16 December 2012

Geno 2.0 - The Website

My Geno 2.0 test results arrived Tuesday night.  HURRAY!!!!

The website which is still in Beta testing has the following sections:

YOUR STORY includes how and when your distant ancestors moved out of African and the various populations with which they interacted over thousands of years of migration.  The migration is determined by tracing mutations in your Y-chromosome DNA (if you are a male) for paternal lines and on your mitochondrial DNA for maternal lines.  Your haplogroup (basically your twig on the World Family Tree) is given as an alternating series of letters and numbers.  A short video is available on the site.

YOUR MAP are pages begin with your oldest known ancestors in Africa and shows your ancestors’ migration out of Africa for your maternal line and if you are a male, also for your paternal line.   Each page is a haplogroup and as you click on the next section, you see how that haplogroup changed to the next haplogroup and how your ancestors migrated.  Below the map on each page is interesting background about each haplogroup is given including its location of origin and time.  A Heat Map indicates the frequency of your haplogroup in the areas it has been found.  The FUTURE section shows the entire migration for all haplogroups, but the information on the page indicates that as more data is found, more detail will appear.  There is also a request for you to complete your profile and contribute your story.  This enables you to tell what you know about your maternal and paternal lineages and as others add their story, you will be able to read them if you match them.

WHO AM I? displays how you affiliate with nine world regions.  As this is determined from your entire genome that is tested, your percentages include information from both of your parents going back six generations.  This reflects both recent influences and ancient genetic patterns as various groups mixed over thousands of years.  As your ancestors mixed with extinct hominid cousins such as the Neanderthals and Denisovans (/dɪ̈ˈniːsəvən/) these are included.  A short video is found on this page.

Two major populations are listed for each person.  My personal population percentages are:

43% Northern European which states that my results are found at the highest frequency in areas of the UK, Finland, Russia and Germany in the current reference populations, and to lesser degrees throughout the rest of Europe.  This is probably the earliest hunter-gatherers in Europe and who moved from the Middle East during the Neolithic period about 3,000 years ago.

37% Mediterranean with the highest frequencies in southern Europe and the Levant people (people from Sardinia, Italy, Greece, Lebanon, Egypt and Tunisia.  It is at lower frequencies in the rest of Europe, the Middle East, Central and South Asia.  This group migrated from the Middle East around 8,000 years ago during the Neolitic period and likely form the western part of the Fertile Crescent.

18% Southwest Asian is found at the highest frequencies in India and the area including Tajikistan and Iran.  It is at fewer frequencies in Europe and North Africa.  Again, the movement was probably during the Neolithic period and possibly from the Fertile Crescent.  The site states:  “Individuals with heavy European influence in their ancestry will show traces of this because all Europeans have mixed with people from Southwest Asia over tens of thousands of years.”

Below this the site explains what all this means and clarifies that it does not mean that I belong to these groups or are from these regions, but that these groups have a similar genetic match to me.  It further asks me to remember that this is a mixture of my past six generations and ancient patterns established over thousands of years.

My first reference population is considered British (UK).  This reiterates that my line is among the first hunter-gathers who arrived more than 35,000 years ago and that the Mediterranean and Southwest Asian percentages came later with the spread of agriculture from the Fertile Crescent.

My second reference population is considered German.  This connects me to people who are native to Germany.  This essentially states the same as the information for British and states that both northern and central European populations link to the earliest Europeans and the later movement from the Middle East.

You can click on a link to see information on all the reference populations as well as information on how the analysis was conducted, a description of all the nine regions and an example of a participant’s result discussed by Dr. Spencer Wells.

Below all that is my Hominid Ancestry for which I can click on a link to learn more details about the Neanderthal and Denisovans.

I am 2.2% Neanderthal.  National Genographic states:  “Everyone living outside of Africa today has a small amount of Neanderthal in them, carried as a living relic of these ancient encounters. A team of scientists comparing the full genomes of the two species concluded that most Europeans and Asians have between 1 to 4 percent Neanderthal DNA.”

I am 1.6 Denisovan.  National Genographic states that this may well change as they are “working to determine the best way to assess the percentage Denisovan ancestry that you carry. “

OUR STORY contains your paternal and maternal matches.  It is the section where you can read the personal stories your matches post about their lineages.  You are the center circle and those most closely related are nearer to you.  A legend indicates the level of relationship based on the size of the circle. By clicking on your circle you are offered a space of up to 1400 characters to write your story.  Another link allows you to see all those who have posted a story.  You can scroll to your haplogroup to see who has posted.  There is a guided tour to view.

PROFILE is the section which asks for cultural information on yourself and your recent ancestors in order for National Genographic to learn more about recent migrations and further refine their understanding to where people migrated today.  You can also click to be put in the scientific research study, and then complete sections entitled:  Account Settings, About Me, About My Family, About My Ethnicity, and Expert Option.*  
.......*Note that it is not extremely clear as to your oldest male and female for which to answer these questions of location.  I believe the goal is to do your oldest known female from your ALL-FEMALE line and the same for your ALL-MALE line even though this is not clear.  I have requested that it be make clearer.  Otherwise, we will have information that stems from other branches of our lineage and even the oldest male and female could be a married couple on the same line.

Transfering your Geno 2.0 results to FTDNA
Go to PROFILE and then to EXPERT OPTIONS.  Follow the prompts and add information (kit and passwords) for appropriate tests you have taken:  Geno 2, Geno 1, Y-DNA and/or mtDNA.
At this point in time there seemed to be a bug in some attempts to transfer data, but that appears to be resolved.  If you find a problem report it to FTDNA and try what I did:  I did not test Geno 1.0 with National Genographic, but transferred my HVR1 to them.  I was able to transfer my Geno 2.0 data to Family Tree DNA only when I did not enter the kit number for my Geno 1.0.

Also know that for males when they transfer their Geno 2.0 test to FTDNA, they will see all the National Genographic SNPs (Single Nucleotide Polymorphism) for which they test positive for their Y-DNA portion.  This will definite add to the string of letters and numbers for many haplogroups, but remember that everyone will soon be using the first letter of your haplogroup and the terminal (last) SNPs for which you test positive.  One of my I2b people is now I-Z183.

Other Features
On many pages you can click SHARE in the upper right to email your page to others, post on one of the social networks or download to your computer.

Be sure to check the FAQs and other items under RESOURCES.

REMEMBER, the current National Genographic website is in Beta so there will be bugs, and there may be some changes as issues are fixed and features added. The email to report problems is  Genographic@ngs.org

Haven't ordered your test yet?  Go to the National Genographic webiste and join the other 559,515 participants!

copyright 16 Dec 2012

11 December 2012

23andMe Lowers Test Price to $99

Today’s exciting news is that 23andMe has lowered their test in a goal of reaching a million testers.  Not only does this have implications for the medical field, but for those of us involved in genetic genealogy.

Although we see generally around 20-30% of those testing will accept your invitation to share basic genomes, it will still increase our matches.  For those of you who have also tested at Family Tree DNA, you can have your 23andMe matches also transfer a copy of their data to Family Tree DNA and do additional testing as well.  23andMe does not test the Y chromosome or mitochondria in the same manner, but they do give you haplogroups for each as does Family Tree DNA.  Many of us are interested in adding to our Y-DNA and mtDNA projects so increasing testing from any company can mean future additions to those projects.

The other benefit to this price reduction could be that it will spur other companies to reduce their prices or at least do some great sales.  We have to realize that 23andMe has obtained funding from outside sources and other companies may not take that approach so we cannot fully expect a price war.

Purchasing kits from 23andME outside the US does raise the cost greatly as compared to Family Tree DNA's (FTDNA) comparable test called Family Finder.  However, understand that the Family Finder test does not deal with any health issues, but gives you the names and emails of the matches you have in their database.  You need not ask permission to share genome information as you do with 23andMe.  Other features are similar in both companies, although they do vary a bit.  For example, 23andMe rounds the beginning and ending positions of where you match people, and FTDNA does not.  Each company uses a slightly different set of populations to compare you so your percentage for your ancestral locations (i.e, Middle Eastern, Asian, African, etc.)  may vary somewhat.  Both companies accurately report your genome results and allow you to download your raw data so you can do chromosome mapping and phasing..

By testing with both companies most of your matches will be different as each company has a different clientele. A few people have tested with both companies. FTDNA allows you to transfer your results form 23andMe to them. 23andMe doesn't take results form FTDNA at this point in time.

These are the costs for the UK for each company:

Family Tree DNA's Family Finder:  $199 + $6.00 postage = $205 (+ return postage equivalent to about $2)
23andMe:  $99 + $79.95 = $178.95

FTDNA charges a flat rate of $6 for postage anywhere in the world. 
23andMe charges variable rates depending on the country. Shipping within the US costs just $9.95, but it costs $59.95 to send the kits to Canada, $94.95 to Cyprus, Malta and Iceland, and $118.95 to Bosnia and Belarus.

It will of course be more cost effective if people order multiple kits from 23andMe and have them sent to the same address.

The press release from 23andMe:

23andMe Raises More Than $50 Million in New Financing
Company Sets Growth Goal Of One Million Customers, Reduces Price to $99 from $299

MOUNTAIN VIEW, Calif. – December 11, 2012 – 23andMe, Inc., the leading personal genetics company, today announced it has raised more than $50 million in a Series D financing. Participants in the financing include Yuri Milner, a new investor, as well as existing investors Sergey Brin, 23andMe CEO Anne Wojcicki, New Enterprise Associates, Google Ventures and MPM Capital. This investment will help the company achieve its growth goal of one million customers.
The Power of One Million People

Expanding the company’s ability to reach and serve one million individuals supports 23andMe’s goal to revolutionize health and wellness. It also will accelerate 23andMe’s ability to create a powerful platform that enables researchers around the globe to make meaningful discoveries significantly faster than is currently possible. With this expansion, 23andMe, which currently has more than 180,000 customers, will aim to:

Enable groundbreaking research by creating an exponentially larger collective of actively engaged, genotyped individuals;
Help accelerate development of new treatments;
Improve understanding of wellness and disease prevention; and
Broaden access for people seeking to manage their health and well-being through direct access and greater understanding of their own genetic data.

“A community of one million actively engaged individuals will be transformational for research. A community of this magnitude will improve researchers’ ability to quickly answer questions about genetic function and the role of environmental factors. In addition, it will enable researchers to understand medication efficacy and side effects, in both medications that exist today and medications are that are in development,” Wojcicki added.

Broadening Access: Lowering Price to $99
The Series D investment, combined with rapidly decreasing costs associated with genetic testing technologies, enables 23andMe to reduce the price of its Personal Genome Service to $99, effective immediately. The company will continue to evaluate optimal pricing strategies.
The investment also enables 23andMe to expand the necessary infrastructure to support growth in its research and operational capabilities, including product development, genetic research, software development, recruitment and marketing.

About 23andMe
23andMe, Inc. is the leading personal genetics company dedicated to helping individuals understand their own genetic information through DNA analysis technologies and web-based interactive tools. The company's Personal Genome Service® enables individuals to gain deeper insights into their ancestry and inherited traits. The vision for 23andMe is to personalize healthcare by making and supporting meaningful discoveries through genetic research. 23andMe, Inc., was founded in 2006, and the company is advised by a group of renowned experts in the fields of human genetics, bioinformatics and computer science. More information is available at www.23andme.com.

05 December 2012

National Geographic Unveils New Phase of Genographic Project

Geno 2.0  Combines Powerful New Technology, Citizen Science
More than a Half-Million Participants Traced Deep Ancestry in First Phase

WASHINGTON—The National Geographic Society today announced the next phase of its Genographic Project — the multi-year global research initiative that uses DNA to map the history of human migration. Building on seven years of global data collection, Genographic continues to shine new light on humanity’s collective past, yielding tantalizing clues about humankind’s journey across the planet.

“Our first phase drew participation from more than a half-million participants from over 130 countries. It is evidence of enormous interest in deep ancestry among the global public — tracing the paths their ancestors took as they migrated around the world over the past 60,000 years,” said Project Director Dr. Spencer Wells, a population geneticist and National Geographic Explorer-in-Residence.

“Now, the Genographic Project’s second phase creates an even greater citizen science opportunity —and the more people who participate, the more our scientific knowledge will grow.”

Geno 2.0
The Genographic Project enters this groundbreaking new stage of research by harnessing powerful genetic technology to further explore and document the historic pathways of human migration. Based in part on a unique database compiled during the project’s first phase, the next generation of the Genographic Project Participation Kit — Geno 2.0 — examines a unique collection of nearly 150,000 DNA identifiers that offers rich, ancestry-relevant information from across the entire human genome. In addition to learning their detailed migratory history, participants will learn how their DNA is affiliated with various regions in the world, and even if they have traces of Neanderthal or Denisovan ancestry — from our ancient hominid “cousins” who lived in Europe and parts of Asia tens of thousands of years ago before going extinct.

Participants will receive their results through a newly designed, multi-platform Web experience. In addition to full visualizations of their migratory path and regional affiliations, participants can share information on their genealogy to inform scientists about recent migratory events. These stories also can be shared with the broader Genographic Project community; as the number of contributions grows, the experience will become richer, as participants learn more about themselves and their shared ancestry. Results also can be shared as an infographic for social platforms.

Already, project results have led to the publication of 35 scientific papers, reporting results such as the origin of Caucasian languages, the early routes of migrations out of Africa, the footprint of the Phoenicians in the Mediterranean, the genetic impact of the Crusades and the genetic origins of the Romanian royal dynasty that included Vlad the Impaler. The project’s DNA results and analysis are stored in a database that is the largest collection of human anthropological genetic information ever assembled.

"The Genographic Project truly represents another facet of a new age of exploration. The newest Genographic technology will push the limits of our research, inspiring us to learn more about ourselves and leveraging the insights gleaned so far to take citizen science and genetic testing to a whole new level,” said Terry Garcia, executive vice president of Mission Programs at National Geographic.

Applications from Scientists Welcome
New to the second phase of Genographic, the project will invite applications for grants from researchers around the world for projects studying the history of the human species, which use innovative anthropological genetic tools such as the custom-designed “GenoChip,” a technology developed by scientists using Illumina’s Infinium iSelect HD BeadChips specifically for the study of human migration patterns. Sample research topics could include the origin and spread of the Indo-European languages, genetic insights into regions of high linguistic diversity such as Papua New Guinea, the number and routes of migrations out of Africa, the origin of the Inca or the genetic impact of the spread of maize agriculture in the Americas.

During Genographic’s first phase, Wells and project scientists traveled the globe to collaborate with tens of thousands of indigenous people, whose genetics are particularly significant in determining human migratory routes. Wells and Pierre Zalloua, principal investigator in the Middle East, for example, collaborated with the Toubou people of northern Chad, whose DNA has revealed insights into ancient migrations across the Sahara. Genographic’s principal investigator in the Oceana region, Lisa Matisoo-Smith, worked intensively with people on the remote south Pacific island of Emirau, collecting DNA samples and sharing the results with them.

The Genographic Project team worked with individuals, institutions and organizations all over the world to find and tell their genetic stories, including the prime minister of Kazakhstan, who invited Wells and his colleagues to collect DNA samples in his country after becoming fascinated with his family story as revealed by his Genographic kit results; the people of Barbados, who requested a study on the pattern of diversity in the country using the public participation kits; and members of the public in South Africa, who learned that they carry links to the region’s earliest inhabitants, the San people, in addition to genetic lineages from elsewhere in Africa, India and Europe.

The project also tested 200 random people on a single day on a block of Queens, New York, to demonstrate the area’s diversity. In a collaboration with cellist Yo-Yo Ma’s multidisciplinary education foundation The Silk Road Project, more than 400 students at four New York City public schools swabbed their cheeks and traced their ancient ancestry.

A portion of the proceeds from the sale of Genographic Participation Kits funds project research and the Genographic Legacy Fund, which awards grants to support community-led cultural conservation and revitalization initiatives among indigenous and traditional communities around the world. So far, the Genographic Project has provided 62 Legacy Fund grants worth $1.7 million. Efforts supported by the grants include the creation of teaching materials on the ancient wisdom of the Chuj in a Maya community in Guatemala and the revitalization of indigenous languages in Nepal, India, Taiwan, French Polynesia, Mexico and Bolivia.

‘GenoThreads’ Connects Students, Teachers
A new education program called GenoThreads enables science, culture and geography to be naturally woven into a shared educational experience. GenoThreads connects students and teachers around the world who are using Genographic participation kits; this allows a cross-cultural exchange between students via email and videoconference for a truly global experience. In the first GenoThreads project, high school students in Switzerland are sharing their results with those halfway across the world in Singapore.

Members of the public are encouraged to visit the Genographic Project’s newly created website at www.genographic.com. Featuring National Geographic photography, the website gives Genographic participants the opportunity to learn more about their own ancestry and find ancestral connections. The Genographic Project remains nonmedical and nonprofit, and all analysis results are placed in the public domain following scientific publication. The Genographic Project serves as an unprecedented resource for geneticists, historians, anthropologists and citizen scientists.

Visit the Genographic Project’s website: www.genographic.com.

5 Dec 2012 Press Release courtesy of National Geographic Society.