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Mike, I agree. The appropriate contact at the company can be reached via:
genealogy_info@dnaprint.com
W2P, thank you for pointing that out. Dr Lancaster has also worked on ovarian cancer:
http://www.ocrf.org/research03.shtml
Jonathan M. Lancaster, M.D.
Senior Fellow, Division of Gyneclogic Oncology, Duke University Medical Center
"Defining Genetic Pathways that Underlie Ovarian Carcinogenesis Using Microarray Expression Analysis"
Ovarian cancer is the most lethal gynecologic malignancy, resulting in the death of more than 14,000 women in America every year. Like all cancers, ovarian cancer is a genetic disease, which develops because of alterations in the genes that normally function to control cell division and tissue growth. This gene disruption occurs as the ovarian lining repairs itself following ovulation during each menstrual cycle. Despite intensive research efforts to date, study of individual genes has failed to fully elucidate the precise mechanisms that lead to ovarian cancer development. This is likely because cancer results from disruption of thousands of different genes within discrete pathways and networks, rather than in a handful of single genes.
Recently, microarray technology has been developed enabling the simultaneous analysis of up to 30,000 genes in a single sample. We aim to apply this technology to identify the "genetic signatures" of disrupted gene pathways that lead to loss of normal cell growth control and ovarian cancer development. We will study ovarian cancers from women with high and low lifetime numbers of ovulatory (menstrual) cycle, as well as cells which carry known genetic alterations, in an effort to identify the "genetic signatures" of discrete gene networks that have been disrupted in the process of ovarian epithelial repair following ovulation. Characterization of these disrupted gene networks will reveal opportunities for the development of novel medications for treatment and prolongation of survival from ovarian cancer. I thank OCRF and The Liz Tilberis Scholars Program for providing me with this invaluable opportunity to pursue these important studies.
End of aricle
"Ovarian cancer is the most lethal gynecologic malignancy, resulting in the death of more than 14,000 women in America every year..."
Who knows how many fatalities might be avoided if classifiers were available to help with selection of appropriate chemotherapy regimes. Just 1% would be one person roughly every other day.
Grateful, Moffitt obviously know a bit more than we do...
Terry, all things are possible with a bit of accounting legerdermain, e.g. a pooled asset merger...
ifida, a lot of things were mentioned in the TWST article! If they are still going to become a drug company, and I have no reason to believe they do not plan to do so, then acquisition of an entity with a drug pipeline is the obvious way to do it. Like everything else with the company we have to wait and see what happens.
Dorsey, yes and as the PR was put out on March 29 the projects had been running for over three months at that point.
NikLinna, yes but as the company themselves say:
"The increase of approximately $115,300 of cost of sales is primarily due to the increase of revenues in 2004 compared to 2003. Because of the small sales volume and our dependence on the type of testing conducted in a particular period, these results are not indicative of the margins that we expect to attain if our long-term goals are achieved. Some differences could also arise from our refinement of our estimate and allocation of research and development costs."
We have to wait until sustained volumes over a couple of quarters are such that the true margins are reflected in the bottom line results.
Another interesting item from the 10Q
From the Moffitt agreement:
"The Projects shall be carried out from November 17, 2003 to November 17, 2006..."
That means that as of tomorrow the Moffitt projects (all four of them presumably) have been in progress for six months.
Doug, makes sense. There is also the timing issue to consider. They may well want to move prior to the availability of the USF facility.
patiencepays, dealt with this subject here:
http://www.investorshub.com/boards/read_msg.asp?message_id=1837734
It is not clear what the 20 categories are going to be, and is something that is eagerly awaited by several people.
I wondered about that as well. They obviously are going to move into USF so perhaps the text is historic (probably not), they will move into an interim location while the research park buildings are built (doesn't make sense), or perhaps they will have two buildings? In the latter scenario the USF site would perhaps be the R&D function. Maybe there is another explanation. Another mystery...
Stockboy, you might want to read all of the "capital expenditures" section of the 10Q. You will see that there is more than just the $3,900 mentioned (which was actually for laboratory equipment and not computer equipment). Here is the full text:
During 2004, we anticipate developing the required infrastructure to realize our 2004 operational growth plan, including acquiring or leasing property, equipment and other operating assets.
We are actively seeking to acquire or lease a new building that has 15,000 to 20,000 square feet with additional expansion potential. We estimate that lease costs will be between $15 and $25 per square foot. This does not include leasehold improvements or other associated costs such as utilities, taxes and maintenance. The initial build out of 7,000 square feet is estimated at approximately $780,000 which includes laboratory, office and warehouse space. Additional costs for equipment, furniture and fixtures are estimated at approximately $257,000. Timing of the incurrence of the expense will depend upon the length of time required to find the appropriate facility.
In addition, it is anticipated that new laboratory and computer equipment will be purchased during 2004. Computer purchases for programming, modeling and business use is estimated at approximately $100,000 and scientific and business programs and software at approximately $65,000. Capital expenditures for laboratory equipment are estimated at approximately $500,000 that includes a new robotic SNP machine at a value of approximately $250,000.
During the first quarter of 2004, in line with our capital expenditure plan, we purchased new laboratory equipment for approximately $3,900 and financed new computers for approximately $20,500. Capital expenditures are expected to continue throughout 2004 as our operational plans are realized and cash flow allows.
I liked this little piece in the Moffitt agreement:
"...the Parties acknowledge that Exhibit A may be amended from time to time to add additional studies to the Project."
Retro, didn't take too much time, and I had to look at it to reassure myself anyway lol! It is hard to keep track of the number and scope of agreements. Perhaps we will learn a bit more about the reason(s) for the termination of the PSRF agreement in due course.
Grateful, yes.
The PSRF and Mark Shriver agreements
From the 10K for 2002 filed on 15 April 2003:
http://www.sec.gov/Archives/edgar/data/1127354/000107087603000035/dnap10ksb2002.htm
"...in collaboration with The Pennsylvania State University, the Company is studying the genetic basis underlying natural skin shade variation."
The key source document is the 10Q filed on 14 August 2002, which contains the agreement with Penn State Research Foundation (PSRF) and the agreement with Mark Shriver (together with the amendment to the latter):
http://www.sec.gov/Archives/edgar/data/1127354/000107087602000071/0001070876-02-000071-index.htm
This document also summarizes the agreement with Mark Shriver:
"During June 2002, we entered into an agreement with an individual, who is also a member of our Scientific Advisory Board, to collaborate with us to develop a kit product that could be used to infer Ancestry Admixture Ratios in individual human beings."
So there is ostensibly a clear difference in the scope of the agreements with PSRF and Mark Shriver. Let's turn to the agreements themselves.
Here are the key points from the Mark Shriver ("CONSULTANT") consulting agreement was signed on June 12 2002:
http://www.sec.gov/Archives/edgar/data/1127354/000107087602000071/shriverconsultagmt.htm
"DNAPRINT is the patent owner of certain SNP markers and methods, and desires to collaborate with CONSULTANT to develop a kit product that could be used to infer Ancestry Admixture Ratios in individual human beings."
"CONSULTANT is the inventor of certain compositions and methods useful for determining Ancestry Admixture Ratios in individual human beings. CONSULTANT is also the owner of certain DNA samples collected from individuals of various ancestries, and of certain rights therein. CONSULTANT wishes to commercialize his compositions and methods."
The parties agreed to develop a diagnostic kit for the inference of Ancestry Admixture Ratios. The goals of the project were to create a panel of AIMs that can infer admixture with respect to a list of target ancestral groups, to evaluate the panel for fitness as a commercial product, to obtain a license from a 3rd party manufacturer to allow DNAP to commercialize the product, and to commercialize and provide support for the product.
It was agreed that DNAP could modify Shriver’s software with the intent of commercializing them.
The term of the agreement was 2 years, after which the agreement would renew for consecutive two year terms unless terminated.
"CONSULTANT agrees and understands that any and all data, software improvements, methods, compositions and commercial rights are the property of DNAPRINT, and that CONSULTANT acquires no rights therein and that it can use DNAPRINT data, including any Documentation, only for legitimate scientific research as previously approved by DNAPRINT, and for no other purpose whatsoever."
"Genotyping data is the property of DNAPRINT, and CONSULTANT may not sell, loan, disclose or present DNAPRINT data in any manner whatsoever, unless requested by or agreed to by DNAPRINT."
"CONSULTANT warrants to DNAPRINT that he is the inventor of record for the compositions and methods contributed by CONSULTANT to the project."
In the amendment to this agreement the parties executed a confidentiality agreement, DNAP agreed to indemnify and hold Consultant harmless for any damages or losses arising as a result of modifications it made to his software, there was a formal definition of the term "net sales", and the parties agreed that the terms of the original contract would apply to any future projects which might be developed by the parties.
So much for the Mark Shriver agreement. Here are the main points of the PSRF agreement:
http://www.sec.gov/Archives/edgar/data/1127354/000107087602000071/psulicenseagmt.htm
Mark Shriver, a PSU employee, in the course of basic research, has collected certain human DNA samples and certain subjectively measured and self-reported biogeographical ancestry and ethnicity data, eye color, hair color & skin color pigmentation data, and sun exposure history information relating to said samples.
PSRF is the owner of said SAMPLES & TECHNICAL INFORMATION and has the right to grant licenses;
WHEREAS, LICENSEE wishes to collaborate with the UNIVERSITY and to perform further internal research and development on the SAMPLES & TECHNICAL INFORMATION, as part of its effort to develop commercial products in the FIELD that will be related to, rely on, using, incorporating and/or referencing the SAMPLES & TECHNICAL INFORMATION;
WHEREAS, LICENSEE wishes to obtain and PSRF is willing to grant a license to said SAMPLES & TECHNICAL INFORMATION
"FIELD" shall mean the research, development and commercialization of genomic informational kits for purposes of identifying eye colors, hair colors, skin pigmentation, skin response to burn, for uses in forensics and prenatal diagnostic.
"SAMPLES & TECHNICAL INFORMATION" shall mean certain human DNA samples and certain subjectively measured and self-reported biogeographical ancestry and ethnicity data, eye color, hair color & skin color pigmentation data, and sun exposure history information relating to said samples.
PSRF hereby grants to LICENSEE an exclusive right and license in the TERRITORY for the FIELD, without right to sublicense, to SAMPLES & TECHNICAL INFORMATION and PATENTS RIGHTS and to the extent not prohibited by other patents, to collaborate with the UNIVERSITY and to research, develop, make, have made, use, lease, and sell LICENSED PRODUCTs for the term set forth herein, unless this License Agreement shall be earlier terminated according to the terms and conditions contained herein.
PSRF reserves the rights for itself and the UNIVERSITY to use SAMPLES & TECHNICAL INFORMATION and to practice under the PATENT RIGHTS for their own research and educational purposes, including, without limitation, any new information, methods and compositions developed, whether patentable or not, as a result of the use of SAMPLES & TECHNICAL INFORMATION by the collaborative efforts and LICENSEE's internal research efforts contemplated under this Agreement.
In partial consideration of the rights granted by this License Agreement, LICENSEE shall pay to PSRF a non-refundable, License Issue Fee of ten thousand one hundred and fifty dollars ($10,150.00 USD) upon execution of this License Agreement. Said License Issue Fee shall be paid upon the Effective Date of this License Agreement.
In addition to the foregoing License Issue Fee, LICENSEE shall pay PSRF a running royalty of twenty-five percent (25%) of NET SALES of LICENSED PRODUCTS within the field of skin pigmentation.
(There was also an agreement to give PSRF a minimum amount, which was based on a sliding scale that rose to a maximum of $40,000 per annum.)
LICENSEE shall pay PSRF Additional Running Royalties of three and a half percent (3.5%) of NET SALES as defined herein for LICENSED PRODUCTS sold within the field of eye and hair pigmentation.
PSRF and LICENSEE shall be joint owners and joint named assignees of all PATENT RIGHTS filed, prosecuted and maintained as a result of LICENSEE's collaboration with the UNIVERSITY and LICENSEE's research and development work relating to, relying on, using, incorporating and referencing SAMPLES & TECHNICAL INFORMATION.
There were also clauses that stated that manufacturing was to be mainly undertaken in the USA, and limits on export of data and commodities related to PSRF.
"LICENSEE shall have the right to terminate this Agreement at any time on six (6) months' notice to PSRF, and upon payment of all amounts due PSRF through the effective date of the termination."
"Upon termination of this License Agreement for any reason, nothing herein shall be construed to release either party from any obligation that matured prior to the effective date of such termination; and Articles I, VIII, IX, X, XV and paragraphs 14.5 and 14.6 shall survive any such termination.
LICENSEE may, however, after the effective date of such termination, sell all LICENSED PRODUCTs, and complete LICENSED PRODUCTs in the process of manufacture at the time of such termination and sell the same, provided that LICENSEE submit the reports required by Article V hereof."
The things that survive termination of the agreement are: contract definitions, indemnifications, export controls, non-use of PSU/PSRF names, and normal miscellaneous provisions. Article V relates to reports and records that allow PSRF to confirm it's royalty payments.
So where does that leave us?
There seems to be a discrepancy between the two agreements about who the owner of samples is (and the rights therein), unless different samples are referred to - but I do not think this is the case.
It seems to me that DNAP has clear rights in relation to the AIMs as per the agreement with Mark Shriver, which is still in place.
Even though the PSRF samples include biogeographical ancestry and ethnicity data, the agreement is very clear in the scope of products: kits for identifying eye colors, hair colors, skin pigmentation, skin response to burn, for uses in forensics and prenatal diagnostics.
PSRF/PSU do not seem to be assignees of the pigmentation patent (DNAP are sole assignees), which was originally filed on 25 May 2001. I am not sure whether or not PSRF/PSU should be assignees. I would assume that they should be?
It seems to me that PSRF (and PSU) can use any new information, methods, and compositions arising from collaboration or DNAP's internal research efforts.
It also seems that DNAP can complete any products in development at the time of termination and sell the same. There are a few items that survive the contract that DNP need to be aware of and (confusingly) we still seem to have to submit royalty reports even though payments do not survive termination of the contract.
Unless I have missed something there is no big deal here. The question remains though, why did DNAP give notice to terminate the contract?
Jim, the personal details that are included on a profile are typically those of the alias that an individual has chosen to use, although a few people do use their real name. Hence the email etc are not personal details.
Grateful, it certainly does look as if DNAP did do the cancelling. No, I do not know what this is about, and am as intrigued as everybody else.
frog, I am genuinely pleased that you are able to take mild enjoyment from the turn of events. Of course (in the real world), you can't always get what you want...
Frog, if you have an issue with a particular post that you feel is an issue vis-a-vis violation of privacy I am more than happy to review it and (if necessary) delete it. Now if you are referring to the occasion when I alluded to your christian name and you posted my surname...
For the avoidance of doubt, the following are reasons why posts may be removed from IHUB:
Duplicate – an accidental duplicate post by a member
Personal Attack – when someone attacks a person, with name calling, or relating to the messenger and not the message.
Spam – a message that is being posted promoting other sites, stock-related or not, that has no use in the discussion (for example, if your board is about Ford Motors, a link promoting amazing returns running a home-based business is worthless to the discussion).
Vulgarity – cursing of any kind unacceptable on your board
Violation of Privacy – posting of any personal identifiable information (email, real name, phone, address, etc)
Threat – someone threatening another member in some fashion
Vulgarity.
If anybody would like to do a little DD these are the current projects with Moffitt:
STUDY PROPOSAL ON COLON CANCER
PRINCIPAL INVESTIGATOR AT MOFFITT: TIM YEATMAN
STUDY PROPOSAL ON MULTIPLE MYELOMA
PRINCIPAL INVESTIGATOR AT MOFFITT: DANIEL SULLIVAN
STUDY PROPOSAL ON CYCLOPHOSPHAMIDE
PRINCIPAL INVESTIGATOR AT MOFFITT: RICHARD M. LUSH
STUDY PROPOSAL ON TAXANES
PRINCIPAL INVESTIGATOR AT MOFFITT: JONATHAN M. LANCASTER, MD
And we have terminated the license agreement with PSU...
DNAPrint genomics, Inc. and The Penn State Research Foundation(PSRF) entered into a License Agreement effective on July 25, 2002. You notified us in an email dated February 4, 2004 that you would like to terminate the License Agreement as soon as possible.
Paragraph 14.1 of the License Agreement states that "LICENSEE shall have the right to terminate this Agreement at any time on six (6) months' notice to PSRF, and upon payment of all amounts due PSRF through the effective date of the termination." However, PSRF and DNAPrint genomics, Inc. agree that the License Agreement will terminate effective upon the date of last signature herein and upon the return of the samples described in Appendix B (attached) to Professor Mark Shriver.
The Pennsylvania State University and the Penn State Research Foundation look forward to future interaction with DNAPrint genomics, Inc.
Interesting...
Has anybody noticed the 10Q is out...
http://www.sec.gov/Archives/edgar/data/1127354/000114420404006612/0001144204-04-006612-index.htm
And it includes the Moffitt agreement...
New-Medical.Net picked up the bald eagle PR:
http://www.news-medical.net/view_article.asp?id=1510
More evidence about the utility of AIMs:
Seldin MF, Morii T, Collins-Schramm HE, Chima B, Kittles R, Criswell LA, Li H. Putative Ancestral Origins of Chromosomal Segments in Individual African Americans: Implications for Admixture Mapping. Genome Res. 2004 May 12
Rowe Program in Human Genetics, Departments of Biological Chemistry and Medicine, University of California at Davis, Davis, California 95616-8669, USA.
Theoretically, markers that distinguish European from West African ancestry can be used to examine the origin of chromosomal segments in individual African Americans. In this study, putative ancestral origin was examined by using haplotypes estimated from genotyping 268 African Americans for 29 ancestry informative markers spaced over a 60-cM segment of chromosome 5. Analyses using a Bayesian algorithm (STRUCTURE) provided evidence that blocks of individual chromosomes derive from one or the other parental population. In addition, modeling studies were performed by using hidden real marker data to simulate patient and control populations under different genotypic risk ratios. Ancestry analysis showed significant results for a genotypic risk ratio of 2.5 in the African American population for modeled susceptibility genes derived from either putative parental population. These studies suggest that admixture mapping in the African American population can provide a powerful approach to defining genetic factors for some disease phenotypes.
The reference to out-sourcing of contracts probably refers to something else. As far as genotyping is concerned, from the 10K:
"We will accomplish our analysis of individual SNPS, as previously defined under "Our Research and Development Approach", through ultra-high throughput (UHT) machines. Genotyping consists of two phases: screening, wherein a relatively small number of cases and controls are genotyped at a large number of SNPs, and validation, wherein a considerably larger number of cases and controls are genotyped at a small number of SNPs. The Orchid UHT machine we purchased and installed at DNAprint Genomics, for example, will accomplish validation genotyping."
"Our Plan of Operations over the next twelve months will focus on common cancers such as lung, prostate, colon, breast and pancreas. We will conduct screening genotyping, followed by validation genotyping."
In the plan of operations section they also provide a breakdown of estimated expenses of $1,403,907 over the
next year (to be met from the ADOT and Pierpoint funding and from any revenues). This includes the amount of $800,000 for genotyping. Note that the corresponding estimate for genotyping in the last 10Q was $2,000,000.
So, we know that genotyping will take place this year. We do not know what the percentage split is between "screening" and "validation genotyping" so therefore cannot estimate what percentage of the total genotyping might be contracted to DNAP. We also do not know for certain that DNAP will be the party selected for this work, or if the work might be shared between multiple people. We can reasonably suspect though that DNAP will get at least some of this work. Thus all that we can say is that DNAP will possibly get an unknown share of $800,000 worth of genotyping work this year.
mahastock, Sean Connery once described the stock market as a fixed horse race. I would not disagree with him.
What do you think?
Yes, and we should show him some respect. He is a genuine guy.
mahastock, the terms of the La Jolla financing are a matter of public record. I agree with the poster that there is a difference between "death spiral financing per se" and what he refers to as "death-spiral-type financing."
Articles about Genomed hires
Two articles pick up on the press release, the St Louis Journal:
http://stlouis.bizjournals.com/stlouis/stories/2004/05/10/daily16.html?jst=b_ln_hl
GenoMed names CFO, other executives
GenoMed Inc. has hired three new executives to its management team as it prepares for growth, the company said Tuesday.
Robyn Owens was named chief financial officer, Ellen Jones was named vice president for marketing and Andy O'Guin was named chief technical officer. O'Guin was most recently with a St. Louis biotechnology company. He will oversee research outsourced to GenoMed's partners, the company said.
St. Louis-based GenoMed Inc. (Pink Sheets: GMED) is a medical genomics company working to find genes that cause disease.
And News-Medical.net:
http://www.news-medical.net/view_article.asp?id=1429
GenoMed adds to management team
Posted By: News-Medical in Miscellaneous News
Published: Tuesday, 11-May-2004
GenoMed, Inc., a Next Generation Disease Management™ company that uses its expertise in genes to improve patient outcomes, said today that it has hired three additional full-time employees: a Chief Financial Officer, a Vice President for Marketing, and a Chief Technical Officer.
Ms. Robyn L. Owens was hired as Chief Financial Officer. She has twenty-two years' experience in the health care industry, half on the payor's side and half on the providers' side. Her experience includes contracts, claims, customer service, and bringing private physicians into managed care. Her expertise is in finance, in particular hospital and physician contracting. She is a member of Medical Group Managers Association, Group Health Association of America, and National Association of Female Executives.
Ms. Ellen Jones was hired as Vice President for Marketing. She has experience marketing Internet solutions to banks, tax and regulatory information to accountants and tax lawyers, as well as temporary staffing solutions. She has extensive experience translating complex technical information into everyday language.
Mr. Andy O'Guin was hired as Chief Technical Officer. He comes from a private St. Louis biotechnology company engaged in anti-viral drug discovery. He has experience in genotyping, assay development, and drug discovery. He will oversee research outsourced to GenoMed's partners.
Said Dr. David Moskowitz, GenoMed's CEO and Chairman, "After a careful search, GenoMed now has a wonderful management team, one that is nimble, experienced, and personable. We are poised for growth."
Miss Scarlet, no the name's Faux, David Faux!
I did wonder about contacting the courthouse and seeing if the information could somehow be remotely released without going via the internet, but I suspect I know what the answer would be...
Cgr, thanks. Hopefully it is quality rather than quantity here, and hopefully the 10Q will be out at the end of the week and we will have something concrete to talk about!
Who's watching who?
http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2004-05/1084036457
It may seem odd that I am going to leap to the defense of DNAPrint on the issue of releasing allele information and their algorithm(s).
Correct me if I am wrong Charles, but what you and I and others have requested is that they tell us which version of the algorithm they are using as part of the results they send us - otherwise we will be comparing apples to oranges. I suspect that since they began with 2.0 there have been in the order of 10 or more algorithms used as they continued to try and fine tune the test. This tinkering plays havoc with what people such as myself are doing - comparing family members from different lines down from a known Native American ancestor to assess percentage and compare with the genealogy as a cross validation.
DNAPrint either has, or is in the process of, patenting the test. The information they use is proprietary and it would be counter productive on their part to release the data that people are requesting. Don't forget that they are a commercial, for profit (although they have not yet shown one), operation - not a scientific endeavor. They are attempting to tap the forensic and recreational market - their prime focus is not in publishing peer reviewed articles in scientific journals.
As I understand it things have changed dramatically since the days when Tony "joined" the List and allowed us to hammer him with questions. I don't even know who is steering the ship at this point. There was a massive shake up when the venture capitalists from San Diego bought in and bailed out the operation after the Louisiana serial killer success story. I spoke to one of these investors, who resides in the Orient, who had somehow found out that I was interested in bringing a competitive product to the marketplace. I think we might be very surprised to learn who is lurking on the List and monitoring posts like this one.
Lets just say that DNAPrint, "Witness" version, did not make a big splash at the recent peace officer's convention here in LA. I am worried that the health of the company may be in question. Personally I would like to see them stay in business since they may be on to something. Unfortunately to date I don't see any reason to put much faith in any racial - geographic percentage under 25%. That being said, even if perchance I do succeed in bringing an alternative to market, I would like to see another product there that will help to fuel the engine of competition.
However, for the moment, lets face it, whether the information comes from 2.0, 2.5 or whatever, there is no way to know whether your minority results are meaningful or misleading. We will never know this until they increase their sample size and the representativeness of the sample - this is what we all hope will be accomplished in Version 3.0. Until then we can argue till the cows come home with respect to results from the other versions - but it will be a lot of wasted energy.
It may seem unusual, considering the (skeptical) source, but I may upgrade myself and other family members to 2.5 to see how the results differ with the two versions of the product (not ascribing any meaning to minority results unless there is genealogical support). It is in our best interest that the company remain afloat so that ultimately our wish for a truly reliable and valid test of biogeographical ancestry will eventually be fulfilled.
David.
End of post
OK, I was the "investor from the Orient" who spoke to the good Doctor. I found out that he was thinking of bringing a competitive product to the market because he himself posted this on RootsWeb. My original mail to Dr Faux was in fact to advise him of the patent situation. Incidentally, Tony Frudakis has made reference to this initiative on RootsWeb. I don't agree with all of David's assertions, but you can detect that even one of our "critics" wants the company to succeed and for version 3.0 of the product to be more (ahem) "reliable and valid". We all await version 3.0 with much interest. Until then here's watching you David, watching us, watching you...
You're going away again? Good! The last time you were away the share price spiked as I recall! lol
W2P, I somehow though the signficance of the rather obvious coincidences would not be lost on you! lol
Ranajit Chakraborty and others have long worked on STRs and their variation within populations (note that Shriver was working on this in the 1990s). Here are some relevant papers:
Silva DA, Crouse CA, Chakraborty R, Goes AC, Carvalho EF. Statistical analyses of 14 short tandem repeat loci in Brazilian populations from Rio de Janeiro and Mato Grosso do Sul states for forensic and identity testing purposes. Forensic Sci Int. 2004 Jan 28;139(2-3):173-6.
Budowle B, Chakraborty R. Population variation at the CODIS core short tandem repeat loci in Europeans. Leg Med (Tokyo). 2001 Mar;3(1):29-33.
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.
Budowle B, Chidambaram A, Strickland L, Beheim CW, Taft GM, Chakraborty R. Population studies on three Native Alaska population groups using STR loci. Forensic Sci Int. 2002 Sep 10;129(1):51-7.
Cerda-Flores RM, Budowle B, Jin L, Barton SA, Deka R, Chakraborty R. Maximum likelihood estimates of admixture in Northeastern Mexico using 13 short tandem repeat loci. Am J Human Biol. 2002 Jul-Aug;14(4):429-39.
Ramana GV, Su B, Jin L, Singh L, Wang N, Underhill P, Chakraborty R. Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India. Eur J Hum Genet. 2001 Sep;9(9):695-700.
Budowle B, Shea B, Niezgoda S, Chakraborty R. CODIS STR loci data from 41 sample populations. J Forensic Sci. 2001 May;46(3):453-89.
Chakraborty R, Stivers DN, Su B, Zhong Y, Budowle B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis. 1999 Jun;20(8):1682-96.
Desmarais D, Zhong Y, Chakraborty R, Perreault C, Busque L. Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA). J Forensic Sci. 1998 Sep;43(5):1046-9.
Busque L, Desmarais D, Provost S, Schumm JW, Zhong Y, Chakraborty R. Analysis of allele distribution for six short tandem repeat loci in the French Canadian population of Quebec. J Forensic Sci. 1997 Nov;42(6):1147-53.
Chakraborty R, Stivers DN, Zhong Y. Estimation of mutation rates from parentage exclusion data: applications to STR and VNTR loci. Mutat Res. 1996 Jul 5;354(1):41-8.
Chakraborty R, Stivers DN. Paternity exclusion by DNA markers: effects of paternal mutations. J Forensic Sci. 1996 Jul;41(4):671-7.
Budowle B, Monson KL, Chakraborty R. Estimating minimum allele frequencies for DNA profile frequency estimates for PCR-based loci. Int J Legal Med. 1996;108(4):173-6.
Shriver MD, Jin L, Boerwinkle E, Deka R, Ferrell RE, Chakraborty R. A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol Biol Evol. 1995 Sep;12(5):914-20.
Jin L, Chakraborty R. Population structure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics. Heredity. 1995 Mar;74 ( Pt 3):274-85.
Hammond HA, Jin L, Zhong Y, Caskey CT, Chakraborty R. Evaluation of 13 short tandem repeat loci for use in personal identification applications. Am J Hum Genet. 1994 Jul;55(1):175-89.
Shriver MD, Jin L, Chakraborty R, Boerwinkle E. VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics. 1993 Jul;134(3):983-93.
Edwards A, Hammond HA, Jin L, Caskey CT, Chakraborty R. Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics. 1992 Feb;12(2):241-53.
Here is the abstract abstract of one of the above papers which is particularly interesting:
Global genetic variation at nine short tandem repeat loci and implications on forensic genetics.
Sun G, McGarvey ST, Bayoumi R, Mulligan CJ, Barrantes R, Raskin S, Zhong Y, Akey J, Chakraborty R, Deka R.
Center for Genome Information, Department of Environmental Health, University of Cincinnati, Ohio 45267, USA.
We have studied genetic variation at nine autosomal short tandem repeat loci in 20 globally distributed human populations defined by geographic and ethnic origins, viz., African, Caucasian, Asian, Native American and Oceanic. The purpose of this study is to evaluate the utility and applicability of these nine loci in forensic analysis in worldwide populations. The levels of genetic variation measured by number of alleles, allele size variance and heterozygosity are high in all populations irrespective of their effective sizes. Single- as well as multi-locus genotype frequencies are in conformity with the assumptions of Hardy-Weinberg equilibrium. Further, alleles across the entire set of nine loci are mutually independent in all populations. Gene diversity analysis shows that pooling of population data by major geographic groupings does not introduce substructure effects beyond the levels recommended by the National Research Council, validating the establishment of population databases based on major geographic and ethnic groupings. A network tree based on genetic distances further supports this assertion, in which populations of common ancestry cluster together. With respect to the power of discrimination and exclusion probabilities, even the relatively reduced levels of genetic variation at these nine STR loci in smaller and isolated populations provide an exclusionary power over 99%. However, in paternity testing with unknown genotype of the mother, the power of exclusion could fall below 80% in some isolated populations, and in such cases use of additional loci supplementing the battery of the nine loci is recommended.
I have for some time wondered whether a combined STR/SNP approach might well be able to shed more light on population affinity, and whether this has any possible bearing on the development of ABD/DNAWitness 3.0.
Terry, what the end of this paragraph is alluding to is the fact that during the 1950s and 1960s a lot of people emigrated from the Caribbean to London. A lot of these folks ended up living in South London. Hence the supposed connection.
As we can increasingly see, this is not as cut and dried as the first press articles suggested...