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review of scientific and news articles on dna testing and popular genetics

Fifteenth Anniversary of New Genome Sequencing

Monday, November 21, 2011

At a time when it seemed that American science had bitten off more than it could chew with the Human Genome Project, Craig Venter and his innovative company published "A New Strategy for Genome Sequencing." Appearing in the journal Nature in 1996, the Venter multi-center approach bypassed laborious gene mapping and allowed the HGP to meet its goal of full sequence information on the human genome in 2000.

"In the race to sequence the human genome," write the editors of Nature's DNA Technologies Milestones, "research groups had to choose between the random whole genome shotgun sequencing approach or the more ordered map-based sequencing approach." The choice of randomness versus order was present from 1982, but the Venter strategy was resisted for many years. Finally, in 1996 it was accepted and given an equal emphasis with the more orthodox approach.

After a standoff between the two groups of scientists, "a showdown ensued, with the biotechnology firm Celera Genomics wielding whole-genome shotgun sequencing and the International Human Genome Sequencing Consortium wielding map-based sequencing. Yet when the dust settled, it was a draw -- both groups published their initial drafts of the human genome concurrently in 2001."

The maverick technology helped make high throughput genomic sequencing at commercial labs an economy reality and gave birth to a range of new DNA tests within the reach of ordinary consumers like you and me. Today, fifteen years later, those interested in autosomal ancestry testing and personal genomics have biologist and entrepreneur Craig Venter and his irascible persistence as a scientific pioneer to thank.




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US, EU Move to Regulate Direct-to-Consumer Genetic Testing

Sunday, November 28, 2010

Discussion is accelerating in the United States and European Union to regulate private genomic testing that provides consumers medical information, according to Science magazine and the European Journal of Human Genetics. No mention is made in the reams of white papers about ancestry testing, but some of the pitfalls and bureaucratic morasses in the thinking about true genetic/medical testing are fairly ominous, if not silly.

"Although there has been speculation about the potential psychosocial harms of testing [that is, genomic medical testing], such as an increase in anxiety or encouragement of fatalistic behavior, there are, to date, few studies addressing these concerns," writes the reporters for Policy Forum in the Oct. 8 issue of Science. "The limited evidence tends to be reassuring, even for risk information associated with relatively serious ailments...however, the scope for potential harm from unnecessary or unproven treatment after genetic risk assessment is an important unstudied question" (pp. 181f.).

We commend scientists and physicians for finding a new field of study divorced from reality but have to wonder what they will do about ancestry testing once they have conquered and tamed Frankenstein's elder monster. We suggest the following guidelines:

  • Labeling on Internet sites and Zen Shopping Carts that explicitly states, "The claims for this ancestry product have not been evaluated by the U.S. Government Accountability Office (GAO), U.S. Federal Trade Commission (FTC), House Energy and Commerce Committee, Food and Drug Administration, National Institutes for Health or Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA 98195 USA."
  • Predictive ancestry information may be hazardous to your progeny.
  • No animal has been harmed in the production or clinical evaluation of this ancestry test.
  • If you discover you have ancestry you did not expect, take a deep breath. Then take a healthy dose of skepticism, followed by two aspirins and a glass of water.
We're waiting for the next gambit from the genius bar in Washington!
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Autosomal DNA Testing is Newest Wave

Wednesday, April 07, 2010

DNA Consultants’ 18 Marker Ethnic Panel Reveals Native American, Jewish, Other Hard-to-Find Lines in Your Family Tree

PHOENIX – (April 7, 2010) – The market leader in autosomal DNA testing for ancestry, DNA Consultants announced that it has introduced the latest enhancement to its DNA Fingerprint Test™ ancestry tool. The add-on to its popular all-in-one ancestry tracing product is called the 18 Marker Ethnic Panel and sells for $50.00.

“With the 18 Marker Ethnic Panel, you can easily verify Native American, Ashkenazi Jewish, African and other ethnic lines that may be hidden in your family tree,” said Donald Yates, the company’s founder and principal scientist. “If you get a check mark for Native American marker I or II from either parent, you have Native American ancestry…it’s that simple.”

Like the DNA Fingerprint Test upon which it is based, the 18 Marker Ethnic Panel uses the same unique DNA profile familiar from television police shows like CSI. The markers were discovered by the company last August after statistical validation showing they reflected population splits in early human migrations.

“We’re not talking about ancient history,” said Yates. “These markers reflect recent genetic contributions to your overall ethnic mix within a relatively shallow time frame of about the last ten generations.” The reason, he said, was that Native American and the other types of DNA are “so distinctive their genetic signature lasts and never completely goes away.”

The 18 Markers include tell-tale evidence for Native American, Mediterranean, East European, Ashkenazi Jewish, Sub-Saharan African, Asian and several other definitive ethnic groups.

 “The test doesn’t tell you how much of that ancestry you have,” Yates added. “It only tells you if you have it, even if it is a minor line.” The panel also reports whether you have a given ethnic heritage from one parent or both.

To obtain the 18 Marker Ethnic Panel you must first order or submit results from a DNA Fingerprint Test. The core test is a comprehensive analysis of all your ancestral lines and gives you matches to populations and countries around the world where you have accumulations of ancestry. It sells for $250.00. Combined with the new 18 Marker Ethnic Panel, the test is called DNA Fingerprint Plus and costs $300.00.

Order online at dnaconsultants.com or call toll free 1-888-806-2588.

For more information, maps and sample report, visit DNA Consultants’ product page for the DNA Fingerprint Plus at:

http://dnaconsultants.com/_product_60282/DNA_Fingerprint_Plus.

DNA Consultants’ complete and total ancestry analysis is based on human prehistory but detects recent ethnic contributions to your DNA.

Donald Yates discovered

new DNA markers in 2009.

NATIVE AMERICAN I

NATIVE AMERICAN II (Hispanic)

EUROPEAN I ( Mediterranean )

EUROPEAN II

EASTERN EUROPEAN I

EASTERN EUROPEAN II

ASHKENAZI JEWISH I

ASHKENAZI JEWISH II

ASHKENAZI JEWISH III

TATAR/KHAZAR

ASIAN I

ASIAN II

SUB-SAHARAN  AFRICAN I

SUB-SAHARAN AFRICAN II

SUB-SAHARAN AFRICAN III

SUB-SAHARAN AFRICAN IV

AUSTRALOID/SOUTHEAST ASIAN 

FINNIC/URALIC

Ethnic admixture markers included in the DNA Fingerprint Plus 18 Marker Ethnic Panel range from Native American to Sub-Saharan African.

Press Release dated April 7, 2010

DNA Consultants

Home of the DNA Fingerprint Test

26438 N. 42nd Way

Phoenix, AZ 85050

Tel. (480) 292-9820

Website:  www.dnaconsultants.com

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Does deCODE's Bankruptcy Signal False Promise of Genetic Medicine?

Sunday, December 06, 2009
Future Shock or Future Letdown?

New York Times reporter and DNA author Nicholas Wade raised an interesting question in his report on the bankruptcy last month of Iceland's deCODE Genetics, which attempted to make it possible for an ordinary consumer to buy the latest applicable information on the connection between their personal genes and their personal disease risk. The article was titled "A Genetics Company Fails, Its Research Too Complex."

In the November 17 edition in the Science and Technology section, Wade wrote:  "The company's demise suggests that the medical promise of the human genome may take much longer to be fulfilled than its sponsors had hoped." But there may be more to the story. "The discovery that major diseases do not have any simple genetic pattern of causation has dealt a serious setback to the gene-hunting field as a whole," he added.

Signs of the deflation of the field of "gene hunting" over the past 10 years since the Human Genome Project was completed and the second phase of the HGP was announced as focusing on the "conquest" of disease are:

  • Discovery that genes are not found in continuous sequences or segments or even on the same chromosome.
  • Realization no DNA can be considered "junk DNA" and even "non-coding" loci have at least place-holder functions and hence their values are not neutral.
  • Greater respect for the role of environment in inheritance, including the nano-environments within the cell where DNA is stored and replicates.
  • Jumping the gun on numerous claims concerning genome-wide association studies in scientific journals like Nature and Science, and subsequent retractions by editors and authors.
  • Ever increasing sample sizes with ever increasing lack of robustness for the data and clarity for conclusions.
  • A push for extending genetic surveys to rare and under-represented populations, with few surprises in the analysis of the implications for medical research or consequent benefit for public health.
  • Diminishing returns on research investment (ROI) on nearly every front.
  • Not a single viable gene therapy product ever introduced.
  • Realization that only very rare genes are discoverable and selection usually takes care of them and extinguishes them over time; hence the bulk of medical research funds goes toward the rarest of cases and not widespread disease such as cancer or diabetes.
Harvard biology professor Richard Lewontin maintained as long ago as the 1960s, and continued to warn even on the eve of the completion of HGP I in 2000, that gene hunting was essentially a scientific fetish with little true power or efficacy. In 1992, he wrote "The Dream of the Human Genome" as a review article in response to The Code of Codes:  Scientific and Social Issues in the Human Genome Project, edited by Daniel J. Kevles and Leroy Hood, and seven other recently published books on the subject of genetics and medicine. The essay was reprinted in Lewontin's own book It Ain't Necessarily So (second edition, New York Review, 2001). 

I think it is time to elevate gene hunting to the danger of something beyond a harmless fetish for the members of a narrow profession or scientific sect. Its waste and failures have taken on the proportions of a national form of folly and collective denial. While huge expense and sensational efforts continue to be thrown away on the molecular biology revolution, the need to renovate our neglected infrastructure and reform political mechanisms goes unanswered. Resources that might be better allocated keep dwindling. The supposedly most advanced society in history turns a blind eye on such relatively easy measures of public health as universal health care and uncontaminated chemical-free food and water supplies. While geneticists continue to cackle about inch-sized strides in their progress toward scaling the distant peaks of genetic medicine we are slipping into the abyss of logical disconnects. 



Comments

naturopathic physician commented on 06-Dec-2009 02:34 PM

The area of personalized genomics for health intervention has not really panned out. For example, the BRCA 1 and BRCA2 genes were hailed with great fanfare a few years ago as causal agents of breast cancer. But the true percentage of BRCA 1 and 2 mutations contributing to breast cancer are between 5 and 10%, leaving an astounding 90-95% of breast cancer due to other environmental factors. It is those factors that bear looking into, not the "faulty" genes.

The available personalized SNP (single nucleotide polymorphism) panels that are available today for use without a physicians input, are leading people into unproven territory as the true associations between these SNPs and the disease they purport to contribute , is not supported by science.


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FOX News Showcases DNA Consultants

Thursday, December 03, 2009
Dr. Yates was interviewed by WBRC reporter Jeh Jeh Pruitt of FOX News Alabama at the company offices in Phoenix on October 22. The report was broadcast on affiliate stations in late November. Watch it on MyFoxAlabama.com.


Comments

M. Moore commented on 15-Dec-2009 01:44 PM

I hope there are many more interviews with DNA Consultants. Kudos and Cheers!


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Iceland's deCODE Defunct

Saturday, November 28, 2009
Icelandic genomics firm goes bankrupt

Nature 462/401 
23 November 2009

In a report by Erika Check Hayden, the journal Nature gloated that the innovative personal genomics company deCODE Genetics went out of business, leaving the disposition of valuable genetic data unclear. "After struggling financially for years, the genomics company deCODE, based in Reykjavik, Iceland, filed for bankruptcy on 16 November," wrote Hayden, who follows the genealogy-and-genetics business beat for Nature. "The question now is whether other companies looking to commercialize genomics will follow the same path." 

DNAPrint of Sarasota, Fla., went down that path last February without even an obit in scientific journals.

But according to Kari Stefansson, deCODE's CEO, the fate of the data never was in play since it belonged to individuals who had their DNA tested at their own expense with the service lab of deCODE. The lab, Islensk Erfdagreining, continues to operate today "under the same data and privacy protections as ever, rooted in the Icelandic community and within a tried and tested regulatory environment," wrote Stefansson in a comment on the online report by Nature. 

Such an accidentally-on-purpose misunderstanding is more than sloppy science journalism or bad science. It reveals the fundamental hostility of academic geneticists and related disciplines to commercializing or even popularizing DNA. Geneticists should stop thinking they are doing God's work. They should give up the illusion that the great generality of humankind can only understand, profit from and benefit from their work if they, the scientific intelligentsia, condescend to allow it and specify the conditions and goals of its use. 

Those on the payrolls of governments and public institutions have received so much money they think now they can be governors -- governors of the applications of their research.
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