Â Â Â Â Â Â Â Â Â I consider my new friendship with Hsien and other fellow bloggers to be one of the great successes of this blog, and I thank her for the opportunity to share my enthusiasm for genetic genealogy with her readers!
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 : 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).”
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:
â€œFamily 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.â€œThe Genographic Project Public Participation Mitochondrial DNA Databaseâ€ can be found at http://genetics.plosjournals.org and it will be uploaded to the Family Tree DNA public library as well.
Two fellow genealogists recently nominated me for a “The Thinking Blogger Award.â€My honored thank you to Tim at Genealogy Reviews Online and Randy at Genea-Musings.The rules of this meme are pretty simple:
1.If you get tagged, write a post with links to 5 blogs that make you think;
2.Link to the original post at The Thinking Blog (see above) so that people can easily find the exact origin of the meme, and;
3.Optionally, display the â€œThinking Blogger Awardâ€ graphic.
There is a certain occurrence in genetic genealogy called a Non-Paternal or Non Paternity Event.This is a break in the ancestry of a personâ€™s Y chromosome and surname.A person named â€œSmith,â€ for instance, might have a Y chromosome that is clearly â€œJohnson.â€
A non paternal event can occur when an adopted male takes the surname of his adoptive family, or a male child takes his step-fatherâ€™s surname, or a male child takes his motherâ€™s surname (undoubtedly there are other circumstances as well).
When a break in the Y chromosome is suspected or confirmed, it is possible that the break might have occurred 1,000 years ago, 100 years ago, or with the testeeâ€™s birth.
Two companies recently teamed up to offer their services to families with roots in the African Diaspora.Slave Descendants Freedom Society and Diversity Restoration Solutions are bringing a seminar series to 50 cities in the
â€œThis interactive seminar series is a stepping stone in that it seeks to help African Americans find their self identity, understand the benefits of restoring the core family base, and move forward in leveraging resources as a people,â€ said Sheppard, author of â€œAncestorâ€™s Call,â€ a genealogy and historical accounting of the Grandy family and Moses Grandy, an ancestor whose story was originally told in a rare 1843 slave narrative. â€œItâ€™s important that we lay the foundation for generations coming after us; our children and grandchildren need to know who they are in order to receive their inheritance. This seminar honors the contributions of our ancestors but with an emphasis that this recognition should not occur just during Black History Month, but as a way of life, everyday. Participants will come away with a greater understanding of themselves, an action plan for tracing their family tree and hopefully a stronger appreciation for family and desire to pay it forward in their community.â€A pdf brochure is available.
If you missed Ira Flatow’s interview with Megan Smolenyak on NPR’s Science Friday, you can download the podcast in a number of different formats at NPR.Â The interview is the result of this week’s big announcement that Ancestry.com is teaming up with Sorenson Genomics to offer DNA testing.Â Great job Megan!
Today represents a brief break from genetic genealogy, in a way, but I thought the topic was interesting enough to talk about.
BRCA2 (Breast Cancer Type 2 susceptibility protein) is a tumor suppressor gene involved in the repair of DNA damage.BRCA2 binds to and regulates another protein (the product of the RAD51 gene) to fix DNA breaks caused by any number of factors.BRCA2 was discovered in 1995 by Professor Michael Stratton and Dr. Richard Wooster in cooperation with the Wellcome Trust Sanger Institute.
To date, researchers have identified 450 different mutations in the BRCA2 gene, some of which unfortunately cause an increased risk of cancer.Typically, the mutated gene produces an abnormally short protein that is unable to help the cell fix DNA breaks.Thus, mutations can accumulate and eventually lead to cancer (breast, ovarian, prostate, or pancreatic).
I am a genetic genealogist because I thought it would be a fun and interesting thing to do.Some people, however, are genetic genealogists because it is a matter of life and death.
The Amish/Mennonites and Genetic Disorders
The Amish migrated from Europe (Germany/Switzerland) to the United States in the 1700s.One such group, the Old Order Amish of Lancaster County, Pennsylvania, began with 200 Swiss immigrants.Today, there are roughly 200,000 Old Order Amish.Because of the difficult lifestyle, the lack of evangelism, and the language barrier, there is essentially no conversion to the Amish religion.In addition, marriage outside the community is forbidden.As a result, the community has remained closed for over 10 generations and is still using the same 200 genomes of their founders!This is known as founder effect, which means that a population is started by just a small number of individuals and as a result that new population will be different (both genetically and phenotypically) from the parent population, potentially with low genetic variation.
Often, at least at the current stage of genetic genealogy, DNA sequencing does not reveal enough information to identify a personâ€™s particular Y chromosome or mtDNA haplogroup.The example I will be using in this post is Haplogroup E.Haplogroup E split into E1, E2, and E3 about 28,000 years ago.Current tests offered by many sequencing companies are able to place a person in the general â€œEâ€ Haplogroup, but might be unable to determine exactly which subclade of E a person descends from.In such a situation, a â€œDeep SNPâ€ test can be used to fill in that information.
A SNP is single nucleotide polymorphism, or a change in the DNA sequence at a single nucleotide.For instance, the switch of a C for G, a cytosine for a guanine.You can see a chart of some of the most common SNPs tested for genetic genealogy here or here.The Deep SNP test (which can go by other names) analyzes a personâ€™s DNA, such as the Y chromosome, for the presence or lack of these mutation(s).