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OT Dick, I feel the same way about the bits of the US I have not been to. I am sure you could spend a lifetime exploring just Montana and not see all of it!
W2P actually brings up a good point, which has also been mentioned in private emails by a few people. This is namely the non-disclosure agreement, which those involved in the PP have to sign (myself included, despite not perhaps having the degree of sofistykayshun that is ostensibly required). I know of at least one shareholder who does not post anything at all on any board to ensure that he abides by the terms of this agreement. I will only post things that are in the public domain (such as links to newspaper articles) while the agreement is in force. This does somewhat limit responses to some of the FUD that is posted on (especially) RB and (increasingly) IHUB; but so be it.
OT Dick, it is called Sharp Peak, and is in the Sai Kung Country Park in Hong Kong. It's Chinese name, interestingly enough, is Nam She Tsim - which means 'snake tongue peak'.
frogdreaming, I was going to respond to some of your (many) posts, but then decided that I would go here instead today:
This is the view from the top:
David, I agree. eom
Sarasota Herald Tribune article
http://www.heraldtribune.com/apps/pbcs.dll/article?AID=/20031204/NEWS/312040738/1200
DNAPrint Genomics gets $8M financing deal
BY MARGARET ANN MIILLE
SARASOTA -- DNAPrint Genomics Inc. plans to expand its operations with up to $8 million it will get from a California investment group over the next two years.
The Sarasota research and development company announced on Wednesday that it had signed a financing agreement with La Jolla Cove Investors Inc. of La Jolla, Calif.
The group will pay $400,000 a month for 20 months for DNAPrint common stock. DNAPrint will price the shares at an undisclosed discount based on the then-current trading price.
Funding will begin after the shares to be issued to La Jolla Cove Investors are registered by the Securities and Exchange Commission. Richard Gabriel, DNAPrint's chief executive, said the SEC registration process usually takes four to six months.
"This is definitely a big step up," said Tony Frudakis, DNAPrint's chief science officer. "We will invest it in growing the company. The goal isn't to use this money to become profitable. It's to grow us so that we can become wildly profitable."
The company's sole product is a genetics test that analyzes bodily fluids to determine to what extent a person is of Native American, East Asian, Indo-European and sub-Saharan African heritage. It's marketed under the name of ANCESTRYbyDNA2.0 to genealogy buffs and as DNAWitness to forensics experts.
The product generated $565,084 in revenues during the first nine months ending Sept. 30, compared with $132,201 during the same 2002 period.
For the first three quarters of this year, DNAPrint had a $5.47 million loss, compared with a $2.33 million loss during the same 2002 period.
Frudakis said DNAPrint will use the new capital to hire more workers, especially scientists who will continue the company's research in personalized medicine. DNAPrint will also seek a site to establish a second laboratory.
DNAPrint and La Jolla Cove Investors were brought together by Athena Capital Partners Inc., a private merchant bank in Tampa.
As part of the agreement, La Jolla Cove Investors will also provide $500,000 in cash. DNAPrint has received half that amount; the remainder will be paid after the SEC registration.
DNAPrint's shares, which trade over the counter, were selling for 5.1 cents at the close of regular trading Wednesday, up about 16 percent.
Bradenton Herald article
http://www.bradenton.com/mld/bradenton/business/7408452.htm
DNAprint genomics secures financing
DNAPrint genomics Inc. has secured a commitment for up to $8 million in financing over the next two years from La Jolla Cove Investors Inc. DNAPrint says the financing will enable it to hire more people and expand its clinical pharmacogenomics program. Information: www.dnaprint.com.
Gatorvestor, it was a post on RootsWeb from Tony, not an email from him to me!
Miss Scarlet, it is a reference to this post:
http://www.investorshub.com/boards/read_msg.asp?message_id=1855724
ifida, And, the $,64,000,000 name in that piece is...........
GlaxoSmithKline
Here is an interesting speech by Mark McClellan where he talks about the future role of information technology in relation to the FDA:
http://www.fda.gov/oc/speeches/2003/urbaninstitute1112.html
Nik, just when you think you are getting a handle on this whole area something else pops up that means you have to do a whole lot more reading! lol
I hope your answer is more acceptable than mine lol
IOM, yes Matt is still there!
Chris, the DNAP/Shriver/PSU relationship is a little unusual. The following is taken from the agreement between Mark (CONSULTANT) and DNAP:
http://www.sec.gov/Archives/edgar/data/1127354/000107087602000071/0001070876-02-000071.txt
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.
Note that there is no mention of PSU at all in the agreements, despite the wording of the original PR about the relationship:
http://www.dnaprint.com/pr_7_10.htm
Both groups will fund the research and DNAPrint will pay PSU a minority share of revenues derived from products that result from the collaboration.
I have often wondered about the "boundaries" here myself!
Walter, the simple answer is that we do not know at the moment. We can reasonably suspect that AIMs are going to be key and we know that we have a patent application related to them. We know about existing relationships with three universities, and might infer that there could be others - at least on the genotyping front - from what the company has said publicly. Universites will undertake basic research irrespective of how this might result in products downstream, and however these are brought to market. Time will tell...
Nik, agree that the important thing is that all possibilities are under consideration. I am always suspicious about concepts like "junk DNA" - underlying mechanisms usually tend to be simple, and such a degree of non-functionality or redundancy seems to be "wrong". BTW, here are some examples of "active" things (transposons or mobile DNA elements) that hint at other possible roles for non-coding DNA:
http://www.nsf.gov/od/lpa/news/03/pr0303.htm
http://www.uphs.upenn.edu/news/News_Releases/june97/dna.html
http://dragon.zoo.utoronto.ca/~J02T0301A/Mobile.html
There are also some interesting papers here:
http://instruct.uwo.ca/biology/281b/Tomppt/Notes/
for instance:
http://instruct.uwo.ca/biology/281b/Tomppt/Notes/Class9.pdf
The Seventy-Third Annual Meeting of the American Association of Physical Anthropologists (to be held in April 2004) has three presentations/posters by Mark Shriver.
http://www.physanth.org/annmeet/aapa2004/ajpa2004.pdf
Pigmentation variation in Island Melanesia and associated candidate gene variation. H. Norton1, J. Friedlaender2, D.A. Merriwether3, G. Koki4, C. Mgone4, M. Shriver1.
1Department of Anthropology, Penn State University, 2Department of Anthropology, Temple University, 3Department of Anthropology, Binghamton University, 4Institute of Medical Research, Papua New Guinea.
Pigmentation of the skin and hair is one of the most variable phenotypic traits observed in human populations. This variation is most often explained via natural selection acting on melanin content of the skin at different latitudes. This paper describes pigmentation variation of the skin and hair of 1135 Papuan and Austronesian speaking individuals living in the Bismarck Archipelago, Bougainville, and New Guinea. These pigmentation measurements were examined for sex-, linguistic-, and geographic-based differences. Skin pigmentation in Island Melanesia is extremely variable; significant differences were found between males and females; between the major island populations; and between language groups. Regional variation in skin pigmentation is also being studied at the genetic level, using 3-5 SNPs from the pigmentation candidate genes MC1R , TYR, and TYRP1 typed in representative samples from the major island and language groups. An initial study using individuals from West New Britain and New Ireland suggests an association between the MC1R variant Thr314Thr and decreased skin pigmentation in these two groups. Current investigations are pursuing whether this relationship and others are due to a true association between the MC1R SNP and skin pigmentation, or if they are instead due to an artifact of population differences between these two groups.
Charting genomic variability for clues on population history and genetic adaptation.
M.D. Shriver. Department of Anthropology, Penn State University.
The completion of the human genome sequence and recent technological advances have provided the opportunity to perform genomic-level studies of human variation. There is substantial potential for such "population genomic" approaches to assist efforts to uncover the historical and demographic histories of human populations. Additionally, these genomewide datasets allow for investigations of variability among genomic regions. Although all genes in a population may have experienced the same demographic events, they have not been affected by these events in precisely the same way. Much of the variability among genomic regions is simply the result of genetic drift, but some is also the result of genetic adaptation, which will only affect the gene under selection and nearby regions. We (a consortium of over 20 investigators) have performed one such study using a new DNA typing assay developed by Affymetrix, Inc (Santa Clara, CA). 203 individuals from a selection of 12 geographically diverse populations (including the Nasioi from Bougainville) were assayed using this new method, which facilitates typing 11,555 SNPs after a single whole genome amplification PCR reaction. We have investigated the evolutionary histories of these individuals and the populations they represent using neighbor joining trees, principle coordinates analysis, ancestral allele frequency and linkage disequilibrium analysis. For each of these analyses we have examined not only the average parameter estimate for the population, but also the degree to which there is variability about this average that might in some way reflect locus-specific random and directional effects. Our findings will be discussed with particular emphasis on Island Melanesia.
The new DNA typing assay referred to above is the Affymetrix Mapping 10K Array, which W2P has mentioned previously:
http://www.affymetrix.com/products/arrays/specific/10k.affx
Ventilatory control and exercise response in lowland born admixed Peruvians tested at 4,338 meters. T.D. Brutsaert1, M. Kiyamu1, E.J. Parra2, M.D. Shriver3, A. Gamboa4, M. Rivera-Ch4, F. León-Velarde4.
1Department of Anthropology, The University at Albany, SUNY, 2Department of Anthropology, University of Toronto, 3Department of Anthropology, The Pennsylvania State University, 4Dpto. de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayétano Heredia.
High altitude (HA) Andean natives have a blunted ventilatory (VE) response to hypoxia, reflected in both the acute hypoxic ventilatory response (AHVR) and the hypoxic ventilatory depression (HVD). This blunting effect is partly irreversible as de-acclimatized HA natives show ~76% and ~30% of the lowland control AHVR and HVD, respectively. The functional and genetic correlates of HVD are largely unknown. In this study, the VE response to sustained isocapnic hypoxia (20 min, end-tidal PO2=50 Torr) was measured at sea-level in 32 male and 33 female lowland born Peruvians of mixed Spanish-Quechua ancestry. Individual admixture proportion (ADMIX, %Spanish) was estimated using a panel of ancestry informative genetic markers. After studies of VE control, subjects were transported to 4,338 m and given a graded exercise test to exhaustion. In males, HVD was negatively correlated with ADMIX (r=0.36, p<0.05). HVD was also negatively correlated to arterial oxygen saturation (SaO2) at HA, both at rest and during exercise (r=0.27-0.38, p<0.05). However, the SaO2-HVD relationship depended on ADMIX, and there were notable sex differences. In males, the SaO2-HVD relationship was significant only at rest in subjects with high ADMIX (r=0.743, p<0.01). In females, the SaO2-HVD relationship was significant only during exercise in subjects with high ADMIX (repeated measures, p<0.05). Results suggest that HVD is a determinant of SaO2 at HA. Results also suggest that population history (as measured by ADMIX) modifies the response to hypoxia in these lowland born subjects. Supported by grants from NSF BCS-0129377 to TDB and NIH/NHGRI (HG002154) to MDS.
BTW, this site has a great deal of information about "races":
http://www.racearchives.com/calc/
IOM, I know that Matt was involved in correspondence with the RootsWeb posters about Ancestry; here is one example:
http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2002-11/1037930381
IOM, I think that people like Matt Thomas have been quite involved with Ancestry (arguably not the best use of his time, but then again given the importance of Ancestry...)
Doug, yes agree re the timescales. From my perusal of a lot of posts on RootsWeb my impression is that the company has bent over backwards to explain their position and to try to accommodate people. As I said on RB, this is a tough audience! However, when the people on RootsWeb are generally happy with the results of the product within known statistical limits and with known caveats, and leaving aside the issue that it is primarily a forensic application, then perhaps they will generally agree that is is a useful tool for their hobby.
BGA groupings in ANCESTRYbyDNA 3.0
This is a complicated topic, mainly due to the fact that there seem to be several taxonomic classifications for human "races". The current product is limited to four categories, Sub-Saharan African, Native American, East Asian, and Indo-European. What categories will be in future versions? Some relevant reference material is copied below. My further comments are in italics.
http://www.ancestrybydna.com/
Ongoing research at DNAPrint has suggested a more logical grouping based on the four BGA delineations shown on the map in the home page – where South Asian, Middle Eastern and European are grouped into a single group called Indo – European. This grouping makes sense in light of anthropological evidence and cultural connections between these groups (for example, their languages are derived from a common base), and our data suggest these groups are far more similar to one another in genetic sequence content than to other groups. We have also found that the test performs more accurately when Pacific Islanders are grouped with East Asians. Because our desire is to produce the most accurate results possible, we will use the following four groupings for the ANCESTRYbyDNA 2.0 test: 1) Native American (those peoples that migrated to inhabit South and North America), 2) Indo – European (Europeans, Middle Easterners and South Asians such as Indians, 3) East Asians (Japanese, Chinese, Koreans, Pacific Islanders) and 4) Africans (sub-saharan). Constructive criticism from other Molecular Anthropologists have also suggested this new 4-way grouping is a more reasonable task for our current test, and we agree. Thus, we have decided to wait to attempt to distinguish between South Asian and European, as well as Pacific Islander from East Asian with the ANCESTRYbyDNA 3.0 test.
http://www.familytreemagazine.com/articles/aug03/dna.html
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.
http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2003-08/1061655028
It's my understanding that the next test will be called 2.5, not 3.0.
The 2.5 version will add a number of markers, but it will still be using the same four population divisions (Indo-European, Native American, African, and East Asian). The additional markers will tighten the confidence intervals. We'll undoubtedly be discussing whether an upgrade is worthwhile for Ancestry 2.0 customers.
The 3.0 version will subdivide those four categories into more groups. They originally planned to have six, including Pacific Islander and South Asian, as I recall, but decided that version 2.0 didn't have that kind of resolution. I don't know what the timetable is for 3.0
So, it looks as if a six-way grouping would be Sub-Saharan African, Native American, East Asian, European, South Asian and Pacific Islander. If this was to be expanded it looks as if the following nine groups might be implied:
Sub-Saharan African
Europeans, Middle Easterner, South Asians
Japanese, Chinese, Korean, Pacific Islander
Native American
http://www.dnaprint.com/pr_9_19.html
DNAPrint scientists are collaborating with Dr. Shriver to develop more advanced versions of ANCESTRYbyDNA that may be useful for discerning regional heritage proportions in individuals. For example, ANCESTRYbyDNA 3.0 is expected to be capable in the near future of determining whether an individual is of Irish/British, Middle European (French, German), Scandinavian, Mediterranean (Italian, Greek, Spanish) or Eastern European heritage as well as of Western/Central versus East African heritage or of Japanese, Chinese or Korean heritage. For more information about the ANCESTRYbyDNA 2.0 service please visit http://www.ancestrybydna.com.
So now we have an implied fourteen-way grouping:
Western/Central African, East African
Irish/British, Middle European, Scandinavian, Mediterranean, East European
Middle Easterner, South Asians
Japanese, Chinese, Korean, Pacific Islander
Native American
Which would become a seventeen-way grouping if they were able to sub-classify the Middle European and Mediterranean groups.
http://www.dnaprint.com/2003/corporate/participate.html
We are working to expand our current base of four (4) distinctions to twenty (20).
Close enough perhaps to suggest the sort of groupings that DNAP might have in mind for version 3.0? I thought so until I saw the following.
http://archiver.rootsweb.com/th/read/Melungeon/2003-10/1065754240
The recent questions here about the so-called DNA print test prompted some back-channel discussion in search of authoritative answers, which in turn prompted Mike Nassau, a population geneticist himself, to research this topic. His rather lengthy response is below. I certainly want to thank Mike for all his work on this and Karlton Douglas for his assistance as well. The bottom line is, if you thinking of having this test done, wait for version 3.0 at least, for reasons Mike explains in detail.
Dennis Maggard
List Owner
October 9, 2003
Dear Friends,
I got an e-mail today from Karlton Douglas asking my opinion about the new ANCESTRYbyDNA test offered by DNAPrint Genomics. Being me, I wrote a three page response to his one line query. I thought some of the rest of you might be interested. Since writing, I have read that they will soon bring out ANCESTRYbyDNA3, which will be able to distinguish Mediterranean from Northwestern European. If you are interested in doing this test, I would strongly recommend that you wait until version 3 is ready. Maybe it will also be able to distinguish at least Na-Dene from Amerind types of Native Americans, which would greatly increase my confidence that it can distinguish Native American from North and East Asian. My earlier paper on Race and Miscegenation, written a year ago for a discussion on the Melungeon Family Genealogy Forum about the validity of race, is now attached as a file to this group, as is the write-up where I learned about the new version 3 of the test.
Any of you may feel free to copy this or part of it to any other list, but answers or questions should be directed back to the Melungeon Origin group.
http://groups.yahoo.com/group/MelungeonOrigin
melungeonorigin@yahoo.com
Mike Nassau
P.S. October 10,2003
I have had an interesting response indicating that version 2.0 can not distinguish Amerind from "East Asian" , that someone of known Algonquian ancestry was told they were East Asian, not Native American. This is exactly what I would expect from a test which does not distinguish Na-Dene (Navajo, Apache, Athbaskan, Tlingit and other groups which came to America from Asia only some 8000 years ago) from Amerind (the rest of Native Americans, whose ancestors came over twice as long ago). These two groups are closer to related groups in North and East Asia than they are to each other.
I now have had time to wade through the blurbs put out by DNAPrint including the one on their "science". Their "science" article is reassuringly sound and well written. They do know what they are doing. Their work will tell people a lot about their ancestral composition, with one major problem or exception. First, wait for version 3.0, version 2.0 doesn't distinguish between different "Indo-European" groups. (They seem to lump all "white" or "Caucasian" racial groups under this umbrella, which is very wrong.) If version 3.0 will distinguish Na-Dene from Amerind, and both of them from related groups in North Asia, it will serve for people of mixed NW European, Mediterranean, Sub-Saharan Black and Native American ancestry given that the mixing has not been followed by visual selection. That proviso pretty well rules it out for Mestees old mixed groups) like Melungeons [including Carmel Indians and Goinstown Indians], Brass Ankles, Redbones, etc., but maybe not for Lumbees, Haliwa Indians, Occaneechi Saponi, etc. The difference is that the lighter groups like the Melungeons and Brass Ankles have been visually selected, with the more "Black" appearing members tending to leave and join Blcak communities. This means that the appearance has become more "White" over time while the actual ancestry hasn't changed.
Pollitzer's blood type studies had the advantage that blood types are not seen and people are not selected based on their blood type. So visual selection can explain why a group like the Hancock County Melungeons he tested were over one eighth Black in ancestry but appeared much less. This study, with its use of Duffy blood type, which is found only in people of Black West African ancestry, is still the definitive study on Melungeon ancestry. Guthrie's reanalysis in no way diminishes this finding of a large Black component, what it does show is that if Pollitzer had included a Mediterranean component like Portuguese in his model instead of just Black, English and Cherokee, he would have had a much better fit. That better fit would have been at the expense of the English, not the Black component.
ANCESTRYbyDNA uses some 2000 SNPs (Single Nucleotide Polymorphisms) to type people for their ancestry. The problem is that they have not used only sites which do not impact appearance. In fact, they have looked for sites which do have an effect on appearance. So visual selection will shift the results of the test significantly. So a Melungeon who is 14% Black, 1% Native American, 25% Mediterranean and 60% NW European in ancestry may well test out to be 5% Black, 0% Native American, 30% Mediterranean and 65% NW European.
Be warned. The advertisements for this product are dishonest and deceptive. Do not believe what you read. I think this more likely the fault of the advertising agency than of the scientists, but it is very real. When they say this test will tell you your precise ancestral mixture, that is patently false. Any scientist or statistician would be looking for their statistical margin of error. My guess is with 2000 SNPs used, they would have about 1 to 3% error in their estimate for each generation since the mixing occurred. So for people whose ancestry was recently mixed, the estimates will be pretty good, for those with old mixing, not so good.
I do hope this test is improved in future versions. I particularly hope they may bring out a version which excludes SNPs in loci for visually identifiable traits.
Mike
Dear Karlton,
I have just started to look at the info I have collected on the internet. The genetics, using a wide variety of SNPs (Single Nucleotide Polymorphisms), seems valid enough. What I have read of their interpretation of the data seems very, very simplistic at best, racist and ignorant at worst.
The immediate glaring problem is their lumping of people into races or groups. South Chinese are closer to Pacific Islanders than they are to North Chinese. North Chinese are closer to Navajo than they are to Japanese. Navajo are closer to Chinese than they are their Hopi neighbors. Eskaleuts (inuit, Yupik, Aleuts) are very close indeed to Chukchi, Kamchatkans and other peoples of extreme NE Asia and closer to Uralic peoples like Finns and Samoyeds and Indo-Europeans like Russians and English than they are to Amerinds like the Algonquians and Siouans. These Amerinds are probably closer to Kets and Huns (language extinct, but many descendants) than to Na-Dene (Athbaskans, Apache, Navajo).
The races of humankind are divided first by the direction from the point of origin of modern man, somewhere around Lake Victoria, probably in Kenya or Uganda. To the south are the two Southern African races, the Twa (pygmies) and Khoisan (San ["Bushmen"] and Khoi-Khoi ["Hottentots"]). To the west and northwest are the two Black African races, Guinean and Sahelian. To the east and northeast are the Trans-Saharan races. The Trans-Saharan can be broken into the Australoid, the Papuan [New Guinea and related areas], the Austric (Southeast Asia, South China and the Austronesian [Malayo-Polynesian] area) and the Rest. The Rest includes North Africa and the Horn of Africa, Eurasia except for SE Asia and South China, and the Americas. Coming up with a name which makes sense for a group as diverse as this, including Icelanders, Basques, Moors, Somalis, Dravidians, Kets, Finns, North Chinese, Turks, Japanese, Inuit, Navajo and Quechua, is very difficult.
I do not see these eight races in AncestorsbyDNA, rather, I see the traditional breakdown slightly modified. I am particularly disturbed by the treatment of Native Americans. If they have SNPs which will lump Na-Dene with Amerinds instead of North Chinese, I would be very surprised. The Far East race is another puzzle. If this is meant to include Japanese (with their affinities to Turkics and Eskaleut), the North Chinese and the South Chinese, I do not believe they have the common ancestry to provide SNP common identity.
OK. So this implies an eight-way grouping:
Twa, Khoisan
Guinean, Sahelian
Australoind, Papuan, Austric, "the Rest"
Other sub-divisions, such as distinguishing between Na-Dene and Amerind (other Native Americans) also seem to be important. If we take the groupings from the last paragraph above we would have the following twelve-way grouping (ten-way if the Austric group is not sub-divided):
Twa, Khoisan
Guinean, Sahelian
Australoind, Papuan
Southeast Asia, South China, Austronesian
North Africa/Horn, Eurasia, Americas
However, the implied further sub-divisions within "the Rest", some of which match the categories mentioned by DNAP, would expand this to at least twenty-two groups ("The Rest includes..."):
Twa, Khoisan
Guinean, Sahelian
Australoind, Papuan
Southeast Asia, South China, Austronesian
Icelanders, Basques, Moors, Somalis, Dravidians, Kets, Finns,
North Chinese, Turks, Japanese, Inuit, Navajo, Quechua
Again, if the Austric group is not sub-divided this becomes a twenty-way grouping...
I think this is coincidence and not necessarily the same twenty groups that DNAP has in mind. It will though be interesting to see what they eventually are. Finally, a more definitive fifty-two-way classification:
http://www.legioneuropa.org/mxrabd/rosenberg.pdf
Genetic structure of human populations", Rosenberg et al., Science 298, pgs. 2381-2385
African: Bantu, Mandenka, Yoruba, San, Mbuti Pygmy, Biaka Pygmy
Europe: Orcadian, Adygei, Russian, Basque, French, Italian, Sardinian, Tuscan
Middle East: Mozabite, Bedouin, Druze, Palestinian
Central/South Asia: Balochi, Brahui, Makrani, Sindhi, Pathan, Burasho, Hazara, Uygur, Kalash
East Asia: Han, Han (N. China), Daj, Daur, Hezhen, Lahu, Miao, Oroqen, She, Tujia, Tu, Xibo, Yi, Mongola, Naxi, Cambodian, Japanese, Yakut
Oceania: Melanesian, Papuan
America: Karitiana, Surui, Colombian, Maya, Pima
Meanwhile, some of the people mentioned in the Scientific American article have been busy looking at Ancestry Informative Markers (as mentioned before Seldin et al even refer to relevant SNPs as "AIMs"):
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14631557&....
Rosenberg NA, Li LM, Ward R, Pritchard JK. Informativeness of Genetic Markers for Inference of Ancestry. Am J Hum Genet. 2003 Nov 20 [Epub ahead of print]
Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA. noahr@usc.edu
Inference of individual ancestry is useful in various applications, such as admixture mapping and structured-association mapping. Using information-theoretic principles, we introduce a general measure, the informativeness for assignment (I(n)), applicable to any number of potential source populations, for determining the amount of information that multiallelic markers provide about individual ancestry. In a worldwide human microsatellite data set, we identify markers of highest informativeness for inference of regional ancestry and for inference of population ancestry within regions; these markers, which are listed in online-only tables in our article, can be useful both in testing for and in controlling the influence of ancestry on case-control genetic association studies. Markers that are informative in one collection of source populations are generally informative in others. Informativeness of random dinucleotides, the most informative class of microsatellites, is five to eight times that of random single-nucleotide polymorphisms (SNPs), but 2%-12% of SNPs have higher informativeness than the median for dinucleotides. Our results can aid in decisions about the type, quantity, and specific choice of markers for use in studies of ancestry.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14628215&....
Collins-Schramm HE, Chima B, Morii T, Wah K, Figueroa Y, Criswell LA, Hanson RL, Knowler WC, Silva G, Belmont JW, Seldin MF. Mexican American ancestry-informative markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians.
Hum Genet. 2003 Nov 20 [Epub ahead of print]
Rowe Program in Human Genetics, Departments of Biological Chemistry and Medicine, University of California at Davis, One Shields Avenue, 95616-8669, Davis, CA, USA.
Markers with large differences in allele frequencies between ethnicities provide ancestry information that can be applied to genetic studies. We identified over 100 biallelic ancestry informative markers (AIMs) with large allele frequency differences between European Americans (EA) and Pima Amerindians from laboratory and database screens. For 35 of these markers, Mayan, Yavapai and Quechuan Amerindians were genotyped and compared with EA and Pima allele frequencies. Markers with large allele frequency differences between EA and one Amerindian tribe showed only small differences between the Amerindian tribes. Examination of structure in individuals demonstrated a clear separation of subjects of European from those of Amerindian ancestry, and similarity between individuals from disparate Amerindian populations. The AIMs demonstrated the variation in ancestral composition of individual Mexican Americans, providing evidence of applicability in admixture mapping and in controlling for structure in association tests. In addition, a high percentage of single-nucleotide polymorphisms (SNPs) selected on the basis of large frequency differences between EA and Asian populations had large allele frequency differences between EA and Amerindians, suggesting an efficient method for greatly expanding AIMs for use in admixture mapping/structure analysis in Mexican Americans. Together, these data provide additional support for the practical application of admixture mapping in the Mexican American population.
Related articles listed on PubMed are quite interesting as well:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Display&dopt=pubmed_pubmed&f...
I thought that was the one you meant to paste! lol
I agree with most of this except the assertion that non-coding DNA must be playing a passive role. Below is one real-world example where it does not. First some terminology:
"...each SNP can be classified by whether it is coding or not. Coding SNPs can be classified by whether they alter the sequence of the protein encoded by the altered gene. Changes that alter protein sequences can be classified by their effects on protein structure. And non-coding SNPs can be classified according to whether they are found in gene-regulating segments of the genome — many complex diseases may arise from quantitative, rather than qualitative, differences in gene products."
Single nucleotide polymorphisms: to a future of genetic medicine. Aravinda Chakravarti. Nature 409, 822 - 823 (2001)
BTW Chakravarti is interesting in his own right:
http://www.hopkinsmedicine.org/humangenetics/facultypages/chakravarti.html
"We hypothesize that most complex diseases arise from common, missense mutations in genes encoding proteins within a pathway."
However:
http://www.hopkinsmedicine.org/hmn/W02/top_2.html
Edward Rubin, The Lawrence Berkeley National Laboratory
"The non-coding sequences of the genome remain a vast, mysterious sea,"said Edward Rubin. In his talk titled "Jewels in Junk," Rubin gloried in metaphors in hopes investigators would give sequences of DNA that apparently don't code for genes a closer look.
Focusing on an especially large stretch of chromosome five that carries interleukin genes, Rubin showed the value of a comparative approach to flush out useful non-coding areas outside of the genes. He pinpointed the non-coding sections in human, cow, dog and rabbit DNA—sections long preserved by evolution—and showed they held similar sequences. Deleting those preserved bits in mice strongly reduced the activity of nearby interleukin genes. "That means, in short, that we've found a genetic switch outside of the genes."
Looks like the non-coding DNA sometimes controls the coding DNA?
OT bag8ger, I have a lot of (recent) experience of going over mountains on foot. I hope Nik likes the view from the helicopter. I seem to recall that you prefer jumping out of perfectly good aircraft yourself!
itsonlymuni, let's go back to one of the paragraphs in my post:
According to the principle it is not a case of coding DNA interpreting non-coding DNA, as both are involved in a dualistic (contravariant to borrow a technical term from the article) role. Hence the additional complexity leading to a "challenge of colossal proportions".
Not sure what "logic" you are referring to.
Let's go back to one of the paragraphs in the article:
"The Principle attributes coding- and non-coding DNA a mutually supportive role in which neither is inferior to the other, thereby changing Genomics from a fishing expedition for fewer and fewer genes into an Information Challenge of colossal proportions to decipher the genetic code in which both "coding" and "non-coding" DNA play an essential part."
According to the principle it is not a case of coding DNA interpreting non-coding DNA, as both are involved in a dualistic (contravariant to borrow a technical term from the article) role. Hence the additional complexity leading to a "challenge of colossal proportions".
Indeed they should, and I cannot see them at either WIPO or the US Patent Office...
bag8ger
It is just plain difficult to get published at all these days with the volume of papers competing for the limited journal space.
The Geonme Duality Principal is an interesting idea. Science does tend to proceed as implied in the article, with paradigm shifts caused by "left-field" ideas that get a lot of flak at first before they eventually become the accepted norm. If true it means that it is going to be a lot harder to do all of the things that the genome revolution promised - although there will still be some "simple" applications possible through the use of coding DNA alone. Time (and more scientific minds) will tell if this new theory is correct.
Lab21 article:
http://www.genomenewsnetwork.org/articles/11_03/dna_face_cream.shtml
Lab21 was mentioned on page 18 in:
http://www.hciv.com/pdfs/2003_digital_dawn.pdf
This one also talks about Lab21 and DNAP:
http://www4.od.nih.gov/oba/sacghs/meetings/June2003/Presentations/Juengst_t.pdf
Another possible connection
Ahmed SS, Tan FK. Identification of novel targets in scleroderma: update on population studies, cDNA arrays, SNP analysis, and mutations. Curr Opin Rheumatol. 2003 Nov;15(6):766-71.
Department of Internal Medicine, University of Texas Medical School-Houston, Texas 77030, USA. sohail.ahmed@uth.tmc.edu
PURPOSE OF REVIEW: Systemic sclerosis, or scleroderma, is an uncommon autoimmune connective tissue disease that results in systemic fibrosis. Its etiologic basis remains unclear. The pathogenesis of systemic sclerosis involves a proliferative and obliterative vasculopathy resulting from endothelial cell dysfunction, extensive fibrosis secondary to fibroblast activation, and autoimmunity as demonstrated by the presence of disease-specific autoantibodies. Although there is no clear and convincing evidence for an environmental trigger in most cases, accumulating data emphasize the role of genetic factors in systemic sclerosis. As in other complex human diseases, multiple genes likely contribute to disease susceptibility and the clinical manifestations of systemic sclerosis. This review will cover the application of genomics to the complex genetics of systemic sclerosis. RECENT FINDINGS: The following review is an update on novel targets identified in scleroderma based on published reports (May 2000-May 2003) of mutation/polymorphism analysis (using SNP and haplotyping), the results from a recent genome-wide scan on a Native American population with systemic sclerosis, and gene expression studies (microarrays). SUMMARY: The use of genomics has revealed novel targets and genetic associations that may contribute to the cause, the onset, and the subsequent pathologic changes that constitute systemic sclerosis. The identification of potential candidates for gene therapy or disease-specific targets amenable to pharmacologic intervention will benefit patients with systemic sclerosis who are currently being treated for their symptoms and not the disease process itself.
Here's the genome-wide scan the paper refers to:
Zhou X, Tan FK, Wang N, Xiong M, Maghidman S, Reveille JD, Milewicz DM, Chakraborty R, Arnett FC. Genome-wide association study for regions of systemic sclerosis susceptibility in a Choctaw Indian population with high disease prevalence. Arthritis Rheum. 2003 Sep;48(9):2585-92.
University of Texas-Houston Medical School.
OBJECTIVE: Systemic sclerosis (SSc) is a complex, multisystem connective tissue disease in which genetic factors contribute to disease susceptibility. The aim of this study was to localize chromosome regions associated with susceptibility to SSc in a relatively isolated and homogeneous population of Choctaw Indians with a high prevalence of SSc. METHODS: A genome-wide microsatellite screen at 10 cM resolution (400 markers) was performed in 20 Choctaw patients with SSc and 76 ethically matched controls. Based on the results of the initial screen, fine-scale microsatellite mapping at < or =1 cM resolution was performed in 10 selected chromosome regions. Allele and marker haplotype frequencies were compared between SSc patients and controls. RESULTS: From the genome-wide screen, 12 markers showed evidence of highly significant associations with SSc in this population (P < 0.01), while 5 other markers showed significant associations (0.01 < P < 0.05). Among these markers, loci D5S410, D6S422, D15S978, and D20S107 are near the SPARC, MHC, FBN1, and TOPOI genes, respectively, confirming the results of our previous studies, which used different markers. D1S2800 and D14S63 have been reported to show linkage to systemic lupus erythematosus (SLE) in family-based studies, and D1S206, D6S422, and D6S264 are loci on 1p21.2, 6p22.3, and 6q23-27, respectively, which are in regions reported as showing linkage to SLE and other autoimmune diseases. Other markers showing unique associations with SSc were D7S510 (7p12-11), D7S661 (7q35), D8S514 (8q24.12), D19S221 (19p13.2), D19S220 (19q13.2), D22S423 (22q13.1), DXS1068 (Xp11.4), and DXS8055 (Xq21-23). Further analysis with fine-scale microsatellite mapping revealed at least 14 potential haplotypes associated with SSc. CONCLUSION: Our findings indicate that a number of genetic loci may contribute to the high prevalence of SSc in the Choctaw and are consistent with the paradigm that some autoimmune rheumatic diseases are likely to share genetic determinants.
She is one of the RootsWeb posters (DNACousins is her alias).
RootsWeb postings about the Niteline interview
http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2003-11/1067872939
Date: Mon, 3 Nov 2003 10:22:19 EST
I wrote to Dr. Tony Frudakis of DNAPrint and asked him if he had any comments on this case. Here is his reply:
Ann,
I am very familiar with this case, and have spoken with Wayne several times already. Wayne is a very light skinned man of very much unknown but surely mixed pedigree (according to him). He believed himself to be a European/Native American/African mix, but the test showed him to be mainly Native American/European. We in fact did an interview with ABCs Nightline on how this case illustrates the disconnect between peoples geopolitically derived expectations and anthropological realities. I cannot guarantee that it will air, or when it will air, but we spent a day here doing that interview and it was very productive. As I said in the interview, it is actually unusual to show no African for a person that expected it.
Tony.
There are a few separate threads discussing the program. The main one starts here:
http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2003-11/1069479658
You'll have to wait quite a while for your test results in the immediate future. DNAPrint genomics will be flooded with orders, now, as they were after the CBS report, earlier this year.
Health warning: the RootsWeb posters Raymond Whritenour and John Chandler (both well known to anybody who follows this forum) tend to be less than positive about DNAP.
Shrinkage at the Biometrics council?
http://www.biometricscouncil.org/
There seem to be fewer people on the Board and the Scientific Advisory Council. If you look at the javascript source for the wweb page you see that this is because a number of people have been "commented out". There must be a good reason for this you would think, and also for not just deleting the relevant source code?
This was a recent radio spot
http://www.werctalk.com/jholland_main.html
ANCESTRY by DNA! Now, you can find out YOUR OWN Ancestry!! Dr. Tony Frudakis (froo DAH kuss), Ph.D., has developed this technology and he will join us to talk about it! Go to his website at www.ancestrybydna.com and take the test! It determines genetic heritage and is a great tool for anyone interested in learning what their true ancestral lineage is! Don’t miss this one!
I thought it was froo DAY kiss, not froo DAH kuss?
OT: bag8ger, re your mail - I can see Hwan's point.
I seem to remember the Billirubin alias from RB before it was TOS'ed there...
Interesting that Lee Silver was on the programme.
I can't remember if this was mentioned before. From the UTEK press release:
"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."
Apollo are one of Athena Capital's clients.
http://philadelphia.bizjournals.com/tampabay/stories/2003/05/19/focus2.html?page=2
"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.sunbiz.org/scripts/cordet.exe?a1=DETFIL&n1=P03000116663&n2=NAMFWD&n3=0000&....
The Directors of Apollo Pharmaceuticals Inc are the principals of Athena Capital.
http://www.sunbiz.org/scripts/cordet.exe?a1=DETFIL&n1=L03000016462&n2=NAMFWD&n3=0000&...
In October 2003 Apollo Pharmaceuticals LLC has changed it's name to WCW Enterprises LLC, the Registered Agent for whom is Lisa Weiss. I just know that WCW stands for Weiss, Cimino and Weiland.
OT Just have too much spare time! eom