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!
Archive for the "DNA for Newbies" Category
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).
Each SNP is detected either by sequencing or by cutting the DNA with enzymes â€“ the presence of a certain mutation will cause the enzyme to cut the DNA differently, either stopping it from cutting or allowing it to cut. The scientists can then analyze the results and determine whether or not the person has that particular mutation. Certain marker results will lead the person to be group in the haplogroup containing other people who have similar results.
Haplogroup E, for instance, is characterized by the mutation M96. If a person has this mutation, they would be M96+, it is extremely likely that they are directly descended from the founder of Haplogroup E. If they do not have the mutation, they are M96-, and they belong to another haplogroup. It isÂ helpful to follow along on the ISOGG Haplogroup E Tree.
Haplogroup E split into E1, E2, and E3 about 28,000 years ago. E3 is characterized by the SNP mutation P2, meaning that people who test positive for P2 (i.e. P2+), then it is extremely likely that they are directly descended from the founder of Haplogroup E3.
E3 split into E3a and E3b about 26,000 years ago. E3b is characterized by the SNP mutation M35. From Wikipedia: â€œE3b is believed to have first appeared in the Horn of Africa approximately 26,000 years ago and dispersed to the
So, therefore, if you belonged to subclade E3b, your Deep SNP test results would be (M96+, P2+, M35+). And E3b splits into even more subclades, meaning that you would have more SNP results.
Anytime you get Deep SNP results and arenâ€™t sure how to interpret them, use the ISOGG Haplogroup Trees. The identifying SNP for each branch of the tree is listed right next to the branch. ISOGG updates the Haplogroup Tree yearly, and even includes source information! Itâ€™s a great resource for genetic genealogists.
By the way, this post came about after a great email conversation with Tim at Genealogy Reviews Online. Thanks Tim!
The following is an interview with Katherine Hope Borges, founder of ISOGG (The International Society of Genetic Genealogy), done at the 2007 SoCal Genealogical Jamboree. ISOGG has about 5,000 members and is growing rapidly. ISOGG has MANY great services on their website, including the “Founding Fathers DNA Page”, and an up-coming Presidential DNA page.
If you liked the video, there are lots more at Roots Television!! If you’re interested in genetic genealogy and haven’t checked out Roots Television yet, you don’t know what you’re missing.
Thanks to Megan for letting me snag this video!
Not only is the network a great way to discover new blogs, but it is an opportunity to stay current on events and developments in the field of genetics. The following blogs are currently members of the network:
My Biotech Life
DNA Direct Talk
Eye on DNA
Gene Sherpas: Personalized Medicine and You
henry: the human evolution news relay (genetics)
Mary Meets Dolly
Microarray and Bioinformatics
And me, The Genetic Genealogist.
If youâ€™d like to subscribe, the feed is available here.
Do you have a burning question about genetics that’s been keeping you up at night? Ever wonder why the combination of red hair and brown eyes is so rare? There are two great resources currently available online for anyone who is curious about genetics.
AsktheGeneticist is a partnership between the Department of Human Genetics at
The Tech Museum of Innovation in
The site also has an interactive eye calculator you can use to predict the color of your childâ€™s eyes (for fun, of course). For example, both my wife and I have brown eyes, but both our mothers have blue eyes. According to the calculator (which takes other factors into account), our child had a 75% chance of have brown eyes, 10.9% green, and 14.0% blue. Note that these percentages suggest that he might have had a 0.1% chance of no eye color (just kidding, of course!). Our son, against the odds, has blue eyes.
Although these websites could be both entertaining and a great source of information, I donâ€™t recommend their use for the diagnosis or treatment of any type of genetic disorder.
1. You got those big blue eyes from your grandmother, but chances are you inherited less desirable genes as well. We inherit our DNA from our parents, who inherited it from their parents. Since we all possess genes that can cause or contribute to disease, knowing oneâ€™s DNA and family medical history can be a great resource for someone who learns they have a genetic disorder.
2. Full genome sequencing is right around the corner! The X-prize quest for the $1000 genome will lead to efficient and affordable whole-genome sequencing. As commercial companies crop up and compete for customerâ€™s business, leading to even lower prices.
3. Your grandmotherâ€™s DNA contains clues to her ancestry. X-chromosome, mtDNA, and autosomal genealogy tests contain clues to a personâ€™s ancestry, both recent and ancient.
4. Even if you arenâ€™t interested in this whole genetic genealogy craze, somebody you know will be! Genealogy is one of the most popular hobbies in
5. All the undiscovered possibilities. No one knows what uses will be discovered for DNA in the future. Save that DNA just in case!
Disclaimer: Some people are very uncomfortable with the thought of gathering and storing a loved oneâ€™s DNA, and those beliefs should be honored and respected. It is ALWAYS best to obtain your grandmotherâ€™s permission before you gather her DNA. So donâ€™t delay, call her now!
This is a contribution to Problogger’s Top 5 Project.
If you’re a regular reader of this blog, then you know that I am a strong proponent of genetic testing for genealogical purposes. I believe that when used correctly genetic testing can serve as a valuable tool in the genealogist’s toolbox.
A recent visitor found my blog with the search term “is genetic genealogy a scam?” When I recreated the search, I discovered that a previous post on this blog is the leading link for this search. The process made me think about the many people who are skeptical or wary of genetic genealogy. As a scientist, I appreciate and encourage healthy skepticism. After all, genetic genealogy has been available for less than a decade, and it has changed considerably since it was first offered. I believe that anyone who forays into the world of genetic genealogy should have a basic understanding of the science and the application of the results. Just reading about genetic genealogy in the media can give one a distorted view of the technology. Along this point, I recommend reading an interesting article by Rebecca Skloot (author of the upcoming book “The Immortal Life of Henrietta Lacks,” which I can’t wait to read). I was referred to that article by a post on her blog (Culture Dish) entitled “The Bogus-ness of DNA Testing for Genealogy Research” in which she reiterates the point that genetic genealogy tests “simply can’t tell you anything definitive about your heredity unless you’re testing your DNA and comparing it to someone else’s to find out if you’re related.”
I agree with Ms. Skloot – the skepticism and wariness about genetic genealogy comes from the interpretation of the results. As a scientist, I believe that a DNA sequence is a DNA sequence and a person can’t argue with those results. But, using that DNA sequence to tell a person that they are 50% Native American is the type of data interpretation that should be viewed skeptically. It can be exciting, but the science is still too new. For me, the verdict is still out on autosomal testing (click on About Genetic Genealogy at the top of the page to learn more about autosomal testing).
On the other hand, I strongly believe in mtDNA and Y-DNA testing. The results are nothing but DNA sequence and an approximate haplogroup determination. These tests CAN tell you if your Y chromosome or your mtDNA is Native American or distinctly European. The information from these test can serve a multitude of functions. For example, I run a surname project to determine if all people in North America and Europe with my surname are descended from the same German family. I am able to answer this type of question using genetic genealogy as a tool.
Genetic genealogy best serves people who are ready for genetic testing to add to their basket of knowledge. It is not as well suited for people who have no experience in genealogical research or who know nothing about their past (unless, of course, they are unable to know anything about their past – then it’s perfect), although it can still be a useful tool for the beginner.
Genetic genealogy is definitely not a hoax. DNA sequence can be a very useful and exciting addition to a genealogist’s research, IF that genealogist is aware of meaning and consequences of genetic testing. If you have any questions or thoughts about the usefulness of genetic genealogy, leave a comment below.
Note: When writing this post I attempted to find other online sources or blogs that had discussed this topic. Unfortunately, I failed to discover a fantastic review of the subject written by Megan Smolenyak Smolenyak at the Family History Circle (available here). If your interest was piqued by my post, please be sure to read hers.Â Interestingly, the format of the posts are remarkably similar and both mention the article and blog post by Ms. Skloot (although in much more detail at Family History Circle)! Nothing like re-inventing the wheel!
Want to know more about DNA, DNA replication, and mutations? Here are few videos that I thought might be helpful. Seeing a 3D animation of a biological process can be even more informative than reading about it.
1. DNA Structure I
2. DNA Structure II (a little more technical)
3. DNA Replication
4. PCR â€“ Polymerase Chain Reaction
5. DNA Mutation
6. Genetic Diversity
9. Mitochondrial DNA Inheritance
10. Mitochondrial Eve:
Click here to view.
And finally, because itâ€™s just too cool not to include:
11. The Inner Workings of the Cell
The Guardian, a newspaper based in
The journalist quotes Chris Pomery, author of the up-coming book â€œFamily History in the Genes: Trace Your DNA and Grow Your Family Tree.â€
“In specific cases, genetics is a very useful tool, but it is not a panacea,” he says. “We’re not even close to the situation where, if you’re starting to research your family history, you should begin with a DNA test. At Â£100 or so a throw it’s a lot of money, and you can progress your research a long way first for free.”
However, as is often the case in these types of stories, there were a number of errors in the story.
â€œWhat does it mean, for example, for Oprah Winfrey to announce â€œI am a Zuluâ€ after having a mitochondrial test?
“It’s nonsense,” says Mark Jobling, a geneticist at
Oprah Winfrey thought she was Zulu BEFORE the mtDNA test. The test conclusively told her that her mtDNA was NOT related to the mtDNA found among the Zulu people! [Correction: See the comment section for an update regarding Oprah's first mtDNA test, which reportedly DID tell her that her mtDNA was related to the Zulu].
I agree with the author that the results of genetic testing should always be interpreted wisely, and I try to reinforce that point as often as I can. No current genetic test can tell you who you are! Genetic tests can only give you a description your DNA, and based on that you can estimate relationships with others (temporally and geographically).
One of the problems facing the field of genetic genealogy, however, is the number of inaccuracies perpetuated by the media. These articles are often written by non-scientists who donâ€™t completely understand the topic and are making conclusions that arenâ€™t backed up with science.
I recently blogged about some questions that a genetic genealogy newbie had asked about genetic testing. If you have any questions about genetic genealogy, please ask and I will do everything I can to help you discover an answer (that is supported by science)!
Jasia began by asking whether she should test both her and her mother’s mtDNA (I advised her no, because they would be the same sequence), and then we talked about testing her father’s mtDNA. Since her father could not be tested directly, Jasia wondered if her brother could provide a sample of her father’s mtDNA. I explained that although her brother could provide a sample of her father’s Y-DNA, she would have to find other sources for her father’s mtDNA, including her father’s sisters or brothers, or the children of her father’s sisters. She responded:
“Fortunately, my dad came from a large family including 6 sisters 4 of which had children. So I have cousins a plenty and can probably find one of them to help me out with a little saliva
“So is the mtDNA more valuable to the genealogist than the Y-DNA? Does it give more/different information? Would there be a benefit to having my brother’s Y-DNA tested as well as one of my paternal cousin’s mtDNA?”
With lots of sisters and cousins, it looks like Jasia won’t have any problem finding someone willing to help her out with this endeavor. She’s very lucky in this respect – in many families, the sources of DNA either don’t exist or have disappeared forever.
Her next question is also one that many people ask. Why test both mtDNA and Y-DNA? How are the results different and is either test more informational than the other? Here’s how I answered:
“I’m not sure I would say that mtDNA is more informative than Y-DNA, or vice versa. They’re just different. The result of an mtDNA test reveals your maternal lineage all the way back to a haplogroup founder. My mtDNA test, for example, revealed that my maternal lineage belongs to Haplogroup A, a Native American haplogroup. My wife’s mtDNA belongs to Haplogroup H, a European haplogroup.
“The results of a Y-DNA test will tell you much the same thing, except that Y-DNA traces the paternal lineage. The results will put the Y-DNA into a haplogroup family, and that information will tell you about the origin of the Y-DNA. One of the benefits of Y-DNA testing is that it is associated with a surname. There are many surname groups that a person can join once they have the results of their Y-DNA. The theory goes that people with the same surname are more likely to have the same Y-DNA (that is, they are more likely to be paternally related).
“So, each test will tell you something about the line that it traces, either the maternal line or the paternal line. For me, having both pieces of information was fun, mostly for the sake of knowing it and learning more about my own ancient roots.“
Jasia then suggested that I write up the correspondence as a blog post to help out all the other newbies out there. I’d like to thank her for the fun and interesting correspondence, and for the idea and permission to write about it! If you can, I suggest you go check out her site, The Creative Gene.
You can read Part I in this series here.