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I did see this one, but it is worth repeating:
http://observer.guardian.co.uk/uk_news/story/0,6903,1208036,00.html
Mobile DNA labs set to change face of sleuthing
Twist of science marks a revolution for detectives
Robin McKie, science editor
Sunday May 2, 2004
The Observer
Police are investigating an armed robbery. The unconscious victim has been taken to hospital, and detectives have discovered a spot of blood they believe to be the robber's. They place a sample in a briefcase-sized test kit and wait for results. Twenty minutes later, a print-out shows the DNA came from a 6ft-tall, middle-aged man with a Scottish background, brown eyes, and a distinctive hooked nose. The manhunt begins.
It sounds like science fiction, yet this technology is soon likely to become reality, say scientists. A report by the Laboratory of the Government Chemist, commissioned by the Police Foundation and due to be delivered in a few days, will review a variety of new DNA markers that could soon be used to help police pinpoint the appearance and origins of suspects.
At the same time, the laboratory's director of life science, Dr Paul Debenham, will tell the Association of Chief Police Officers that new mobile DNA test kits, currently being developed so that doctors can make bedside identifications of bacteria and viruses, could be used as the basis for mobile DNA fingerprinting laboratories.
DNA profiling is changing - as has already been revealed in a series of criminal investigations. In one case Craig Harman, a 20-year-old man from Frimley, Surrey, who threw a brick through a lorry window, killing its driver, was recently jailed after his DNA was linked to a family member with a criminal record.
DNA technology - which has already been used to pinpoint thousands of criminals since first used in Britain in 1987 to solve the murders of Lynda Mann and Dawn Ashworth - is now entering a new phase of sophistication.
'We already have a DNA test that can tell us if a sample comes from a person with red hair,' said Debenham. 'At the same time, tests are being developed that will show eye colour. Other tests will tell us their ethnic origins. These new tests could provide crucial leads.'
'Most crime investigators would give their left arms to have a witness for certain crimes, and spend untold hours attempting to locate witnesses who, in the end, may not be telling the truth,' said Dr Tony Frudakis, chief executive of Florida biotechnology company DNAPrint. 'Our tests will serve as an eyewitness for every crime scene where DNA was left, but they will be more reliable.'
Of course, the use of hair dye and coloured contact lenses by criminals would affect the usefulness of such tests, but if employed in conjunction with other forensic data they should still prove to be key tools.
'In the end, there is no reason why you could not develop DNA tests that would let you build up a complete picture of a person's face,' said Oxford geneticist Sir Walter Bodmer.
'You would still have difficulties in working out their age, but that is not an insurmountable problem. The real issue is commitment. It would take a great deal of effort and money to work out all the markers that control face morphology. Governments will have to decide soon if they think it is worth the cost.'
I don't remember seeing this article posted before:
http://www.guardian.co.uk/life/thisweek/story/0,12977,1210021,00.html
Can your DNA reveal where you're from?
David Adam
Thursday May 6, 2004
The Guardian
Not really, at least not yet. Although broad ethnic ancestry can be determined from our DNA, geneticists can't refine that information to say with certainty that an individual hails from a specific country. Or indeed the Caribbean, which is where the Metropolitan Police claimed last week that new DNA testing had placed the origins of a serial rapist known as the Minstead offender.
"Ancestral testing concluded that the Minstead offender's origins probably lie in the Caribbean," the Met's Simon Morgan said.
It sounds plausible, but this particular piece of sleuthing is beyond current technology. Who says so? The company that analysed the Met's sample. "That's not what our test indicated," says Zach Gaskin, technical director of forensics at DNAPrint Genomics in Florida.
Analysing DNA for telltale genetic markers can only reliably judge whether someone's background lies in one of four distinct historical population groups: East Asian, European, Native American and African. Beyond that, it's far trickier and a case of trying to judge the relative percentages of each and then comparing the results with people whose backgrounds are known.
This does at least allow certain possibilities to be ruled out. Will O'Reilly of the Met says they had reports that the attacker was black or of mixed race, and when DNAPrint compared the results with a database of 500 people, the markers did not match those from West Africa or those of mixed race. They were similar to those in African-American populations, but O'Reilly says the most likely match, given the population of south London, where the attacks took place, is African-Caribbean. Other geneticists helping the Met apparently agree; O'Reilly says one has even pinpointed the exact Caribbean island.
"That would be extremely difficult because they are very similar populations," warns Alec Jeffreys, the geneticist at Leicester University who pioneered DNA fingerprinting. The Met is not giving up; it has persuaded 200 African-Caribbean officers to submit samples to DNAPrint for comparison.
Babe, you are most welcome and thank you for your thoughts.
66fan, thanks. Matt takes care of the multiple aliases - and they seem to be very efficient at managing this.
Here's another project using SNPs to estimate ancestry:
http://www.ccc.columbia.edu/HICC_collaboration/projects/p20-joe.html
P20
2003-2004
The African-American grouping is a reasonably valid variable for conducting small-scale biological studies
Andrew Joe (PI, Columbia University), Nathan Consedine (Co-Pi, Long Island University)
We will identify and characterize two cohorts of African American (AA) individuals: US-born AAs and Jamaican individuals. The latter, presumably more homogenous cohort, will serve as the comparison group Using serum samples and polymerase chain reaction (PCR)-based methods, we will characterize the degree of genetic admixture of each group by determining the relative allelic frequency distributions of the D1S80 and HLA-DQA1 gene polymorphisms. We will demonstrate that the contribution of African alleles to both groups is not significantly different. There is an ongoing debate as to whether race is an appropriate and valid research variable for use in biological studies.
Specific Aim 1 was completed. The control population has been changed. Immigrants from many countries, including those from Africa, Europe, and Asia, have settled in Jamaica. Thus, ancestry analyses may not be too different from those conducted in the African-American population in the US. Nigerians from either the Yoruba or Ibo cultures will represent a more genetically homogeneous group and will therefore comprise the control population for this study. Specific Aim 2 project is based on the collection of human blood specimens and questionnaire data. Because the target study and comparison populations are very specific, three institutions – Columbia University Medical Center (CUMC), Harlem Hospital Center (HHC), and Long Island University (LIU) – will be required to complete the planned accrual. Thus, this protocol was presented to and is currently being reviewed by the Institutional Review Boards (IRBs) of the three institutions. Unfortunately, sample and data collection will not be possible until the protocol is approved. (a) Documents were reviewed and approved by the LIU IRB. (b) Documents were reviewed by the CUMC IRB [Protocol IRB-AAAA1500]. Revisions have been submitted. (c) Documents were reviewed by the HHC IRB. Revisions have been submitted. A 25-item questionnaire has been created that will investigate potential factors used by the study subjects to construct racial identity. The method of determining genetic admixture has been changed (Specific Aim 2) to allow a more reliable method for estimating racial ancestry. A panel of 50 SNPs will be studied, and these analyses will be conducted by Dr. Elad Ziv, Assistant Professor of Medicine at the University of California, San Francisco. An addendum to the IRB to include this SNP panel will be submitted.
Contribution of the P20 The results of these studies may help us to determine whether it is valid to study tumor biology using racial classifications.
Project-Generated Resources and Benefits: In this project, DNA and questionnaire data will be collected from the African-American and Nigerian cohorts.
Dr Elad Ziv was mentioned in this post yesterday where he collaborated with Shriver on a piece of work that used 52 Ancestry Informative Markers:
http://www.investorshub.com/boards/read_msg.asp?message_id=3040369
Coincidence?
DNAPrint became a member of the Sarasota Chamber of Commerce in April:
http://www.sarasotachamber.org/yourChamberDirectory.cfm
They are in fact a trustee:
http://www.sarasotachamber.org/yourChamberTrustees.cfm
Frog, being the man of integrity and honor that i am (lol) I would not dream of employing such nefarious means or any subterfuge to influence the outcome of our discussions. To my mind there is no "immediate improvement" necessary as the board moderators have IMO been doing an excellent job to date. Rather, it will be a case of maintaining the existing standard.
Here is an article that has been accepted for publication by the American Journal of Human Genetics. There is clearly growing interest in MALD:
Linkage Analysis of a Complex Disease through Use of Admixed Populations
Xiaofeng Zhu,1 Richard S. Cooper,1 and Robert C. Elston2
1Department of Preventive Medicine and Epidemiology, Loyola University Medical Center, Maywood, IL; and 2Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland
Received September 2, 2003; accepted for publication March 12, 2004; electronically published May 6, 2004.
Linkage disequilibrium arising from the recent admixture of genetically distinct populations can be potentially useful in mapping genes for complex diseases. McKeigue has proposed a method that conditions on parental admixture to detect linkage. We show that this method tests for linkage only under specific assumptions, such as equal admixture in the parental generation and admixture that occurs in a single generation. In practice, these assumptions are unlikely to hold for natural populations, resulting in an inflation of the type I error rate when testing for linkage by this method. In this article, we generalize McKeigue's approach of testing for linkage to allow two different admixture models: (1) intermixture admixture and (2) continuous gene flow. We calculate the sample size required for a genomewide search by this method under different disease models: multiplicative, additive, recessive, and dominant. Our results show that the sample size required to obtain 90% power to detect a putative mutant allele at a genomewide significance level of 5% can usually be achieved in practice if informative markers are available at a density of 2 cM.
Here is another approachable paper on population structure, admixture, confounding, and markers:
http://psg-mac43.ucsf.edu/ticr/syllabus/courses/29/2004/05/25/Lecture/readings/Ziv%20and%20Burchard.....
The authors, Ziv and Burchard from UCSF, also appear on this poster with Mark Shriver:
http://hgm2004.hgu.mrc.ac.uk/Abstracts/Publish/WorkshopPosters/WorkshopPosters04/hgm075.html
Population Stratification Confounds Asthma Studies Among Latino Americans
1S. Choudhry, 1N.E. Coyle, 1D. Lind, 2H. Tang, 1K. Salari, 1S.L. Clark, 1N. Ung, 1H. Matallana, 1P.C. Avila, 3J. Casal, 3A. Torres, 3S. Nazario, 1M. Toscano, 1R. Castro, 3W. Rodriguez-Cintron, 1Pui-Yan Kwok, 1D. Sheppard, 4M.D. Shriver, 5,6N. Risch, 1E. Ziv, 1E.G. Burchard
1University of California, San Francisco, San Francisco, CA, USA, 2Fred Hutchinson Cancer Research Center, Seattle, WA, USA, 3University of Puerto Rico, San Juan, PR, 4Pennsylvania State University, College Station, PA, USA, 5Stanford University, Stanford, CA, USA, 6Kaiser Department of Research, Oakland, CA, USA
Purpose: Case-control association studies are a powerful strategy for identifying genes of modest effect in complex diseases such as asthma. However, such studies may be confounded in racially admixed populations, such as Latinos. We tested whether population stratification may affect the results of asthma case-control studies in Puerto Ricans and Mexican Americans.
Methods: Mexican American asthmatic probands and ethnically matched controls (360) recruited from the San Francisco Bay Area and Puerto Rican asthmatic probands and matched controls (360) recruited from Puerto Rico were typed for 52 ancestry informative markers (AIMs). These AIMs were selected for their high allele frequency differences between West Africans, Europeans and Native Americans. For each population we tested whether the degree of association between pairs of markers on different chromosomes was greater than expected using a permutation test. Population stratification was assessed by comparing the global differences in allele frequencies between cases and controls.
Results: Among Puerto Ricans, the association between markers on different chromosomes was significantly greater than expected (p<0.0001). Among Mexicans, there was a non-significant trend towards association between markers on different chromosomes (p=0.07). Among Puerto Ricans, 9 of 52 markers were significantly associated with asthma, and there was a significant difference between cases and controls (p=0.00031). Among Mexican Americans, 3 of 52 markers were associated with asthma and there was no significant difference between cases and controls (p=0.44).
Conclusion: Case-control genetic association studies of asthma are susceptible to genetic confounding in Latino populations. Empirical assessment of the effects of stratification will be important to appropriately interpret the results of case-control studies.
Here is an interesting recommendation which was discussed at a European Commission conference titled "Human genetic testing: what implications?" last week.
http://www.innovations-report.com/html/reports/life_sciences/report-28913.html
Ethnicity and genetics
There may be differences among patients based on their ethnic origin, with respect to genetic testing. Some genetic variants are more common in certain populations or groups. Specific attention should be paid to such groups in the context of developing new tests to ensure fair access and to avoid stigmatisation or stereotyping based on race. Specifically, genetic tests must never be used to determine ethnicity.
Hello all and thanks to Miss Scarlet and Ann for the thoughts. My email address (mingwan0@hotmail.com) is given in my personal details, which I have updated. I hope that I will do as good a job as DougS, who I wish well in his "retirement".
Two articles have shown up on a news service called New-Medical.net:
West Nile treatment showing 100% response rate among immunocompetent patients
http://www.news-medical.net/view_article.asp?id=1312
Belarus to collaborate with GenoMed on West Nile virus encephalitis
http://www.news-medical.net/view_article.asp?id=1313
dreamsafire, it depends on whether you signed the confidentiality agreement. If you are involved with the PP you must have done in which case you cannot comment (as I cannot). To be on the safe side I would probably not comment further.
Retro, you'll notice I qualified my remarks with the phrase "on account of Genbiomics" as I cannot be sure that the plethora of other things that Hector is involved in do not constitute a distraction larger than that experienced by Richard (who has no other potential distractions that I am aware of). lol
Frog, I think you are as aware of the publicly available validation details as I am. The results of the Validation Studies undertaken in conjunction with the National Center for Forensic Science and the San Diego Police Department Crime Lab on version 2.0 are available on Roger's website:
http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2004-01/1073420735
Incidentally, Experiment II (Comparing Self-Reported Race with the Major Admix Percentage) tells us a little more detail about the parental groups used.
I am not aware of any such information for 2.5 other than the information that was posted on the ABD website and RootsWeb.
As you might expect, I take issue with your assertion that there were "significant accuracy issues with the first version." The only genuine flaw has been discussed by Tony Frudakis:
http://archiver.rootsweb.com/th/read/GENEALOGY-DNA/2004-01/1073420735
"Several months ago we realized that the test was missing African for a small minority of individuals in the teen-30 percent range due to a flaw in the algorithm used. This flaw affected only African admixture and only for a small fraction of individuals with Native American AND African ancestry AND of relatively high (Native American + African) admixture (i.e. very high heterozygosity). It did not affect individuals with substantial African admixture, whether they fit the other criteria just mentioned or not. We were originally alterted to this problem from 2 individuals for whom we confirmed there was an African error. Since then, there have been 2 or 3 others that have stepped forward and the total (of about 6,000 tests run so far) is about 5."
"The flaw, in retrospect, was obvious and very subtle. It was not flagged before because it affects such a very, very small number of possible multilocus genotypes (i.e. people). Since the bug that caused this problem was easily identified, it was easily fixed several months ago - and I think most of you are aware an improvement was made several months ago - the "new" algorithm is what resulted, and nothing has changed since except the style of the presentation.. We havent had any problems detecting dilute African ancestry in these rare individuals of substantial Native American/European admixture since (or anyone else)."
In terms of accuracy and precision of ABD, perhaps you need to refamiliarize yourself with the relevant section of the ABD website:
http://www.ancestrybydna.com/simulation.asp
I believe that the validations do have intrinsic scientific value, as does the test itself.
Retro, interesting. According to the 10K:
"A consulting agreement between GenBiomics, LLC and us was terminated on April 1, 2003. The original consulting agreement was signed on May 17, 2002 and was an agreement that we entered into for consultation and advice on the development of our scientific and business plans. Since that time, two of GenBiomics members have agreed to become executives in our Company and Board of Director members and as a result the prior consulting agreement was terminated. At December 31, 2003, we had accrued $35,475 owed to GenBiomics for the services provided prior to the termination of this agreement. During 2003 and 2002, we recorded consulting expense related to this agreement of $10,000 and 41,250, respectively."
I would imagine that the company was reinstated in November 2003 to allow for the accrued earnings to be paid. There being no further use for the company would then explain the subsequent vountary dissolution. Also confirms that there is no loss of focus by Gabriel and Gomez on account of Genbiomics.
OK, fair enough. DNAP indeed does have to convince the scientific community of the validity of their work. Given that Mark Shriver has a vested interest in the product(s) we can to some extent discount his validation. Such validation extends beyond ABD of course, and beyond the academic community for forensics. To date people like Mirhashemi and Arena, USF, NYU, Moffitt, Chakraborty, Rao, San Diego Police Department, National Center for Forensic Science, multiple other US Police Departments (including Louisiana), Scotland Yard, and the Metropolitan Police have apparently validated the product. I would like to see more papers from the company in journals and some of the patents issued, but things don't look too bad at the moment.
Don't get me started on Kidd and O'Brien (and don't even think of mentioning Goldstein).
We need to bear in mind that DNAP is a small and young company. They have some experience of people trying to rip off their intellectual property, and it is understandable that they are a bit cagey in this regard. Tony Frudakis said on RootsWeb back in January that communication with genealogists had been a problem and had been and would continue to be addressed (presumably the same applies to communication to shareholders - there seems to have been an order of magnitude more communication with RootsWeb posters than there has with the latter). I am sure that DNAP does and will listen to those members of their customer and investor base who have knowledge of these subjects.
I have been trying to have a look at who has been working on timing of admixture events, and there is not a lot in the literature that I can see. It would be nice to get some more information on this. Here is some background for anyone interested:
http://www.garlandscience.com/heg/pdf/ch12.pdf (the best overview)
http://www.pnas.org/cgi/content/full/99/17/11008 (This one has unique-event polymorphisms - UEPs)
http://hpgl.stanford.edu/publications/GR_1997_v7_p996.pdf
http://www.qmw.ac.uk/~ugbt112/ecopop/Goldstein_and_Chikhi_Amended_26_02_02.doc
http://www.genetics.org/cgi/content/full/152/3/1079
http://pritch.bsd.uchicago.edu/publications/FalushEtAl03_Genetics.pdf
I agree that there are some potential issues with ABD 3.0. I previously pointed out the lack of an agreed taxonomy and nomenclature. This is going to create problems I suspect. Hopefully we will see some accompanying papers about this version of the product when it arrives.
St Louis Business Journal
http://stlouis.bizjournals.com/stlouis/stories/2004/05/03/daily67.html?jst=b_ln_hl
Texas physician recruits colleagues to use GenoMed program
An Amarillo, Texas, physician who recently agreed to educate the Amarillo community about St. Louis-based GenoMed's treatment programs has signed up seven more physicians to the program.
Dr. John Young, a partner at Panhandle Pediatrics in Amarillo, is also a clinical assistant professor in pediatrics at Texas Tech University Health Sciences Center in Amarillo. Seven family physicians who are colleagues of Young agreed to distribute GenoMed's treatments to their patients as well. Combined, the physicians treat more than 21,000 patients.
GenoMed Inc. (Pink Sheets: GMED) is a medical genomics company working to find genes that cause disease, particularly hypertension, diabetes and emphysema.
Here's another population researcher:
http://www.thecrimson.com/article.aspx?ref=502369
Published on Thursday, May 06, 2004
Young Profs Net Two Presidential Awards
Two Harvard scientists were among the 57 recipients of the Presidential Early Career Awards for Scientists and Engineers (PECASE) announced by the White House Tuesday.
Cabot Associate Professor of Organismic and Evolutionary Biology John R. Wakeley and Associate Professor of Psychiatry Dr. William A. Carlezon received the high-profile award.
...
Wakeley, who teaches the graduate seminar Organismic Evolutionary Biology 303, "Theoretical Population Genetics" was one of the 20 PECASE award winners that was nominated by the NSF.
He was recognized for his work on developing new methods for analyzing DNA-sequencing data. These methods will help scientists and mathematicians develop new theories about the genetic histories of populations.
"I am working on models that deal with geographically structured populations," Wakeley said. "These models describe the ancestry or genealogy of a sample of DNA."
Wakeley said that his research has found that the genealogies of more complex populations are mathematically similar to genealogies in unstructured populations.
Here is his website:
http://www.fas.harvard.edu/~biophys/John_R_Wakeley.htm
Here is an interesting recent paper from him:
Wakeley J, Lessard S. Theory of the effects of population structure and sampling on patterns of linkage disequilibrium applied to genomic data from humans. Genetics. 2003 Jul;164(3):1043-53.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA. wakeley@fas.harvard.edu
We develop predictions for the correlation of heterozygosity and for linkage disequilibrium between two loci using a simple model of population structure that includes migration among local populations, or demes. We compare the results for a sample of size two from the same deme (a single-deme sample) to those for a sample of size two from two different demes (a scattered sample). The correlation in heterozygosity for a scattered sample is surprisingly insensitive to both the migration rate and the number of demes. In contrast, the correlation in heterozygosity for a single-deme sample is sensitive to both, and the effect of an increase in the number of demes is qualitatively similar to that of a decrease in the migration rate: both increase the correlation in heterozygosity. These same conclusions hold for a commonly used measure of linkage disequilibrium (r(2)). We compare the predictions of the theory to genomic data from humans and show that subdivision might account for a substantial portion of the genetic associations observed within the human genome, even though migration rates among local populations of humans are relatively large. Because correlations due to subdivision rather than to physical linkage can be large even in a single-deme sample, then if long-term migration has been important in shaping patterns of human polymorphism, the common practice of disease mapping using linkage disequilibrium in "isolated" local populations may be subject to error.
Doesn't look too good for DeCode genetics...
A bit more on the London rapist
We knew from previous reports (such as this from the Guardian) the order of magnitude by which the suspect pool had been reduced by viture of using DNA Witness:
http://www.guardian.co.uk/uk_news/story/0,3604,1204770,00.html
Detective Chief Inspector Will O'Reilly said the rapist's origins were in the Caribbean, something which has reduced the range of suspects by 75%.
We also knew from this article in The Mirror something about how many suspects the Police are working with:
http://www.mirror.co.uk/news/allnews/tm_objectid=14187771&method=full&siteid=50143&headl....
Now detectives are working through a list of 100 people with similar DNA to the rapist.
From this article in a local South London paper today we know how many suspects have been eliminated:
http://www.streathamguardian.co.uk/news/localnews/display.var.486600.0.dna_breakthrough_in_hunt_for_....
More than 3,000 suspects have been eliminated from the inquiry and investigators have viewed Interpol and FBI DNA databases in the hope of tracing the man.
So they had over 4,000 current suspects, three quarters of whom were not of Caribbean ancestry.
From this article in The Sun we know the number of suspects that have historically been eliminated:
http://www.thesun.co.uk/article/0,,2-2004192180,00.html
Since 1992, police in London have eliminated 17,000 suspects...
So historically the London Police have on average eliminated some 1,400 suspects per year over the life of the case through traditional methods. The use of DNA Witness has therefore at a stroke obviated the need for some two years work. I would say that the use of DNA Witness is cost effective for the London Police!
Asian/Amerind research
Another example of current population research:
Zakharov IA, Derenko MV, Maliarchuk BA, Dambueva IK, Dorzhu CM, Rychkov SY. Mitochondrial DNA Variation in the Aboriginal Populations of the Altai-Baikal Region: Implications for the Genetic History of North Asia and America. Ann N Y Acad Sci. 2004 Apr;1011:21-35.
Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia.
The discovery of mtDNA types common to Asians and Amerinds (types A, B, C, and D) forced investigators to search for those nations of Asia which, though not considered the ancestors of the Amerinds, have retained a close genetic resemblance with them. We collected samples and studied the gene pools of the Turkic-speaking nations of South Siberia: Altaians, Khakassians, Shorians, Tuvinians, Todjins, Tofalars, Sojots, as well as Mongolian-speaking Buryats. The data indicate that nearly all Turkic-speaking nations of Siberia and Central Asia, as well as the Buryats, have types A, B, C, and D in their gene pool. The highest total frequency of these types is observed in the Tuvinians and Sojots. They, as well as the Buryats, also have the lowest frequency of the europeoid types. The most mixed Asian-Europeoid gene pool examined turned out to be that of the Shorians. An important finding was the presence of type X in the Altaians, which had not yet been detected in Asia. As shown by computer analysis, this DNA sequence is not a late European admixture. Rather, the Altai variant X is ancient and can be close to the ancestral form of the variants of contemporary Europeans and Amerinds. The presented results prove that of all nations in Asia, the Turkic-speaking nations living between Altai and Baikal along the Sayan mountains are genetically closest to the Amerinds.
A couple of observations about the issues raised.
Since February Tony Frudakis has stopped contributing to RootsWeb and the subscriber "DNA Cousins" suggested that the DNAPrint thread be dropped as the discussion had raged there long enough. This seems to have created a bit of a void in terms of a venue for DNAP and ABD discussion by genealogists. This forum is not such a venue. It is for DNAP shareholders. I lurked on RootsWeb and had some email exchanges with some of the stalwarts there (admitting that I was a DNAP shareholder). I did not see fit to subscribe to RootsWeb and enter the fray because I am not a genealogist and did not wish to use their forum to de facto promote the company. By the same token we should not view IHUB (or RB) as a venue for a rehashing of the discussion that previously occured on RootsWeb IMO.
The history of the development of ABD and the issues/concerns raised are well known to those of us who have followed the debate(s) on RootsWeb. Some of those issues are valid and have been or (IMO) are being addressed by the company. The size and diversity of the population samples used to develop the test is IMO such a valid issue. I have previously highlighted where DNAP and it's academic partners are sourcing DNA samples from different populations (not just for ABD) e.g. the Coriell Institute. You can easily see who is working on which populations (especially NAM tribes). We are all interested in seeing the intra-continental subdivisions that will be used in version 3.0 and which population samples they have used. You can learn something about the markers that Mark Shriver and his colleagues have been working with here:
http://146.186.95.23/biolab/voyage/psa.html
The science has been peer reviewed and published in an academic journal:
Frudakis T, Venkateswarlu K, Thomas MJ, Gaskin Z, Ginjupalli S, Gunturi S, Ponnuswamy V, Natarajan S, Nachimuthu PK. A classifier for the SNP-based inference of ancestry. J Forensic Sci. 2003 Jul;48(4):771-82.
Tony Frudakis and Mark Shriver has been asked by an academic publisher to write a textbook on the subject.
There is no comparable test (and I do not think there will be due to the potential for patent infringement).
DNAP are working on timing admixture events (they said this previously). This has big implications - not least for anthropology never mind genealogy.
The other area where this work has some application is in understanding human evolution:
Akey JM, Zhang G, Zhang K, Jin L, Shriver MD. Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 2002 Dec;12(12):1805-14.
Center for Genome Information, University of Cincinnati, Cincinnati, Ohio, USA.
Identifying genomic regions that have been targets of natural selection remains one of the most important and challenging areas of research in genetics. To this end, we report an analysis of 26,530 single nucleotide polymorphisms (SNPs) with allele frequencies that were determined in three populations. Specifically, we calculated a measure of genetic differentiation, F(ST), for each locus and examined its distribution at the level of the genome, the chromosome, and individual genes. Through a variety of analyses, we have found statistically significant evidence supporting the hypothesis that selection has influenced extant patterns of human genetic variation. Importantly, by contrasting the F(ST) of individual SNPs to the empirical genome-wide distribution of F(ST), our results are not confounded by tenuous assumptions of population demographic history. Furthermore, we have identified 174 candidate genes with distribution of genetic variation that indicates that they have been targets of selection. Our work provides a first generation natural selection map of the human genome and provides compelling evidence that selection has shaped extant patterns of human genomic variation.
IMO if you understand which genes have been selected for you might be able to infer something about specific disease causes and processes. Perhaps the company has bigger fish to fry...
I'll look at this tomorrow (it's 2:00 am for me). I personally am quite frustrated with the attitude that has been shown by some individuals on RootsWeb, especially when Tony Frudakis and Matt Thomas have bent over backwards to address the issues raised. The overall tone of your posts is that things are a bit sketchy, things have been screwed up, better to "come clean" now, etc. This is reminiscent of some of the RootsWeb "discussion" so you will forgive me if I am slightly skeptical. The fact that you are aware of the significance of the ability to time admixture events says to me that you are no stranger to this subject matter. You are also therefore aware of the uniquness of ABD, and its relevance to work by the individuals you previously mentioned.
I was going to answer this but IMO you know the answers as well as I do. Your point 7, reiterated in your post this evening, is the real issue that you seem to have (and one that has been discussed ad nauseum on Rootsweb). They are not going to reveal exactly what they have done or publish the specific AIMs for your benefit as this is proprietary information. As Doug says we might expect to see some discussion in relevant journals. The company has previously said that they want to expand their population samples, amd we can reasonably expect this to be an aspect of the version 3.0 development. In due course we will all have more details.
OT Terry, don't really want to get too contentious here. Let me just say that it is both ignorance and manipulation (which is what politics is all about) as Chris says. There are plenty of crazies on all ends of the spectra of opinion. Somewhere along the line common sense always seems to go out of the window and what the majority of reasonable and rational thinking people would want to happen is not the eventual outcome (because it runs counter to the wishes of one or more special interests who influence and control events). Of course, that's "democracy" for you. And before anybody says I'm being anti-American, let me just add that we have the same sort of "democracy" in Britain and the same sorts of crazies (we just don't let them buy automatic weapons).
Here's a small piece
http://www.aberdeennews.com/mld/aberdeennews/news/8584581.htm
Posted on Tue, May. 04, 2004
Aberdeen writing club to meet Wednesday
From staff reports
The Memories Writing Club at the Aberdeen Area Senior Center will hold its monthly meeting on Wednesday at 1 p.m.
Special guest for the day will be Dr. Roy Burt, a pathologist for Avera St. Luke's Hospital. He will speak on DNA and its usefulness in helping determine ancestry.
The Memories Club is an informal group that gathers each month to offer ideas for writing family histories, stories or fiction. New members are welcome to attend.
Members of the group are at all stages of writing from gathering ideas to looking into publishing. Kathy Williams of Stratford is the group leader. For further information, call Shari at the Aberdeen Area Senior Center at (605) 626-3330.
Herald Tribune article
http://www.heraldtribune.com/apps/pbcs.dll/article?AID=/20040504/BUSINESS/405040553/1200
DNAPrint upgrades genetics test
By MARGARET ANN MIILLE
margaret.miille@heraldtribune.com
SARASOTA -- DNAPrint Genomics Inc. is phasing out its original genetics test in favor of a more powerful version that recently gave Scotland Yard a fresh lead in its 12-year hunt for a serial sex offender.
The upgraded ANCESTRYbyDNA 2.5, called DNA Witness when marketed to forensic experts, has helped British authorities narrow their search for a man who has assaulted more than 80 women -- most of them elderly -- in the London area since 1992.
The test, which determines a person's proportional ancestry from among four major population groups around the world, tracked the assailant's ethnic origins to the Caribbean.
The test determines to what extent a person is of Native American, East Asian, Indo-European or sub-Saharan African heritage.
The 177 "ancestry informative markers" in the man's genetic data show that he comes from Native American, European and African stock -- a combination found only in the Caribbean.
Tony Frudakis, DNAPrint's chief science officer, said people with this genetic combination most frequently hail from former British island colonies.
"Then it's just a question of which island," he said.
The test also revealed the genetic makeup of the attacker's parents.
The London Metropolitan Police plans to use the DNA test on its officers with Caribbean ancestry to compare genetic profiles and further pinpoint where the man came from.
The 2.5 version has an average statistical error rate of 3.3 percentage points, compared with 4.7 percentage points for the earlier 2.0 version.
The test is called ANCESTRYbyDNA when it's sold to genealogy buffs exploring their family trees.
"With 2.5, it's more narrow, more precise," Frudakis said. "It does exactly the same job; it just does it better."
But the new test does a few things more. It can distinguish whether a person's European descent is primarily that of continental European, Middle Eastern or Indo-Pakistani origin. Likewise, someone's East Asian ancestry can be further specified as Northern, Central or Southeast Asian.
DNAPrint will continue selling the earlier version of the recreational test until June 1 at a discounted rate of $99.
The 2.5 version, which was launched earlier this year, retails for $219. Customers who buy the earlier version will receive an upgrade for $158.
DNA Witness costs much more -- $1,000 -- because it's much more involved.
Frudakis said although thousands of consumers from around the globe have tried the ancestry test, the English sexual assault case marks the first time it's been used by foreign forensics experts.
That market niche has been a hard sell in the United States, he added, because the test's ability to assemble racial compositions is politically controversial.
DNAPrint, which late last year secured $8 million in financing over two years from a California investment group, had a $7.79 million loss in 2003.
The company's over-the- counter shares were selling for 4 cents at the close of regular trading Monday.
End of article
The last highlighted point is interesting (and disturbing). What do people want, political correctness or rapists and murderers behind bars? OK, in the real world it is not that simple I know but...
The Netherlands
It's a country in Western Europe that should have won the 1974 football World Cup, but that's not important right now...
http://www.dnaprint.com/2003/pressreleases/pr_11_20_03.htm
DNAPrint(TM) Announces Forensic Eye Color Results at Amsterdam Forensic Meeting
World's First Genomics-Derived Test For Forensics Investigation With Predictive Capabilities
SARASOTA, Fla., Nov. 20 /PRNewswire/ -- DNAPrint(TM) genomics, Inc. ("DNAPrint(TM)") announced progress yesterday in developing anthropomorphic genomics testing products to an audience of approximately 500 forensic scientists and detectives at the "DNA ... sporen naar de toekomst II" conference sponsored by the Netherlands Forensic Institute...
From December 2003:
http://www.geneyous.nl/symposium/lecture2.html
Dr. Peter de Knijff (1956) was trained as a medical microbiology technician and clinical chemistry technician. He received his PhD from the Medical Faculty of Leiden University in 1992. Since 1994 he is head of the Forensic Laboratory for DNA Research, the only independent DNA contra-expertise laboratory in the Netherlands. This lab is part of the Department of Human Genetics, Center of Human and Clinical Genetics, Leiden University Medical Center. The FLDO is one of leading laboratories in the introduction of genetic markers from the human Y-chromosome. For this work he is the joint recipient (together with L Roewer and M Kayser) of the Konrad Händel price, awarded by the Deutschen Gesellschaft fur Rechtsmedizin, Hannover, 16 September 1998. His current research interests aim for a better understanding of population genetics and evolutionary genetics. Apart from teaching responsibilities in these two fields, he is also very active in various teaching courses relating to the forensic application and interpretation of DNA analyses. He has published well over 120 peer-reviewed articles many articles in the Dutch language on the topic of forensic DNA research in popular and semi-scientific journals.
The understanding of fundamental population genetics and evolutionary genetics is rapidly growing, mainly through the development of new large-scale genotyping methods. These techniques could ultimately facilitate the rapid detection of genome-wide genetic differences among human populations. One of the exciting applications would be in the field of forensic research, where the development of a set of markers by means of which predictions concerning external characteristics of an individual could be made (colour of hair, skin, eye, etc.), would possibly facilitate the tracing of offenders. Also predictions about the geographical origins of an individual could be possible once reliable markers have been found. In the lecture, both technical and ethical issues will be covered.
Here is just one connection. Apart from forensics, Pete the Knife and his colleagues also collaborate with George Vogler:
Beekman M, Posthuma D, Heijmans BT, Lakenberg N, Suchiman HE, Snieder H, De Knijff P, Frants RR, Van Ommen GJ, Kluft C, Vogler GP, Slagboom PE, Boomsma DI. Combined association and linkage analysis applied to the APOE locus. Genet Epidemiol. 2004 May;26(4):328-37.
Beekman, M. , B.T. Heijmans , N.G. Martin , J.B. Whitfield , N.L. Pedersen , U. DeFaire , H. Snieder , N. Lakenberg , H.D. Suchiman , P. de Knijff , R.R. Frants , G.B. van Ommen , C.C. Kluft , G.P. Vogler , D.I. Boomsma and P.E. Slagboom (2003). "Evidence for a Qtl on Chromosome 19 Influencing Ldl Cholesterol Levels in the General Population." European Journal of Human Genetics 11(11):845-850.
Beekman, M. , N. Lakenberg , S.S. Cherny , P. de Knijff , C.C. Kluft , G.B. van Ommen , G.P. Vogler , R.R. Frants , D.I. Boomsma and P.E. Slagboom (2001). "A Powerful and Rapid Approach to Genome Scanning Using Small Quantities of Genomic DNA." Genetical Research 77:129-134.
George is Professor of Biobehavioral Health and Director, Center for Developmental and Health Genetics at PSU and his research interests are: Genetic epidemiology of complex traits; quantitative trait loci mapping; cardiovascular disease; methodological issues in genetic models and structural equation models; behavioral moderation of expression of biological traits.
http://athens.pop.psu.edu/CtrPRI/DirBio.cfm?PeopleID=57
George has co-authored 15 papers with DC Rao, the (former?) DNAP Scientific Advisor; and 3 with JR Fernandez, the current Shriver collaborator.
A couple of names to look out for.
Here's an interview (in German) with Mark Benecke published in GIS April/May 2004. The article mentions DNAPrint and several observations are made. He says that hair and eye color are of limited interest to Police. It also looks as if ethnic markers have been used in investigations in the US and the Netherlands (but the Google translation I read might have been misleading and it might refer to countries where legislation permitting such analysis exists). The Google "translation" is the second link.
http://www.gen-ethisches-netzwerk.de/gid/TEXTE/ARCHIV/PRESSEDIENST_GID163/SCHWERPUNKT163.HTML
http://translate.google.com/translate?hl=en&sl=de&u=http://www.gen-ethisches-netzwerk.de/gid....
frog, you seem to see no value in preemptive testing in the general population (which does admittedly have attendant logistical issues), and some potential value in crime scene analysis after the event. I thought that I would suggest some more limited cases for your consideration, which might better illustrate the "opportunity" related to DNAWitness. Do you see any possible role for the product as one component of a positive vetting regime in the following instances:
- Applications for commercial airline flight training
- Applications for employment at a Biosafety Level 3 (or above) facility
- Applications for employment at a nuclear facility
I'm sure you can think of some other similar examples.
According to Mark Shriver's CV...
http://www.anthro.psu.edu/cv/shriver.pdf
...we are still waiting for the following papers which I can't see on PubMed:
Shriver, M.D., Kennedy, G.C., Parra, E.J., Lawson, H.A., Huang, J., Makova, K., Akey, J.M., and Jones, K.W. (in review) The Genomic Distribution of Human Population Substructure.
Bonilla, C., Parra, E.J., Shriver, M.D. (in review) Admixture analysis of a rural population of the state of Guerrero, Mexico.
Fernández, J.R. and Shiver, M.D. (in review) Using genetic admixture to study the biology of obesity traits and to map genes in admixed populations.
The first one in particular is interesting as it involves people from Affymetrix...
OT Ann - they have people much brighter than me there already lol!
Yet another Shriver paper:
Bonilla C, Shriver MD, Parra EJ, Jones A, Fernandez JR. Ancestral proportions and their association with skin pigmentation and bone mineral density in Puerto Rican women from New York city. Hum Genet. 2004 Apr 30.
National Human Genome Center, Howard University, DC 20060, Washington, USA.
Hispanic and African American populations exhibit an increased risk of obesity compared with populations of European origin, a feature that may be related to inherited risk alleles from Native American and West African parental populations. However, a relationship between West African ancestry and obesity-related traits, such as body mass index (BMI), fat mass (FM), and fat-free mass (FFM), and with bone mineral density (BMD) in African American women has only recently been reported. In order to evaluate further the influence of ancestry on body composition phenotypes, we studied a Hispanic population with substantial European, West African, and Native American admixture. We ascertained a sample of Puerto Rican women living in New York ( n=64), for whom we measured BMI and body composition variables, such as FM, FFM, percent body fat, and BMD. Additionally, skin pigmentation was measured as the melanin index by reflectance spectroscopy. We genotyped 35 autosomal ancestry informative markers and estimated population and individual ancestral proportions in terms of European, West African, and Native American contributions to this population. The ancestry proportions corresponding to the three parental populations are: 53.3+/-2.8% European, 29.1+/-2.3% West African, and 17.6+/-2.4% Native American. We detected significant genetic structure in this population with a number of different tests. A highly significant correlation was found between skin pigmentation and individual ancestry ( R(2)=0.597, P<0.001) that was not attributable to differences in socioeconomic status. A significant association was also found between BMD and European admixture ( R(2)=0.065, P=0.042), but no such correlation was evident with BMI or the remaining body composition measurements. We discuss the implications of our findings for the potential use of this Hispanic population for admixture mapping.
A selection of past quotes:
"By marketing our platform directly to the public, we intend to make comprehensive genotype screening solutions accessible to people all over the world via the Internet."
"Accessing of the data is going to be accomplished through the internet most likely. First of all the hospital is going to need to know where to genotype a patient, where to look in their chromosome. We will tell them from our results. Our software will be a sort of an operating system. They want to produce a test for Provacol for patients, we'll look up Provacol and see what markers they need to screen. They'll order the test kits from one of our partners, commercialization partners. They'll perform the test at their hospital and they'll have raw genetic data from the patient. Which they won't know what to do with. What they're going to do with it is use our operating system to push it through the internet, compare it against our population level solutions, and to basically classify the patient based on our results."
"The Orchid UHT can process up to 125,000 genotypes per day. More than adequate for immediate processing needs. The bottleneck is in Buccal sample preparation. That is a manual process, is time consuming, and limits overall throughput of the lab."
I believe they work 8 hour shifts so that works out at 4.3 genotypes per second or one every 0.23 seconds. Using a 171 marker test that means some 39 seconds for genotyping plus communication time plus automated buccal swab preparation (the latter would be done at the front end). That's with current technology of course. What if this was a DNA chip based solution rather than an Internet based one? We have already been told that version 3.0 will have to be chip based due to the number of markers. A number of possibilities, it just needs a bit of imagination.
Does it seem more feasible if the test is run in real-time?
You would presumably test selected individuals at the point of entry, and "extended" immigration interviews would await lucky contestants whose results differed from their purported origin? You tell me.
frog, a typical post from you. Leaving aside your innuendo, let me invite you to reconsider this sentence:
"Anyone from the geological regions in question who is even remotely suspicious is already being tracked by homeland security."
This assumes that Homeland Security is aware that individuals in question are indeed from the geographical region(s) concerned. BTW you seem to have a blindspot regarding geological and geographical - this is the second time you have made that mistake. Perhaps there are potential applications related to e.g. cross-checking ancestry against self-reported geographical origin for visa applicants?
This is interesting. Yesterday's PR looked a little odd in isolation and it did suggest that something else was to follow it.
Here is some background to this:
http://www.investorshub.com/boards/read_msg.asp?message_id=1837734
"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."
"The 3.0 version will subdivide those four categories into more groups."
So, it looks as if they are now instead positioning 2.5 as an intermediate intra-continental test rather than waiting for 3.0. I wonder whether we might also see another follow-on announcement related to usage of the test from another agency...
USC Department of Biological Sciences seminars
http://biosci.usc.edu/seminars/mcb.asp
5/6/2004, Thu, 2:00 PM
Choosing informative markers for inference of ancestry
by Noah Rosenberg / USC
http://www-hto.usc.edu/~noahr/projects.html
Current areas of interest:
The shapes of gene trees from one or more species.
Genotype change rates and serial samples in molecular epidemiology.
Human population structure and genetic history, and information content of genetic markers about ancestry.
Rosenberg NA, Li LM, Ward R, Pritchard JK. Informativeness of genetic markers for inference of ancestry. Am J Hum Genet. 2003 Dec;73(6):1402-22.
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.gs.washington.edu/news/oldseminars.htm
Wed, February 25 - Dr. Noah Rosenberg, Research Associate, Program in Molecular and Computational Biology, University of Southern Calfornia
"Genome-wide Analysis of Human Variation and Population Structure"
The 5th HUGO Pacific Meeting and 6th Asia Pacific Conference on Human Genetics
November 17th to 20th, 2004. Biopolis, Singapore
http://www.hugopacific.com/home.htm
Speakers include...
Dr Tony Frudakis (whose country is wrongly given as Australia)