Dr. Wilmot James, head of the African Genome Project and honorary professor of human genetics at the University of Cape Town, is heading a DNA collection project in South Africa.Dr. James is joined by his colleague Himla Soodyall, a scientist at the National Health Laboratory Service and an associate professor in the Division of Human Genetics at the University of Witwatersrand.On September 9th, James and Soodyall collected swab samples from a number of Capetonians.
The African Genome Project is supported by the South African genealogy website Ancestry24.com (although I was not able to find any information there).One of the goals of the project is to create a public genetic database to examine â€œhow the country became populated over thousands of yearsâ€ by filling in the gap in current DNA databases.
23andMe has been the subject of much discussion in the biotech and personalized medicine circles of the blogosphere (See here, here, here, here, here, here, here, and here for plenty of information/speculation/discussion).
In August, 23andMe announced (â€œ23andMe and Illumina Forge Consumer Genomics Goliathâ€) that they have partnered together to offer â€œconsumer genotypingâ€ – more about that in a minute.Illumina produces â€œSNP chipsâ€, chips that can test a genome for thousands of SNPs (single nucleotide polymorphisms) at a time.For example, the company has one chip that tests one million SNPs for as little as $600, and another chip that tests 550,000 SNPs (the HumanHap550) for only $300-$450.Interestingly, Illumina is also able to custom build chips to add specific SNPs if the customer so desires.Additionally, as the announcement touted, Illumina is also exploring the world of inexpensive whole-genome sequencing, suggesting that this partnership with 23andMe could transition from cheap SNP testing to cheap whole-genome sequencing at some point in the future.
A news release announces the completion of a DNA collection project by SMGF (Sorenson Molecular Genealogy Foundation) in Mongolia.The goal of the project is to study the descendants of ancient nomads from the Eurasian steppes.The collection was performed in conjunction with the National University of Mongolia and represents â€œthe most comprehensive [DNA collection project] in the history of Mongolia, incorporating all of the countryâ€™s geographic regions and major ethnic populations.â€In total, more than 3,000 DNA samples and pedigree charts were obtained from 24 different ethnic groups.
According to the news release, the â€œglobal fascination with Mongolian icons such as Genghis Khan and Attila the Hunâ€ played a role in promoting the project:
As I mentioned back in June,Â Ancestry.com has teamed up with Sorenson Genomics to offer DNA testing.Â Today I received the following notification announcing the beta launch of dnaancestry.com.Â A Y-DNA test with 33 markers will be $149, while a Y-DNA test with 46 markers will be $199 (if you look at the sample results page, you’ll see a list of the 46 markers tested).Â An mtDNA test will be $179, although the exact testing parameters for the mtDNA test are unclear at this point (the website only states that HVR1 and HVR2 will be sequenced).
Introducing DNA Ancestry
We want you to be one of the first to know weâ€™re adding a powerful new dimension to genealogical research by integrating the worldâ€™s largest online collection of historical records and family trees with DNA testing. Currently in beta, DNA Ancestry is another way weâ€™re helping people expand their family trees and connect with family across distance and time.
Yesterday we saw that many funeral directors offer DNA retrieval and storage as one of their services.Today, weâ€™ll look into the WHY of DNA storage, and bring up some of the ethical questions it raises.
Why store DNA from the recently deceased?
Undoubtedly, someone who has never heard of DNA retrieval and storage will probably ask WHY we should store a dead relativeâ€™s DNA.
The reason most commonly quoted is that the DNA can be used in the future to identify inherited traits such as genetic disorders and other phenotypic characteristics.In 2006, the New England Historic Genealogical Society published an article by Edwin M. Knights, M.D. entitled â€œDNA Banking for Medical Information.â€In the article, Dr. Knights gives a number of reasons for banking DNA from both living and deceased individuals, many of which he gleaned from the Human Genetic Society of Australasia.He states:
The field of genomics is exploding.Every day, the mysteries of our genome are revealed and we learn more and more about the power of DNA.Soon, with affordable whole-genome sequencing, we will be able to analyze our own personal genome for clues about our ancestry, our propensity for disease, and insight into our body and our personality.In fact, this is already well underway.
Undoubtedly, each of us will be faced with a decision in our lifetime – do we want to learn the secrets of our genome, or do we want to live without that knowledge, as all of our ancestors have done for millions of years.This decision is a personal one, and at this point I donâ€™t think thereâ€™s any right or wrong answer.
But what about those who are unable to make that decision?For example, an infant is unable to give consent for genetic testing, but many states in the USroutinely test newborns for genetic disorders.Today and tomorrow we will be examining another group of individuals who are not able to consent to genetic testing â€“ the recently deceased.
Dogs, just like humans, have interesting genealogical histories.And a new DNA test unveiled by DNAPrint Genomics will help you examine your dogâ€™s genetic past.The test is aimed at uncovering the relative percentages of four ancient ancestral breeds in a modern dog â€“ wolf-like, herders, hunters, and mastiff.The test, which will retail for $99, examines 204 canine Ancestry Informative Markers (AIMs) in the dog genome.For more information, go to www.doggiednaprint.com (not working as of 08/18).
â€œThe test will contain a consent form, mouth swabs, swab envelope, as well as a return envelope.Simply fill out the consent form, follow the step-by-step cheek swab instructions and send the completed consent forms and test swabs in the enclosed return envelope. Within six to nine weeks, participants will receive the results of their dog’s DNA test. These will include raw genetic data, a graphic depiction of the animal’s DNA plus information on how to interpret the results of this DNA test.â€
One of the steps in analyzing the results of a Y-DNA test is to search through Y-DNA databases to look for potential matches. These matches, depending on how well they match, might be relatives, either close or distant (in recent genealogical terms – we’re all distantly related, of course).
One of those databases is YHRD (Y-STR haplotype reference database). The project has two main goals:
- The generation of reliable Y-STR haplotype frequency estimates for minimal and extended Y-STR haplotypes to be used in the quantitative assessment of matches in forensic and genealogical casework, and;
- The assessment of male population stratification among world-wide populations as far as reflected by Y-STR haplotype frequency distributions
According to the YHRD website:
“To this end, a growing number of diagnostic and research laboratories have joined in a collaborative effort to collect population data and to create a sufficiently large reference database. All institutions contributing in this project, participated in an obligate quality control exercise.
“This database is interactive and allows the user the search for Y-STR haplotypes in various formats and within specified metapopulations. Related information i.e. STR characteristics, mutations, population genetic analyses etc. is documented.”
I recently came across a review article by Henry T. Greely, a Professor of Law, Professor (by courtesy) of Genetics, and Director of the Center for Law and Bioethics at Stanford.The article is entitled â€œThe Uneasy Ethical and Legal Underpinnings of Large-Scale Genomic Biobanks (pdf)â€ and was recently published in the Annual Review of Genomics and Human Genetics.
According to Mr. Greely, the identity of participants in large-scale genomic biobanks cannot effectively protected.A biobank is defined as a database of genotypic and phenotypic data.Using genetic information, physical information, or a combination of the two, people can identify an individual in such a large database:
â€œSomeone really interested could get a DNA sample from me – from a licked stamp, a drinking glass, or some tissue – and have it genotyped for a few hundred dollars, but few will have to go to the genomic data; the phenotypic and demographic data will often be sufficient.â€
On June 28, the University of Chicagoâ€™s Newberry Library presented a panel discussion entitled â€œGenetic Genealogy and the Ancestries of African Americansâ€ with Rick Kittles.In addition to being an associate professor of medicine at the University, Mr. Kittles is also the science director of AfricanAncestry.com.
The panel also included Christopher Rabb, a genealogist.The two discussed the difficulties facing African Americans who are interested in discovering their roots.After exhausting paper records, Mr. Rabb used DNA testing to learn more about his paternal and maternal lineages.
Despite the successes of genetic genealogy, â€œ[b]oth Rabb and Kittles recognized that genetic testing for ancestry complicates the history and social reality of race in the United States,â€ noting that 30% of African Americans descend from Europeans.