DNA Databases

The YHRD Database

Blaine Bettinger 5 Comments

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:

  1. 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;
  2. 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.” ... Click to read more!

Ethical and Legal Issues Surrounding Large-Scale Genomic Databases

Blaine Bettinger 3 Comments

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 “The Uneasy Ethical and Legal Underpinnings of Large-Scale Genomic Biobanks (pdf)” 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:

“Someone 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.” ... Click to read more!

“Genetic Genealogy and the Ancestries of African Americans” at the U of C

Blaine Bettinger 1 Comment

On June 28, the University of Chicago’s Newberry Library presented a panel discussion entitled “Genetic Genealogy and the Ancestries of African Americans” 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, “[b]oth Rabb and Kittles recognized that genetic testing for ancestry complicates the history and social reality of race in the United States,” noting that 30% of African Americans descend from Europeans. ... Click to read more!

Genetic Genealogy in the Czech Republic – A Hot Topic!

Blaine Bettinger 3 Comments

Two weeks ago, EyeonDNA posted about genetic genealogy testing in the Czech Republic by two companies, Genomac and Forensic DNA Service. A recent article in the Prague Post details the animosity over ethical concerns which exists between these two competitors.

A few days later, Ludvik Urban responded to the article via Rootsweb, and EyeonDNA shared Mr. Urban’s response with her readers. Today, you can read Genomac’s response (from one of the founders, Dr. Marek Minarik) to Mr. Urban’s concerns about the company.

Whew! Luckily, both sides were able to share their side of the story – it makes for some interesting reading!

The Genographic Project Database

Blaine Bettinger

With Friday’s release of a paper in PLoS Genetics, the Genographic Project also released a spreadsheet with the results of over 16,000 mtDNA tests, including HVS-I and SNP results (available here). In addition to sequencing the HVS-I region of mtDNA samples the Project is now testing 22 SNPs. These SNPs were chosen based upon a number of factors, which are discussed in the paper.

“Twenty one SNPs and the 9-bp deletion make up the total of 22 biallelic sites. For simplicity, we will refer to all biallelic sites as SNPs. The number of SNPs tested was gradually increased from ten at inception of the project to the 22 currently used. The ten initial SNPs were 3594, 4580, 5178, 7028, 10400, 10873, 11467, 11719, 12705, and 14766 (numbers refer to the nucleotide position in the mitochondrial genome). The panel was augmented to a total of 20 coding-region SNPs by including the following additional ten SNPs: 4248, 6371, 8994, 10034, 10238, 10550, 12612, 13263, 13368, and 13928. The panel was further augmented by the addition of SNP 2758, to a total of 21 coding-region SNPs and finally by including the 9-bp deletion at position 8280 to a total of 22 coding-region SNPs (Figure 4). Two further changes were made: positions 8994 and 13928 used in some early work were respectively replaced with their phylogenetic equivalents 1243 and 3970. Therefore, the current panel includes the following SNPs, with their respective gene locations shown in brackets [33]: 2758 (16S), 3594 (ND1), 4248 (M), 4580 (ND2), 5178 (ND2), 6371 (COI), 7028 (COI), 8280 (9-bp deletion) (NC7), 8994 (ATPase6), 10034 (G), 10238 (ND3), 10400 (R), 10550 (NDRL), 10873 (ND4), 11467 (ND4), 11719 (ND4), 12612 (ND5), 12705 (ND5), 13263 (ND5), 13368 (ND5), 13928 (ND5), and 14766 (Cytb).” ... Click to read more!

The Genographic Project Public Participation Mitochondrial DNA Database

Blaine Bettinger 10 Comments

The Genographic Project is probably the largest genetic genealogy project in the world. For $99, the project will sequence seqments of either your mtDNA or your Y chromosome for addition into their publicly available database. The goal of the project, with ten research centers around the world, is to “map humanity’s genetic journey through the ages,” and to “address anthropological questions on a global scale using genetics as a tool.” There has been a huge response to this project, and they just released their first research paper using the results they have collected to date:

“Family Tree DNA is proud to announce that the first paper resulting from data collected through the Genographic Project has been published today at the PLOS GENETICS.“The Genographic Project Public Participation Mitochondrial DNA Database” can be found at http://genetics.plosjournals.org and it will be uploaded to the Family Tree DNA public library as well. ... Click to read more!

For the First Time, a Human Receives (Almost) Entire Personal Genome!

Blaine Bettinger 7 Comments

watson_james.jpgAdmit it, you’re dying to get your hands on Watson’s genome, aren’t you? Who isn’t?! Yesterday James Watson was handed his sequenced genome on DVD from 454 Life Sciences. There’s a great press release from the Baylor College of Medicine where the ceremony took place.

In a very big day for genetics and human beings alike, Watson was the first person to be handed his entire genetic sequence (for those in the know, Venter only received some or most of his sequence according to most sources).

Amazingly, according to the press release, the genome was sequenced over two months for $1 million. Incredible, considering the Human Genome Project took years and billions of dollars, and even Venter’s project took $300 million. ... Click to read more!

Scottish DNA Database Being Created at Glasgow Caledonian University

Blaine Bettinger 3 Comments

Genealogists interested in researching their Scottish roots will soon have a new resource thanks to a new genealogy center created by the Glasgow Caledonian University in Scotland.  The center will join together traditional genealogical research with recent advances in genetic genealogy to help individuals verify their Scottish roots with DNA testing.  According to the Scottish Tourist Board at VisitScotland.com, more than 50 million people throughout the world can claim Scottish ancestry.

This testing will be done by mouth swab and will be conducted in a new forensics lab built at the University.  The center will use both Y-chromosome and mtDNA results to build their database.  Researchers at the University hope that the center will eventually be able to build a genetic map of the clans of Scotland by looking for markers that are specific for each particular clan.  The test should cost around GBP60 ($120USD), and a number of people have already expressed an interest in the test. ... Click to read more!