18

Sequencing the Genome of Sitting Bull and Other Famous People

ScienceNews reports that researchers led by Eske Willerslev at the University of Copenhagen are attempting to sequence the genome of legendary Native American “Sitting Bull” (see “Genome of a Chief”).

Earlier this year (2010), Eske Willersleve announced the successful sequencing of approximately 80% of the genome of “Inuk,” a man from Greenland who left behind a few small fragments of bone and four hairs frozen in permafrost when he died about 4,000 years ago (see “Long-Locked Genome of Ancient Man Sequenced”).  Using these ancient DNA sequencing techniques, Willersleve’s group is analyzing DNA from other samples.

One of these samples is a lock of hair from Sitting Bull.

Sitting Bull (c. 1831 – Dec. 15, 1890) was a Hunkpapa Lokota Sioux born in South Dakota.  Sitting Bull played an important role in the June 25, 1876 Battle … Click to read more!

7

A Review of Family Tree DNA’s Family Finder – Part II

Last week I wrote about the results of my Family Finder autosomal DNA test by Family Tree DNA (see “A Review of Family Tree DNA’s Family Finder – Part I“).  The Family Finder test uses a whole-genome SNP scan to find stretches of DNA shared by two individuals, thus identifying your genetic cousins (and will soon include the Population Finder analysis of admixture percentages).  I currently have over 33 genetic cousins in Family Finder, and I’m working with them to identify our common ancestor(s).

The Affymetrix microarray chip used by FTDNA includes over 500,000 pairs of SNPs located on the X chromosome and the autosomes (no Y chromosome SNPs).  Via SNPedia:

FamilyTreeDNA uses an Affymetrix Axiom CEU microarray chip with 3,269 SNPs removed (563,800 SNPs reported) for autosomal and X (but not Y or mitochondrial) ancestry testing for $289. Other sources have cited 548011 snps. This platform tests 1871 of the 12442 snps in SNPedia.

FTDNA states that the Family Finder test is not intended to be medical.  From the FTDNA FAQ:

Question: Is the Family Finder test medical?

Answer: No, it is not.

This is entirely accurate of course; FTDNA does not analyze the test results for health, traits, or other medically-relevant … Click to read more!

13

How Neanderthal Are You?

On May 6, 2010, the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany presented the world with a draft of the genome sequence of the Neanderthal (press release here (pdf) and full article here (free), NYT article here).  As part of the announcement, the team presented their conclusion that 1% to 4% of the genome of non-Africans is derived from Neanderthals:

“An initial comparison of the two sequences has brought some exciting discoveries to light. Contrary to the assumption of many researchers, it would appear that some Neandertals and early modern humans interbred. According to the researchers’ calculations, between one and four percent of the DNA of many humans living today originate from the Neandertal. ‘Those of us who live outside Africa carry a little Neandertal DNA in us,’ says Svante Pääbo.  Previous tests carried out on the DNA of Neandertal mitochondria, which represents just a tiny part of the whole genome, had not found any evidence of such interbreeding or ‘admixture.’”

Once this study came out, I knew it was only a matter of time before companies began offering tests that examined the percent of Neanderthal contribution to a test-taker’s genome.

The Neanderthal Index

In May 2010, DNA Consultants began offering a test called the Neanderthal Index.  Priced at USD $90.00, the test purports to “estimate how much Neanderthal is in your ancestry.”  From the test description:

“Created in response to the phenomenal interest generated by the revelation in scientific journals on May 8, 2010 that most humans are part Neanderthal (Green et al), our autosomal DNA Neanderthal Index can be added to your DNA Fingerprint Test or DNA Fingerprint Plus. It reports any strong matches you have with populations identified as Archaic, those preserving the earliest earmarks of interbreeding between Neanderthals and humans (Homo sapiens sapiens). The stronger the match the higher the likelihood that your ancestors gave you Neanderthal genes.”

The site also provides an FAQ page, and a sample test result (pdf).  The test returns results on a scale of 0.1 to … Click to read more!

11

American Society of Human Genetics Publishes Updated Genetic Ancestry Testing Statement

Today at noon, the American Society of Human Genetics lifted an embargo on “Inferring Genetic Ancestry: Opportunities, Challenges, and Implications (pdf),” which will be published in the May 14th issue of the American Journal of Human Genetics.

This paper is a follow-up to a 2008 paper called the “ASHG Ancestry Testing Statement and Recommendations” in which a committee from the ASHG addressed concerns about the claims made by genetic ancestry testing companies.  I wrote an article here on the blog at the time – The ASHG Ancestry Testing Statement and Recommendations – that highlighted a number of concerns I had about the statement and the recommendations.

When I wrote the November 13, 2008 blog post, I began by pointing out my personal positions, which have largely remained unchanged in the intervening 1.5 years:

  • After years of experience in this field, I am a proponent of genetic genealogy testing, a scientific endeavor that has been utilized by more than 800,000 customers.
  • I believe that education, not more government regulation, is the most efficient and appropriate answer to the issues raised by the authors of the paper.
  • I believe that autosomal genetic genealogy testing is in its infancy and should only be used with the understanding that the results are only extremely rough estimates that are subject to change as the field develops.

The 2010 paper begins with a brief introduction and a table of most of the companies currently … Click to read more!

2

Announcing the GET Conference 2010


get-genomes-environments-traits_1266501683140
Daniel Vorhaus of the Genomics Law Report is also a member of the steering committee of the GET (“Genomes, Environments, Traits) Conference 2010. This unique conference, to be held on Tuesday, April 27, 2010 will gather together some of the biggest names in personal genomics, as well as most of the limited number of the people who have released their entire genomes to the public. Tickets for the conference go on sale today here.

As part of the GET Conference 2010, the new BioWeatherMap initiative will officially launch. According to the project’s website, BioWeatherMap is “a global, grassroots, distributed environmental sensing effort aimed at answering some very basic questions about the geographic and temporal distribution patterns of microbial life. Utilizing the power of high-throughput, low cost DNA sequencing and harnessing the drive of … Click to read more!

4

The Future of Genetic Genealogy – Tracing DNA To Individual Ancestors

I once told someone that in addition to learning about their ancient origins (such as Y-DNA and mtDNA haplogroups), many genetic genealogists would ideally like to match every portion of their DNA with the contributing ancestor.  Although this might seem to be beyond the reach of current genetic ancestry testing, it has actually already begun.  The family compare function of 23andMe, for example, is already being used by genetic genealogists for just this purpose; people who have matching DNA segments can compare ancestry and attempt to identify the ancestor who might have contributed the DNA.

For obvious reasons, medical geneticists have for many years been using genealogy to trace founder mutations in populations.  For example, in 2008 scientists … Click to read more!

1

Australian Research Study on Consumer Genomics‏

As part of her doctoral research, Sudeepa Abeysinghe is asking people who have purchased genomic tests to complete the “User Experiences of Direct-to-Consumer Genomic Testing Survey”.  According to Sudeepa, the survey focuses on the consumer experience and is completely independent of any testing company.

Although I’m late on reporting this (it was already covered by GenomeWeb, for example), I thought I would mention it in case anyone has missed the previous coverage and might be interested in completing the survey.

This is an opportunity for genetic genealogists to share their experiences and voice their thoughts regarding DTC genomic … Click to read more!

11

Family Tree DNA Discovers Y-DNA Signature That Might Represent the Prophet Mohammed

DNA An article in the United Arab Emirate newspaper The National (wikipedia) does a terrific job of highlighting recent research from Family Tree DNA.  The story – “DNA could illuminate Islam’s lineage” – discusses research that has attempted to elucidate the Y-DNA signature of Mohammed.  Although Mohammed did not have a son, he had a daughter who married her paternal second cousin, thus passing to Mohammed’s grandchildren the same Y-DNA.  From the article:

“For almost 1,600 years, the title Sharif, Sayyed, or Habib has been bestowed on Muslims who have been able to trace their roots back to the Prophet Mohammed through intricate family trees, oral histories and genealogical records. But now an American DNA lab says it may have identified the DNA signature of descendants of the Prophet Mohammed, and perhaps the prospect of a direct, more accurate means of confirming or identifying such a connection.”

The caveat, as the story briefly mentions by the phrase “if their oral tradition is accurate”, is that no one has an authenticated DNA sample directly from Mohammed.  If there were, this type of research would not be needed.  Instead, the conclusion that it might be Mohammed’s Y-DNA is based on testing individuals who … Click to read more!

2

The Close Cousins DNA Project – A Request for Help

Chimpanzee
Image by Aaron Logan

Roughly 6 million years ago, the Hominini subtribe of the Hominidae family tree (the so-called “great apes”) diverged into two known branches, with one branch (genus Pan ) resulting in modern-day Chimpanzees and Bonobos, and the other branch (genus Homo) resulting in modern-day humans.

Since there has only been 6 million years of divergent evolution, Chimpanzees/Bonobos and Humans share a great deal of DNA sequence in common (although estimates vary widely and typically depend on what, exactly, is being considered in the comparison).

The Close Cousins DNA Project

On May 31, 2008, the Close Cousins DNA Project was launched by Bill Davenport as a result of a discussion on the Genealogy-DNA mailing list regarding the relatedness of human and chimpanzee Y-DNA.  From the launching … Click to read more!

1

Interviews with 23andMe Customers

Image representing 23andMe as depicted in Crun...
Image via CrunchBase

DAVIDE at the European Genetics and Anthropology Blog recently posted two interviews (here and here) with customers of 23andMe’s large-scale genome scanning service, one from Finland and one from the U.S.

It’s very interesting to see the responses of these anonymous individuals, particularly since they are from different countries.

For example, both were asked why they decided to purchase the 23andMe test – “Was it to test your ancestry or genetic health risk factors?”  Interestingly, for both individuals ancestry was the motivating factor behind testing.  More support for my conclusion that these companies should strongly promote the ancestral aspects of their products.

Other Questions

Here are a few examples of other questions … Click to read more!