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Recreating a Grandmother’s Genome – Part 2

In my last post (see “Recreating a Grandmother’s Genome – Part 1”), I introduced my grandmother Jane, who died when I was just 8 years old. Although I have only a few memories of my grandmother, I have 25% of her DNA. To explore this rich genetic legacy, I’m trying to recreate as much of my grandmother’s genome as possible using the GEDmatch Tier 1 tool called “Lazarus.”

In the last post we also learned about the new Lazarus tool. In today’s post, we’ll choose what kits to use for my grandmother’s Lazarus kit.

Finding DNA Kits for Lazarus

GROUP 1 – DESCENDANTS ONLY

So GROUP 1 must be descendants of the target Lazarus kit. My grandmother has six children, twelve grandchildren, and eleven great-granchildren. Any of these 29 people are candidates for GROUP 1. Of those 29 people, I’ve tested four of the six children and one of the grandchildren (myself). Yeah, I know, I have more testing to do!

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Small Matching Segments – Examining Hypotheses

Last week I published “Small Matching Segments – Friend or Foe?” to join in the community’s conversation about the use of “small” segments of DNA, referring to segments 5 cM and smaller (although keep in mind that the term “small,” without a more specific definition, will mean different things to different people).

The question that the community has been struggling with is whether small segments of DNA can be used as genealogical evidence, and if so, how they can be used.

As I wrote in my post, a significant percentage of small segments are false positives, with the number at least 33% and likely much higher. In my examination and in the Durand paper I discuss, a false positive is defined as a small segment that is not shared between a child and at least one of the parents.

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Small Matching Segments – Friend or Foe?

There has been a great deal of conversation in the genetic genealogy community over the past couple of weeks about the use of “small” segments of matching DNA. Typically, the term “small” refers to segments of 5 cM and smaller, although some people include segments of 7 cM or even 10 cM and smaller in the definition.

The question, essentially, is whether small segments of DNA can be used as genealogical evidence, and if so, how they can be used.

While it may seem at first that all shared segments of DNA could constitute genealogical evidence, unfortunately some small segments are IBS, creating “false positive” matches for reasons other than recent ancestry. These segments sometimes match because of lack of phasing, phasing errors, or a variety of other reasons. One thing, however, is clear: there is no debate in the genetic genealogy community that many small segments are false positive matches. There IS debate, however, regarding the rate of false positive matches, and what that means for the use of small segments as genealogical evidence.

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DNA Standards and Certification – A Response to an NGS Quarterly Editorial

EDIT 2/8/2014 - I am happy to report that the group originally organized by CeCe Moore is still planning to work on standards, guidelines, and certification for Genetic Genealogists, and thus I will continue to work with that group. Thank you to everyone that expressed support, and I will try to contact you soon.

Original Post:

Below, I’m taking the unenviable position of disagreeing, at least in part, with an editorial by Melinde Lutz Byrne and Thomas W. Jones in National Genealogical Society Quarterly entitled “DNA Standards.” (1)  I’m writing to share my viewpoint and my thoughts about moving forward, and to provide a venue for continued discussion on the subject.

This is also the first post in a series of posts about “DNA and the Genealogical Proof Standard,” culminating with a presentation with the same title at SCGS Jamboree 2014 (on Friday June 7, 2014 at 2:30 PM).

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DNA Presentations at Jamboree (Other than on DNA Day)

DNA_JamboreeAs I wrote previously, the Southern California Genealogical Society has officially announced the 45th Annual Southern California Genealogy Jamboree (June 6-8, 2014), which will again be preceded by Family History and DNA: Genetic Genealogy in 2014.

In addition to many presentations on DNA Day (Thursday), there are DNA-related presentations planned throughout Jamboree (Friday through Saturday).

Browsing through the schedule (links at top of page here), these are the presentations I found either directed to DNA or explicitly utilizing DNA:

  • Blaine Bettinger (FR018) – “DNA and the Genealogical Proof Standard”
  • CeCe Moore (FR019) – “Why Should I Take a DNA Test?”
  • Nicka Smith, Angela Walton-Raji, Bernice Bennett and Shelly Murphy (FR024) – “The Future of African American Genealogy”
  • Bennett Greenspan (SA037) – “The Future of Genetic Genealogy”
  • ISOGG (SA049) – “Ask the Experts about DNA and Genealogy”
  • Maurice Gleeson (SU020) – “Ireland and the Slave Trade”
  • Drew Smith (SU024) – “DNA 102: Understanding and Using Test Results”
  • Blaine Bettinger (SU029) – “Begging for Spit”

My Other Presentations

I’m especially excited about presenting “DNA and the Genealogical Proof Standard.”  This topic has not received nearly enough coverage by the genealogy community, and I think it’s very important. I will absolutely be asking for input from others, so feel free to share your thoughts below (or on a future post I’m planning). Here’s the short summary of the presentation:

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Identifying Ötzi the Iceman’s Relatives

In 1991, German tourists in the Alps discovered the mummified remains of a man who died approximately 5,000 years ago. Named Ötzi, the remains have been studied extensively and have revealed a wealth of information about life in this region.

Ötzi’s DNA

Of note to genetic genealogists, Ötzi’s DNA has also been the subject of extensive analysis.  In February 2012, sequencing of Ötzi’s full genome was announced (see here and here) which revealed, among other things, that the Iceman probably had brown eyes, belonged to blood group O, and was lactose intolerant.  He may also have had Lyme disease, as the genome of the infectious agent  Borrelia burgdorferi was also identified in the sequencing effort.

Ötzi’s Y-DNA belongs to a subclade of Haplogroup G defined by the SNPs M201, P287, P15, L223 and L91 (G-L91).  As far as I know, he has not yet been typed for any of the subclades downstreaming from G-L91. More information can be found at the G-L91 page of the Haplogroup G Project, and elsewhere online.

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A New Patent For 23andMe Creates Controversy

There has been a great deal of coverage this week of the new patent issued to genetic testing company 23andMe.  U.S. Pat No. 8,543,339 is entitled “Gamete donor selection based on genetic calculations” and is directed to methods for predicting traits for a child based on the DNA of candidate parents, and selecting a preferred donor based at least in part on the prediction.

Some of the coverage (including an editorial in Genetics in Medicine) has suggested that the methods are “hugely ethically controversial” and “‘GATTICA’-like,” and could lead to a “design-your-own-baby DNA test” and “designer babies.”  Another popular genetic genealogy blogger, Roberta Estes, also addressed the patent on her blog earlier this week (“23andMe Patents Technology for Designer Babies”).

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The Science Fiction Future of Genetic Genealogy

GeneticGenealogyFutureStamp1Imagine the following scenario:

  • You’ve just received an email that your DNA test results are ready, and you log into your account. The welcome screen guides you through a tutorial and presents you with several tabs to choose from.
  • You click the first tab which reads “Your Ancestors.”  The page shares information about 35 of your ancestors from the past 300 years, identified because you have inherited some of their DNA, although you have not yet provided any genealogical information to the testing company. Each of these ancestors has their own profile page complete with dates, family members, and other information such as computer-generated images and a health report which are based on a genome reconstructed entirely from modern-day descendants.
  • You then click on the tab that reads “Your Reverse Family Tree,” which contains a partial family tree that has been constructed by the testing company.  Based on extensive and well-documented genealogies, there is likely only one way in which the 35 identified ancestors can fit together in a tree (although other possible combinations are provided along with statistical probabilities).  There are a considerable gaps, especially on your recent immigrant grandmother’s line, but the tree appears to be entirely consistent with your many years of traditional genealogical research.  Well, except for the family of John G. Rogers from the 1850’s; you’d copied that off the Internet years ago and never confirmed for yourself anyway.
  • Next you click on “Your Cousins,” which contains numerous close and distant relatives in the database.  Some of these cousins are Genetic Cousins (with whom you share DNA), and some of whom are Genealogical Cousins (with whom you share a genealogical relationship based on your generated family tree).  There are numerous 2nd and 3rd cousins matches.  There are also pending offers to join several citizen science and family research groups, including the “Descendants of Calvin Lane of Old Lyme, Connecticut” group, the “Family of German Immigrant Johann Kehl” group and the “Relatives of the American Franklin Family” group, each of which has a slightly different research goal.
  • Lastly, you click on “Your Memberships,” which offers – among other things – a discount membership to the Daughters of the American Revolution based on your predicted descendancy from Revolutionary War veteran Jedidiah Johnson (although you don’t happen to share any of Jedidiah Johnson’s DNA, he’s in your generated family tree with an extremely high probability (95%)).

While the scenario I described above may sound like science fiction, it’s the inevitable future of genetic genealogy and is much, much closer than you might think (okay, maybe not the DAR offer!).

Next month at the American Society of Human Genetics 2013 meeting, researchers from AncestryDNA will present their work detailing the reconstruction of portions of the genomes of an 18th-century couple using detailed genealogical information and Identity-by-Descent (“IBD”) DNA segments from several hundred descendants of the couple in the AncestryDNA database. In other words, researchers identified several hundred descendants of a certain couple living in the 1700s and then used the DNA shared by those descendants to recreate as much of the couples’ genomes as possible.

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GEDmatch.com Adds Phasing Tool

Today (or perhaps yesterday?) popular DIY genomics website GEDmatch.com released a new tool for phasing DNA data.  Listed under a link entitled “Generate phased data file,” the tool allows users of the GEDmatch.com site to phase their chromosomes if they have their parent’s raw data.

(A similar tool was previously created by David Pike at http://www.math.mun.ca/~dapike/FF23utils/; with David’s tool, users receive their results directly and do not need to upload their DNA test results; accordingly, users have a variety of options depending on their privacy tolerance).

What the Heck is “Phasing”?

Currently, SNP chip testing performed by 23andMe or Family Tree DNA is unable to attribute a test result to either one of your parents.  For example, if your results for SNP rs00000 are “AG,” the test alone cannot determine whether the “A” came from your mother or father.

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Napoleon Bonaparte’s Y-DNA Haplogroup Belonged to E1b1b1c1* (E-M34)

Researchers have recently discovered that Napoleon Bonaparte’s Y-DNA belongs to haplogroup E1b1b1c1* (M34+).

Dominique Vivant Denon was the director-general of French museums under Napoleon.  Denon made a reliquary (a container for relics) that included the beard of Henry IV, a tooth from Voltair, and a lock of Bonaparte’s hair. 1  The “Vivant-Denon reliquary” is currently deposited in the Bertrand Museum of Châteauroux, and contains in the “right lateral compartment” a lock of Napoleon’s hair (two of which were used for mtDNA analysis. 2  Also in the reliquary is three beard hairs belonging to Napoleon.

Interestingly, when the beard hairs were examined using scanning electron microscopy, it was discovered that they were covered by remnants of shaving soap and some microscopic iron debris from the razor used to cut the beard.

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