUSINESS WIRE)--Nov. 20, 2003--UTEK Corporation (AMEX:UTK - News) announced today that Hector J. Gomez, M.D., Ph.D., has joined UTEK's Scientific Advisory Council. Previously, Dr. Gomez served as a Senior Director of clinical research at Merck/MSDRL, Executive Director of Clinical Research at CIBA-GEIGY Corporation, VP of Medical Affairs at Vertex Pharmaceuticals and President and CEO of Transcend Therapeutics. Dr. Gomez is currently a Member of the Board of Directors of PRB Pharmaceuticals and Apollo Pharmaceuticals and is the Chairman of the Board of Directors of DNAprint Genomics.
Another possible connection
Grant Number: 5K07CA091849-03
PI Name: BARNHOLTZ-SLOAN, JILL S.
PI Email: jbsloan@med.wayne.edu
PI Title: ASSISTANT PROFESSOR
Project Title: Analysis of Ethnic Admixture in Lung Cancer
Abstract: DESCRIPTION (provided by applicant): This proposal describes a five-year plan developed for a Cancer Prevention, Control, Behavioral and Population Sciences Career Development Award. It outlines a program that integrates education, teaching and research to develop my skills in statistical genetics, molecular biology, cancer biology, human genetics and genetic epidemiology. My research plan consists of two projects: (l) higher level genetic modeling of early onset lung cancer cases and controls with admixture versus ethnicity as a covariate and (2) application of an admixture, population substructure and disequilibria testing procedure to early onset lung cancer cases, population-based controls and nuclear families. Project l uses data from a funded study on early onset lung cancer of African-Americans and Caucasians. Nine candidate loci believed to be involved in lung cancer risk along with 35 population specific markers (PSAs) for Africans and Europeans combined, are being typed for each case and a matched population and familial control. An admixture algorithm will be written, programmed and tested on cases, controls and parents to estimate individual and population admixture, using the PSAs. Logistic regression models and decision tree models (classification and regression tree) will be compared when modeling the genotypes of the candidate loci and other collected environmental/descriptive variables, in order to assess the difference between using an ethnicity variable versus an individual admixture estimate variable. Project 2 will build on the already developed admixture estimation algorithm (Project l). I will develop a complete procedure that will estimate individual and population admixture and within population substructure and will test for induced linkage disequilibrium (LD) and Hardy-Weinberg disequilibrium (HWD), for all cases, controls and nuclear families. This procedure will be tested in a computer-based simulation, using the early onset lung cancer data as a model, in order to estimate the statistical power and test characteristics such as false-positive and false-negative rates. Linkage disequilibrium mapping will also be performed on the study data. Both of these projects will address epidemiological study design issues about ethnicity and using population-based versus familial based controls. From the studies proposed, a recommendation could be made on how to utilize individual admixture information in the choice of controls for epidemiological studies. These projects will give me experience in developing methodology in statistical genetics and genetic epidemiology, while also helping me to better understand etiology of disease.
Thesaurus Terms:
African American, caucasian American, lung neoplasm, neoplasm /cancer epidemiology
disease /disorder onset, gene environment interaction, gene interaction, genetic model, genetic susceptibility, model design /development, neoplasm /cancer genetics
clinical research, human subject
Institution: WAYNE STATE UNIVERSITY 656 W. KIRBY DETROIT, MI 48202
Fiscal Year: 2003
Department: INTERNAL MEDICINE
Project Start: 25-SEP-2001
Project End: 31-AUG-2006
ICD: NATIONAL CANCER INSTITUTE
IRG: NCI
http://www.parkwayalumni.org/class80.html
Jill Barnholtz-Sloan, North '89, received a Ph.D. in Biostatistics and Statistical Genetics from Univ. of Texas School of Public Health and MD Anderson Cancer Center in May 2000. She is currently an assistant professor of internal medicine and oncology at Wayne State Univ. School of Medicine and Karmanos Cancer Institute in Detroit.
Add in this:
Barnholtz-Sloan JS, Sloan AE, Schwartz AG. Racial differences in survival after diagnosis with primary malignant brain tumor. Cancer. 2003 Aug 1; 98(3): 603-9.
Barnholtz-Sloan JS, de Andrade M, Dyer TD, Chakraborty R. Admixture effects in the traditional linkage analysis of admixed families. Ethn Dis. 2002 Summer; 12(3): 411-9.
Barnholtz-Sloan JS, Tainsky MA, Abrams J, Severson RK, Qureshi F, Jacques SM, Levin N, Schwartz AG. Ethnic differences in survival among women with ovarian carcinoma. Cancer. 2002 Mar 15; 94(6): 1886-93.
Barnholtz-Sloan JS, de Andrade M, Chakraborty R. The impact of population admixture on traditional linkage analysis. Ethn Dis. 2001 Autumn; 11(3): 519-31.
Now it's getting interesting...
Coincidentally Mark Shriver has an association with Wayne and an interest in lung cancer.
BTW, the NIH project details are from the CRISP database:
http://crisp.cit.nih.gov/crisp/crisp_query.generate_screen
OT: Jim, I was a long time lurker on the XKEM board (amongst other boards). I follow the stock posts while doing DD and until it becomes apparent that is is not a good investment for whatever reason (including, and especially, being a scam) or that investment is warranted. XKEM is comfiortably in the former category. I would put say Cytrx in the latter...