Tuesday, July 01, 2014

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.

Saturday, June 14, 2014

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.

Friday, June 06, 2014

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.


Thursday, June 05, 2014

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

Wednesday, June 04, 2014

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.

Monday, May 26, 2014

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.

Tuesday, May 06, 2014

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:


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:

Friday, April 25, 2014

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.