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

VIEWPOINT: Personalized Genomic Information

Wednesday, February 03, 2010

Preparing for the Future of Genetic Medicine

Alan E. Guttmacher et al.

Nature Reviews Genetics 11, 161-65 (February 2010)

Four experts with different insights into the field of genomic medicine answer questions about the prospects for using this type of information. The issues range from scientific to ethical and logistical.

 
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Does Not Compute: Putting Three Sciences Together to Map Migrations in East Asia

Wednesday, February 03, 2010

Book:  Past Human Migrations in East Asia. Matching Archeology, Linguistics and Genetics, ed. Alicia Sanchez-Mazas et al. Routledge, Taylor & Francis, 2008.

According to the reviewer of this compilation of interdisciplinary studies, Frank Roels, writing in European Journal of Human Genetics 18:262f., the three approaches are incommensurate because of differing timeframes and rates of change. Their models cannot be harmonized with sufficient reliability to write a comprehensive, persuasive history of human migrations and settlements in East Asia.

 
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Book Review: The Language of Life by Francis S. Collins

Wednesday, February 03, 2010
Nature 463/298-299 (21 January 2010)

Abdallah S. Daar in reviewing this new book by NIH director Francis Collins maintains that “we have entered the era of rapid, inexpensive genetic testing and genome sequencing” and must simply come to terms with the phenomenon of personal genomics and consumer genetics. In the next decade, he predicts, the cost of sequencing a human genome will drop to a few hundred dollars. The cost for the Human Genome Project was about $3 billion over 13 years.

The Language of Life:  DNA and the Revolution in Personalized Medicine

By Francis S. Collins

Harper/Profile. 2010. 368 pp/288 pp.

$26.99.
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Neandertals Had Symbols, But Did They Use Human Language?

Thursday, January 14, 2010
Neandertal Jewelry Shows Their Symbolic Smarts

Michael Balter

Science 15 January 2010:
Vol. 327. no. 5963, pp. 255 - 256
DOI: 10.1126/science.327.5963.255

A handful of marine mollusk shells, possibly used as necklaces and paint cups, shows that Neandertals expressed themselves symbolically, say the authors of a paper published online this week in the Proceedings of the National Academy of Sciences. They argue that the findings suggest that social and demographic factors, rather than cognitive differences, best explain why so-called modern behavior was relatively rare among Neandertals.

Read abstract.
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Hunter Gatherer DNA from the Don

Saturday, January 09, 2010
The successful extraction of ancient DNA has been a rare accomplishment in genetic circles until recently. In the journal Current Biology, a German-Russian team details how it was possible to avoid the common pitfalls of contamination with modern human DNA in the instance of a 30,000 year-old hunter gatherer's grave in Russia. Svante Paabo, from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and colleagues used the latest DNA sequencing techniques to study genetic information from human remains unearthed in 1954 at Kostenki, Russia. According to a report by the BBC, the hunter gatherer's mitochondrial DNA type was U2. Haplogroup U is seen as a predecessor dominant type among Europeans before the arrival of agriculture and Middle Eastern culture about five to seven thousand years ago. It is hoped the new expertise will help unlock the secrets of other examples of ancient DNA.

Title and authors of the article:  A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia, by Johannes Krause, Adrian W. Briggs, Martin Kircher, Tomislav Maricic, Nicolas Zwyns, Anatoli Derevianko and Svante Pääbo 

Summary The recovery of DNA sequences from early modern humans (EMHs) could shed light on their interactions with archaic groups such as Neandertals and their relationships to current human populations. However, such experiments are highly problematic because present-day human DNA frequently contaminates bones. For example, in a recent study of mitochondrial (mt) DNA from Neolithic European skeletons, sequence variants were only taken as authentic if they were absent or rare in the present population, whereas others had to be discounted as possible contamination. This limits analysis to EMH individuals carrying rare sequences and thus yields a biased view of the ancient gene pool. Other approaches of identifying contaminating DNA, such as genotyping all individuals who have come into contact with a sample, restrict analyses to specimens where this is possible and do not exclude all possible sources of contamination. By studying mtDNA in Neandertal remains, where contamination and endogenous DNA can be distinguished by sequence, we show that fragmentation patterns and nucleotide misincorporations can be used to gauge authenticity of ancient DNA sequences. We use these features to determine a complete mtDNA sequence from a ∼30,000-year-old EMH from the Kostenki 14 site 

Kostenki 14 (Vladimir Gorodnianskiy)
Reconstruction of the hunter gatherer.  Courtesy BBC News.
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Bradshaw Foundation, Stephen Oppenheimer, INORA

Wednesday, December 30, 2009
Bradshaw Foundation
www.bradshawfoundation.com

A Phoenix business contact recently turned me on to the most fascinating website I have yet encountered devoted to prehistoric times and the migrations of humans. Named after the age-old and stunning Bradshaw rock art inscriptions in Australia, the Bradshaw Foundation focuses on rock art around the world and the brilliant discoveries of Oxford geneticist Stephen Oppenheimer. Its website even offers films and podcasts. Here is how the organization describes itself:

The Bradshaw Foundation until now has been discovering, documenting and preserving ancient rock art around the world. In October 2004 it received the Science & Technology Web Award 2004 (Anthropology and Paleontology) from Scientific American Magazine. The award coincides with the launch of the Bradshaw Foundation's latest development on its website: "The Journey of Mankind -The Peopling of the World". The Foundation has created an interactive map charting the global journey of modern humans over the last 160,000 years. It demonstrates the interactions of migration with climate over this period. Based on a synthesis of the mtDNA and Y chromosome evidence with archaeology; climatology and fossil study; Stephen Oppenheimer has tracked the routes and timing of migration, placing them in context with ancient rock art around the world.

Another delight I discovered at the Bradshaw Foundation's site was INORA, International Newsletter on Rock Art.

With 3 publications per year, in French and English, INORA presents an international forum on ancient rock art and associated areas of archaeology, paleaontology and anthropology.

Edited by Dr Jean Clottes, Former Director of the Chauvet Research Team, funded (or subsidized, or sponsored) by the Ministère de la Culture and the Département de l’Ariège, the newsletter presents the latest discoveries of rock art from around the world. It provides a platform for discussion and debate of current theories and controversies. It examines past, present and future documentation and dating techniques, and their interpretation. It provides online database sources for related literature. The bound copy contains photography, illustrations and bibliographies.

DNA Consultants customers and especially those who have taken the DNA Fingerprint Test will want to check out these resources for understanding human prehistory posthaste! The Bradshaw genetic journey is far more detailed, absorbing and convincing than National Geographic's National Genographic Project. 

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Newest Research Confirms Beachcomber Route to Asia out of Africa

Thursday, December 10, 2009
Other Companies Must Revise Their Human Migration Maps

Since Stephen Oppenheimer's The Real Eve suggested that the main out-of-Africa migration of humans proceeded across the mouth of the Gulf of Suez and around the coasts of Arabia, India and Southeast Asia (the "beachcomber route"), controversy has raged about the origin of Asians, whether they split off from the first out-of-Africa groups, sometimes called macro-haplogroup M, in the north central Asian highlands or the Middle East or elsewhere. A massive project spearheaded by the Chinese has put that question to rest. The 40-institution HUGO Pan-Asian SNP Consortium "strongly concludes the southern route made a more important contribution to East and Southeast Asian populations than the northern route," says Li Jin, a population geneticist at Fudan University in Shanghai, China. Jin was one of the lead authors of a study reported in Science, vol. 326, no. 5959, p. 1470, "SNP Study Supports Southern Migration Route To Asia," by Dennis Normile.

DNA Consultants has always followed Oppenheimer's model of the settlement of Asia, but other companies, including the National Geographic Genographic Project with over 200,000 customers purchasing their product, inform their customers differently. Most human migration maps displayed by DNA companies and the news media show Asians splitting off from Europeans and Native Americans in the northern latitudes of Central Asia and do not depict a southern "beachcomber" route at all.

Newly proven southern migration routes.

In July of this year, DNA Consultants discovered ethnic markers it released in its 18 Marker Ethnic Panel that prove a southern divide and origin for Asian populations as in the new study.

According to the Science report, "Anthropologists, ethnographers, and linguists have long struggled to understand the patchwork-quilt diversity of Asia.  Indonesia alone claims some 300 ethnic groups; the Philippines has 180 native languages and dialects. Where did they all come from?"

So the previously dominant theory of two major waves of migration from the Middle East must now yield to just one initial migration along the coastal route with populations moving north into East Asia from India and Southeast Asia (see map).

The new study is vindication for the Chinese genetics community, which has often been dismissed and rejected by European and American geneticists. Vincent Macaulay, co-author with Martin Richards of the seminal paper followed by most DNA testing companies, " Tracing European founder lineages in the Near Eastern mtDNA pool," (American Journal of Human Genetics, 67, 1251-1276), when asked about the new findings admitted that the southern coastal route now "seems very strong," as quoted in Science.






















Human Migration Map from DNA Consultants' 18 Marker Ethnic Panel.

The study used samples from more than 1900 individuals representing 73 populations and involved 93 researches at 40 institutions in 11 countries and regions in Asia. It was "conceived by Asians in Asia and executed, funded, and completed by an Asian consortium," said Edison Liu, executive director of the Genome Insitute of Singapore. Researchers screened each individual for more than 50,000 SNPs.
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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. 



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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.


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Acadian Anomalies

Monday, November 30, 2009
Anomalous Native American Lineages

Now Identified Also among Micmac Indians

After posting “Anomalous Mitochondrial DNA Lineages in the Cherokee,” and after being interviewed on the subject by an Internet radio show host, I was contacted by participants in the Amerindian Ancestry out of Acadia Project who were struck by similarities in results for the two groups.

Established in 2006, the Amerindian Ancestry Out of Acadia DNA Project mission is to research and publish the mtDNA and Y chromosome genetic test results of site participants who descend from persons living in Nova Scotia and surrounding environs in the 17th and 18th centuries, focusing specifically upon the early population of l'Acadie. As part of the mission, the Project develops a database of published mtDNA and Y Chromosome test results and encourages the sharing of this information among other similarly focused studies for the purposes of comparison and the advancement of science and research.

According to Project Administrator Marie A. Rundquist, “We descend from both Amerindians (mostly Mi’kmaq) and the early French settlers who arrived in Port Royal in the 1600s, many of them single French men who married Amerindian wives, whose families would become pioneers of the New World. Our family lines have extended well-beyond the original boundaries of what was known to the French as Acadia, but to our AmerIndian ancestors as Mi’kma’ki, as our ancestors settled the outer-reaches of Nova Scotia, including Cape Breton, Newfoundland, New Brunswick, Prince Edward Island and Quebec. Our family lines continue to extend, traversing the entire North American continent and beyond.”

She adds, “Many who live in the United States trace their genealogies back to the first Acadian AmerIndian immigrants who arrived in Louisiana after being deported from Nova Scotia by the British in 1755 (in the "Grand Deportation') -- and belong to a ‘Cajun’ community known worldwide for its food, flair, fun, and love of all things French.

Several members belong, as it turns out, to rare haplogroups X, U, and other "anomalous types" as compiled by me for DNA Consultants customers and reported in the previous blog post.

Some highlights from the study of Cherokee descendants are:

  • H, the most common European type today, is virtually absent, demonstrating lack of inflow from recent Europeans
  • J present in lines explicitly recognized to be Cherokee
  • X the signature of a Canaanite people whose center of diffusion was the Hills of Galilee, hypothetically correlating with Jews and Phoenicians
  • U suggesting Eastern Mediterranean, specifically Greek
  • K also suggesting Eastern Mediterranean or Middle Eastern, hypothetically correlating with Jews and Phoenicians
  • T reflecting Egyptian high frequencies found almost nowhere else

According to Elizabeth Caldwell Hirschman, the Cumberland Gap mtDNA Project with overlapping territory with the Cherokee and Melungeon homelands in the Southern Appalachian Mountains also shows elevated frequencies of T. Project administrator Roberta Estes recently published the results of a large study of Native American Eastern Seaboard mixed populations “in relation to Sir Walter Raleigh’s Lost Colony of Roanoke” in the online Journal of Genetic Genealogy, 5(2):96-130, 2009. Estes is a board member of the Melungeon Historical Society and has an introduction with links to the study and its data on the society’s blog, titled “Where Have All the Indians Gone?”

Harvard University professor Barry Fell in his book Saga America first published in 1980 presented historical, epigraphic, archeological and linguistic evidence suggesting links between Greeks and Egyptians and the Algonquian Indians of Nova Scotia, Acadia and surrounding regions around the mouth of the St. Lawrence Seaway, particularly the Abnaki ("White") and Micmac Indians. He noted as early as 1976 in his previous study America B.C. that the second century CE Greek historian Plutarch recorded “Greeks had settled among the barbarian peoples of the Western Epeiros (continent).” Fell inferred from Plutarch’s passage “these Greeks had intermarried with the barbarians, had adopted thier language, but had blended their own Greek language with it.” In an appendix, he assembled extensive word-lists comparing Abenaki and Micmac vocabulary in the areas of navigation, fishing, astronomy, meteorology, justice and administration, medicine, anatomy, and economy with virtually identical terms in Ptolemaic Greek. One example is Greek ap’aktes Abenaki/Micmac ab’akt English “a distant shore.”

Fell’s work was continued by John H. Cooper, “Ancient Greek Cultural and Linguistic Influences in Atlantic North America,” NEARA JOURNAL 35/2.

Acadia project’s website is: http://www.familytreedna.com/public/AcadianAmerIndian/default.aspx.
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