Sometimes the answer is a tree in the forest: my paternal mtDNA - U5a1b

In order to find the mtDNA haplogroup of my deceased Father, Denval Perkins, I have been trying to get female line relatives of my Grandmother, Eleanor "Nellie" Walker Inman Perkins, to do either the autosomal test at 23andMe, because it also gives a limited mtDNA haplogroup, or an mtDNA test at Family Tree DNA. Because he and his half and full siblings are all deceased, I have asked his niece, but she has finally decided not to test. I then asked some of my Grandmother's sisters descendants but they also refused to test.

This week I used the Charting program in Legacy Family Tree to go back to my Grandmother's Grandmother, Mariah Moses Manning, and trace her mtDNA descendants. When I examined the chart I realized that two of those female line descendants had already tested at 23andMe and had the mtDNA haplogroup designation of U5a1b. This mtDNA haplogroup is considered one of the oldest European mtDNA haplogroups. It is currently concentrated in the Baltic and Scandinavian countries. This location ties into my Fathers's Y DNA haplogroup of R1a1a (R-176.1) which is mainly found in Scandinavia and Scotland.

My Father's known matriline:
Denval Perkins (1921-1974);
Eleanor "Nellie" Walker (1891-1965) - 1) Francis "Frank" Inman and 2) Henry Franklin Perkins;
Rutha Manning (1867-1928 - Andrew J. Walker;
Mariah Moses (1832-1873) - Jacob H Manning;
Martha Richardson (1814-1869) - 1)Edmund DeBerry Moses and 2) William Manning;
Elizabeth Davis (1778-1860-70) - John Richardson.

Locations covered are Whitley Co., KY and McCreary Co., KY. See the US Census reports for 1850 through 1930.

US National Institute of Health Policy on Genomic Data Sharing

NIH Genomic Data Sharing Policy

Genomic research advances our understanding of factors that influence health and disease, and sharing genomic data provides opportunities to accelerate that research through the power of combining large and information-rich datasets. To promote robust sharing of human and non-human data from a wide range of genomic research and to provide appropriate protections for research involving human data, the National Institutes of Health (NIH) issued the NIH Genomic Data Sharing Policy (GDS Policy) on August 27, 2014 in the NIH Guide Grants and Contracts (available at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-14-124.html), and in the Federal Register (available at https://federalregister.gov/a/2014-20385) on August 28, 2014. The GDS Policy and related documents are available at:

• GDS Policy PDF
  
• Preamble to the GDS Policy
  
• Supplemental Information to the GDS Policy
  
• NIH Press Release on the GDS Policy
  
• NIH Guide Notice on Implementation of the GDS Policy for NIH Grant Applications and Awards
  
• NIH Guide Notice on Development of Data Sharing Policy for Sequence and Related Genomic Data
  

The GDS Policy applies to all NIH-funded research (e.g., grants, contracts, intramural research) that generates large-scale human or non-human genomic data, regardless of the funding level, as well as the use of these data for subsequent research. Large-scale data include genome-wide association studies (GWAS), single nucleotide polymorphisms (SNP) arrays, and genome sequence, transcriptomic, epigenomic, and gene expression data. Supplemental Information to the GDS Policy provides examples of genomic research projects that are subject to the Policy.

10th Annual FTDNA Conference for DNA Project Administrators

The 10th Annual FTDNA Conference for DNA Project Administrators was held last weekend, 10-12 October 2014. I was unable to attend this year.

Two main announcements were

1) the reduction in the cost to transfer 23andme version 3 autosomal dna results and AncestryDNA autosomal results to FTDNA for matching purposes to $39.00 fro $69.00. In addition, a free transfer can be made which will allow one to see their 20 top matches at FTDNA before deciding to either pay the $39,00 to unock all FTDNA matches, or recruit 4 more persons to transfer their results so your matches are shown to you without cost. Details are expected to be on the FTDNA web site this week.

2) The Deep Clade 2.0 test will be developed with the haplogroup admins to allow a quicker determination of the location of a person within the Y DNA haplogroup tree. In the past year over 10,000 SNPs were added to the ISOGG Y Haplogroup tree. This test will be a less expensive route than the Big Y test.

Details of the Conference are on the blogs of Jennifer Zink, Ancestor Central and Roberta Estes, DNA Explained. I am sure more people will be posting this week.

Personal Genome Project: Comments on GA4GH Data Sharing Draft

Comments on GA4GH Data Sharing Draft

JUNE 30, 2014

by Madeleine Price Ball

The following is a copy of our comments as submitted through the online interface at
genomicsandhealth.org.

These comments pertain to the International Code of Conduct for Genomic and Health-Related Data Sharing – DRAFT # 6, produced by the Regulatory and Ethics Working Group of the Global Alliance for Genomics and Health. That draft document can be found at this URL: http://genomicsandhealth.org/our-work/work-products/international-code-conduct-genomic-and-health-related-data-sharing-draft-6

Our most important points are the first two. The first suggests an explicit mandate to inform individuals, families, and communities regarding identifiability of their data. The second suggests individuals, families, and communities from whom data is derived also be considered as potential data sharing recipients.

My current autosomal matching results at AncestryDNA, 23andMe and Family Tree DNA (FTDNA)

My current test stats:

AncestryDNA

• 298 pages of matches with 50 people per page for approximately 14,900 persons. Only two given as 2nd cousins. Neither one confirmed yet. No family tree and one private.
  
• 6 pages of Hints. I have gone through 4 pages checking the pedigree links. Waiting for a known 2nd cousin's results.
  

23andMe

• 2879 matches.
  
• approximately 380 sharing genomes
  
• approximately 30 relationships found in pedigrees.
  
• 3 known first cousins. Matching range from 17.9% to 15.9 to 12.5% 42, 42, 35 segments.
  
• 1 known second cousin, 3.10%, 13 segments.
  
• 2 known third cousins, 3.05% and 1.49%, 13 and 4 segments.
  
• 5 known third cousins once removed. Range is 2.45%, 1.32, 1.26, 0.78, 0.52 and 11, 4, 6, 3, 3 segments.
  
• Some of these are related through both of my parents.
  
• Waiting for a half-first cousin's results to get my paternal grandmother's mtDNA haplogroup and find out if one of her maternal ancestors was Native American.
  

FTDNA

• 113 pages at 10 people per page for approximately 1130 FF matches.
  
• Closest unknown match is predicted 2-4th cousin. 73 cM.
  
• 10 X matches 2 males and 8 females. Relationships not found.
  
• 15 Know relationships.
  

My 2nd cousin's 23andMe Countries of Ancestry graphic is much more complete than mine at 5cM and 1+ ancestor including Colonials.

Big failure at all services:

• No or incomplete family tree. This should at least cover the Great Grandparents and better, the Great Great Grandparents.
  
• Let us know if you are adopted so we can help you.
  
• Check setting to be sure Private is only applied to living persons.
  
• No dates or locations given makes it hard to match a person.
  
• If at 23andMe, include info on Rootsweb or Ancestry tree or GEDMATCH in your Profile.
  
• Response rate is low at all services.
  

23andMe has changed the treatment of "Close Relatives"

Christine at 23andMe has posted a change to the tratment of "close Relatives" [1st cousins and closer] in DNA Relatives.

Prior to tonight you had to opt-in to "Show Close Relatives" if you wanted to see 1st cousins or closer relatives in DNA Relatives. As of tonight everyone will show Close Relative unless you opt-out of DNA Relatives. More details are available in the News and Announcement forum at 23andMe:
https://www.23andme.com/you/community/thread/30426/

While this is a much wanted feature change for genealogists and adoptees, some people may not want to know about previously unknown siblings or children, birth-parents, etc.

Another 23andMe Job Advertisement: Scientist - Human Subjects Research

Another job advert from 23andMe:

Scientist - Human Subjects Research
Organization:
23andMe
Job Location:
Mountain View, CA
Salary:
Great package and free genotyping for you and a friend!
Benefits:
Benefits, stock options, and CalTrain Go Pass!

Job Description:
Do you enjoy laying out the pieces of a scientific story so that non-scientists can understand it? Do you feel that regulation makes sense, but only when it’s sensible? Are you motivated not only by getting things done, but by making sure they’re done right? Do you think the operational part of “human subjects” is “human” and not “subjects”?

In addition to being one of the biggest players in the direct-to-consumer genetics world, 23andMe is also performing cutting-edge research on an unprecedented scale. We are looking for an experienced scientist to work with our research team to help develop and execute creative yet rational solutions to complicated regulatory issues. This individual would assist in preparing and implementing international human subjects research protocols to allow us to execute our wide variety of projects while prioritizing the interests of our research participants and customers. Our research program is incredibly dynamic and we are looking for someone who would enjoy the challenge of doing things right while keeping up with the pace of a Silicon Valley company.

Requirements:
The successful candidate will possess the following:

-Ph.D. in a biomedical science
-Experience writing human subjects protocols, conducting human subjects research and working with IRBs (experience conducting research in non-US countries a plus)
-Excellent communication skills, both written and oral
-Ability to independently set and meet deadlines
-Good working knowledge of statistics and modern human genetics concepts
-Ability to work in a dynamic environment with individuals of diverse backgrounds

Please submit a writing sample, such as a scientific publication or grant proposal, of which you were a primary author.

Contact Information:
https://www.23andme.com/about/jobs/

About Our Organization:
23andMe is the leading personal genetics company. We are dedicated to helping individuals understand their own genetic information through DNA analysis technologies and web-based interactive tools. Our mission is to personalize healthcare by making and supporting meaningful discoveries through genetic research. Combining web development, computer science, genetics, social media, and informatics, 23andMe is at the forefront of a new era in personal genetics.

=====

Looks like they are trying to meet the FDA requirements. Interesting line:

-Experience writing human subjects protocols, conducting human subjects research and working with IRBs (experience conducting research in non-US countries a plus)

Ancestry.com to end Y DNA and mtDNA testing. Will continue autosomal DNA testing [AncestryDNA]

Posted at the Ancestry.com Blog:

We’re always looking to focus our efforts in a way that provide the most impact, while also delivering the best service and best product experience to users. To that end, we’ve decided to retire some of our services: MyFamily, MyCanvas, Genealogy.com, Mundia and the Y-DNA and mtDNA tests.
We will note that the AncestryDNA (autosomal) test will continue to be available for purchase. Only the y-DNA and mtDNA tests will be retired.
- See more at: http://blogs.ancestry.com/ancestry#sthash.OkwjiAEU.dpuf

23andMe Job Advert: Senior Scientist - Analytical Method Validation

Found this at GenomeWeb:

Job Advert: Senior Scientist - Analytical Method Validation

Senior Scientist - Analytical Method Validation
Organization:
23andMe
Job Location:
Mountain View, CA
Salary:
Competitive package and free genotyping for you and a friend!
Benefits:
Benefits, stock options, and CalTrain Go Pass!

Job Description:
23andMe is pushing the envelope for low cost and high accuracy genetic testing. We are looking for experienced scientists who are excited by the opportunity to demonstrate the accuracy of our tests, both current and future. 



This position will:
- Design studies to validate the accuracy of new genotyping/sequencing technologies against existing gold standards
- Perform statistical regression modeling to establish equivalence and explain variance in observed data
- Investigate, explain, and propose solutions for observed discordances
- Develop and track project plans and generate detailed records and documentation for our quality system and regulatory submission.
- Coordinate with lab team and organizations to obtain relevant reference data and samples
- Participate in ongoing regulatory efforts, both domestic and international

Requirements:
The ideal candidate should have:
- a PhD in biology, chemistry, statistics or related discipline
- 2+ years experience with developing in-vitro diagnostic devices used in a clinical setting
- familiarity with genetic testing technologies such as microarrays, Sanger sequencing, and Next Generation sequencing
- experience preparing and submitting to FDA (eg. 510(k), PMA) and international (eg. CE Mark) a strong plus

Contact Information:
Apply at https://www.23andme.com/about/jobs/

About Our Organization:
23andMe is the leading personal genetics company. We are dedicated to helping individuals understand their own genetic information through DNA analysis technologies and web-based interactive tools. Our mission is to personalize healthcare by making and supporting meaningful discoveries through genetic research. Combining web development, computer science, genetics, social media, and informatics, 23andMe is at the forefront of a new era in personal genetics.

Expanded DNA testing for American GIs MIA and KIA: Opportunities to identify war dead abound as DOD overhauls troubled recovery efforts

From Stars and Stripes:

http://www.stripes.com/news/opportunities-to-identify-war-dead-abound-as-dod-overhauls-troubled-recovery-efforts-1.285323

By Travis J. Tritten
Stars and Stripes
Published: May 25, 2014

Excerpt:

More than 83,000 servicemembers are still listed as missing from War World II, the Korean War, Vietnam, Iraq and other conflicts, according to the Defense POW/Missing Personnel Office.

Advances in DNA analysis, the use of global positioning software and aerial drones, and clues gleaned over decades from historical records are already pointing the way toward closure for scores of those servicemembers, speakers at the POW-MIA Awareness Conference said.

FTDNA's revamped Population Finder is now myOrigins

If you have taken the Family Finder test at FTDNA, one of your result sets has been Population Finder. This has been renamed myOrigins. It is found as a link on your Personal Page (MyFTDNA) at FTDNA. I looked at my FTDNA myOrigins results and they are in line with what I have at 23andMe and at AncestryDNA.

So now all three show:

The British Isles;
France and the Low Countries;
Scandinavia;
Portugal and Spain over to Greece and the western Balkans.

Missing is Finnish and Yakut.

I believe Finnish should be there since I'm 90% sure of my Finnish ancestor in New Sweden. The Yakut, maybe not, though it could be Native American.

In 23andMe Counties of Ancestry I match people with all grandparents from Greece, Slovenia, Croatia, Serbia and Armenia, as well as the more western European countries.

For me, myOrigins seems to work.

First and Third Cousin matches at 23andMe

Here is a chart of where my three 1st cousins and I match genetically:

1st Cousins

On average 1st cousins are expected to match at 12.5% of their genome. In order of these matches the percentages are 17.9; 15.9; and 12.5. The first line of matches (green)is from a 1st cousin who is related to me on both the paternal and maternal sides of our families. We shared 6 of 8 Great Grandparents. Our mothers were sisters and our fathers were 1st cousins. The blue line is from a 1st cousin where her father and my mother were siblings. The same is true for the purple line but her father was a different brother of my mother. There is no known paternal relationship in the latter two cases. I am waiting for results from one 1st cousin and a 2nd cousin on my father's maternal line (Walker and Manning). I would also like to test a second cousin on my mother's maternal line (Swain and Kidd).

Here is a chart of matches to my two 3rd cousins and three 3rd cousins once removed:

New 2014 Y DNA SNP tree from FTDNA and National Genographic

Today, FTDNA released the new 2014 Y DNA SNP tree based on results from the GENO 2.0 SNP tests from the National Genographic Project. This has changed most SNP tested individuals' designations on their FTDNA Personal Page. It will also be propagated to the SNP designations on the surname, geographic, and haplogroup pages.

At the same time FTDNA is giving a list of SNPs that are recommended for testing by each individual. CAVEAT: If you tested negative for a SNP in GENO 2.0, check for the SNP in your GENO 2.0 results before ordering it from FTDNA. FTDNA did not include the negative SNPs in their result for you so they may be in the Recommended SNP list even though you have already tested those SNPs.

Before testing contact your Y DNA Haplogroup Administrator for guidance. For more details see, The new 2014 Y DNA haplotree has arrived by my genetic cousin, Debbie Kennett.

A webinar on the Family Tree DNA Feature Launch: Y-DNA Haplotree Update was held today and is expected be available from the FTDNA Learning Center within the next 24 to 48 hours.

There is a Sale on the 37 marker Y DNA test See this post by Debbie Kennett for more information.

Ancestry.com to Present Jermline on DNA Day at the Global Big Data Conference

Posted by Jeremy Pollack on April 9, 2014 in Big Data, Data Science, Development, DNA, Science

Interested in genealogy? Curious about DNA? Fascinated by the world of big data? If so, come check out my talk at the Global Big Data Conference on DNA day this Friday, April 25 at 4pm PT in the Santa Clara Convention Center! I’ll cover Jermline, our massively-scalable DNA matching application. I’ll talk about our business, give a run-through of the matching algorithm, and even throw in a few Game of Thrones jokes. It’ll be fun! Hope to see you there.

http://blogs.ancestry.com/techroots/jeremy-pollack-to-present-jermline-at-the-big-data-innovation-summit-on-april-10th/?sf2685301=1

VH1's DNA Show "Swab Stories" Call for participants

Doron Ofir Casting, Robert Mazza Casting and Powderhouse Productions are searching nationwide for people with the most compelling stories who want to have their double-helix hunches answered for an all-new television series on a major cable network.
Do you need help unlocking the biggest mystery in your life? Put your most life-changing question to the ultimate test – DNA test!

• Do you have suspicions about your blood relation to a family member?
• Have you ever thought that maybe you were switched at birth?
• Did you ever think you look more like your father's best friend than your own father?
• Are you suspicious that you might not be related to any of your relatives?
• Would you ever get a DNA test to prove your theory?

If you want to know who your parents are, who your siblings are or who you are, then this is the perfect opportunity for you.

If you’re ready to make your last strand, and are at least 18 years old, then we want to hear your story! If selected, your search for answers may finally come to an end with a trip to New York or a visit by our genetic team where you will participate in a DNA test and be compensated for your time in doing so.

We’ll finally unlock the answers and put your suspicions to rest.
Send your information to: DNACasting2014@gmail.com

Genetic mixture in the USA

An interesting post at the 23andMe blog:

March 4, 2014
DNA USA*
Published by ScottH under 23andMe Research, Ancestry

Scientists have long used DNA to inform our understanding of big epochs of human change and migration. But what about the smaller changes, can DNA tell us something about recent human history? diversity photo

23andMe researcher Katarzyna “Kasia” Bryc, who is also a postdoctoral research fellow in David Reich’s lab at Harvard Medical School, gathered anonymous aggregated data from our customers to look at the mix of African, European and Native American ancestry in the United States. What she discovered was an illuminating genetic portrait of the U.S. that both confirms some of what we know about America’s social history but also other things that are surprising and new.

“Perhaps one of the greatest discoveries stemming from recent advancements in genetic genealogy is that previously held assumptions about race and identity are being brought into question,” Harvard Professor Henry Louis “Skip” Gates Jr. wrote recently. “It was always known throughout American history that there was at least some intermixing of races, but only now, through DNA testing, can we see the extent to which this actually occurred.”

Continued here.

Looking at Countries of Ancestry (formerly Ancestry Finder) at 23andMe

23andMe has a survey, Where Are You From? that asks people who test where their four grandparents were born. If you take it and agree to let people who match you know the information, the results are placed in the Ancestry Finder database.  The pictures below show the results of looking at my Ancestry Finder matches without and with colonial (USA, Canada, Australia, New Zealand) matches included.

Chromosomes 1 through 22 and the X chromosome are shown. In the application you can select the number of grandparents who must be from the same country and the size of the match in centiMorgans (cM). You can also mouse over a match and see where their grandparents are from, the length of the match, and, if a public match, the name of the person.  Other data can be downloaded in a spreadsheet format for further examination.

The default view is of all 4 grandparents from the same country and a match of at least 7 cM in size and no Colonials.


The first picture below shows the results of looking at my matches with the grandparents matching or non-matching and the size set to the smallest length of 5cM or larger with no colonial matches. You can see that some chromosomes have greater coverage than others. Chromosomes 14, 21, and 22 have no matches. The large gold match on chromosome 1 is with someone with all four grandparents born in Norway.

The second picture has the same parameters but it includes Anglo-American Colonial countries.

Steven C Perkins' Ancestry Finder matches, 1gp, 5cM+, no Colonials

Steven C Perkins' Ancestry Finder matches, 1gp, 5cM+, with Colonials

Debbie Cruwys Kennett on The Big Y results

Posted today by Debbie Cruwys Kennett is an analysis of early results from the Big Y test at Family Tree DNA (FTDNA):

http://cruwys.blogspot.co.uk/2014/03/the-big-y-roll-out-snp-tsunami-is-on.html

Big Y results starting to come out at FTDNA

At the FTDNA Administrators Conference FTDNA announced the Big Y test. This test sequences the Y Chromosome and returns millions of results. As others have written, it will greatly increase the definition of the Y Tree. Results were expected in December 2013, then a series of delays occured and 28 Feb was announced as the release date. As it happened, only 100 results were released on 28 Feb. Other results will be released over the next month. This has caused a number of people to complain that FTDNA has been cavalier in it's treatment of customers with unrealistic release dates. Today FTDNA sent out the following email:

Dear Valued Customer,


Yesterday, February 27th, we began releasing results for the Big Y orders. We have received some incredibly positive feedback and this is much appreciated.

We are also hearing the frustrations from those who have not yet received their results, and we would like to address the matter publicly in the form of a sincere apology. The entire FTDNA team has been working very hard over the last few months with high determination and many late nights. Launching a new product is always a challenge with many moving parts, some more predictable than others. Unfortunately we ran into some surprises beyond our control when one of our suppliers ran out of certain reagents we needed for running the Big Y product. However we recognize that it is our responsibility and duty to meet our deadlines and keep our customers informed when problems arise.

With the Big Y launch, we failed to properly manage the expectations of our customers. This was an honest oversight, in which we internally had a target to release first results in February, but we didn’t pay close attention to the dates being communicated on the status pages for those orders. Big Y was a new product and the status entries were updated automatically. We should have manually adjusted these dates earlier on as needed. So while we were thrilled to release the first results in February, we failed to realize that everyone expected results this week. I personally take responsibility for this miscommunication and mishap with the website delivery dates and hope you accept my sincere apologies.

I am well aware that as a company we have a bit of a history in missing deadlines. A big contributor to that is that we have typically been very ambitious in taking on difficult projects while still wanting to deliver information quickly to customers. The Big Y product is a great example. It was a cutting-edge project that pushed us deep into next-generation sequencing and advanced data analysis. Our ambitious, risk-taking attitude has won many of you over and delivered incredible thought leadership and leading products over the years. Unfortunately, our poor estimates and turnaround time expectations have frustrated many of you along the way as well. We are committed to continuing to be the company that is willing to push the envelope and take risks to bring you the best in genetic genealogy, but moving forward we will strive to be more careful in setting accurate time expectations.

Again, we are sincerely sorry for any frustration we caused with the delays and miscommunication of turnaround time. We are very proud of our achievements with the Big Y and feel confident about the high quality product we are delivering! We hope you will let the wonderful product we produced make up for delays that were needed to refine it! We have updated expected results dates on customer pages and will work around the clock to beat them.

Regards,

Nir Leibovich
Chief Business Officer
www.FamilyTreeDna.com
Gene by Gene Ltd.

Thanks to Tim Jansen, M.D. for the notice.

Good article on using DNA testing to find birth parents

This is an article on Kasandra Rose, an adoptee and a biologist, who has been using autosomal DNA testing to determine her ancestry and to hopefully find her parents:

http://www.freep.com/article/20140223/COL26/302230078/DNA-testing-adoption-finding-family

The side panel contains some useful information for other adoptees. Kasandra has a blog at The Rose Bush

International Genetic Genealogy Conference: 15-17 August 2014

The Institute for Genetic Genealogy will hold the International Genetic Genealogy Conference in August. Details on the Conference with a list of speakers, can be found on the Conference website. This should be a very informative meeting. This blogger will be attending.

Multiple cousins shown at AncestryDNA (UPDATE)

The problem reported below has been corrected.If you have multiple connections to a cousin, the separate connections are now correctly marked for the degree of relationship.

Like numerous others I received two additional pages of Hints today at AncestryDNA. In examining the matches I have found that AncestryDNA is now showing all multiple matches at the furthest degree of relationship. As an example I have one person who is a 3rd cousin once removed and a 6th cousin on another line. When I open the match each is shown as a 6th cousin even though there are two different lines of relationship.

There were two 3rd cousins in my predicted 4th to 6th cousin Hinted match list.

I have started using the Note section to tag the match with the person's name, the degree of relationship and the name of the person or couple the relationship is from.

I now have 5 pages of Hints out of 182 pages of matches. Needless to say, I'll never get through looking at all of those pages of matches.