Showing posts with label Genetic Genealogy. Show all posts
Showing posts with label Genetic Genealogy. Show all posts

20 May 2019

Genetic Genealogy Abbreviations and Terms Quick Reference

Now available, Practical Genetic Genealogy Abbreviations and Terms Quick Reference laminated guide.

I was asked to compile a laminated quick reference guide for DNA and genetic genealogy abbreviations and terminology. Even though the ISOGG Wiki and other online sources contain much of this information, it seems many people prefer to have the information available in a laminated guide.


This quick reference guide has several advantages over online access.
  1. The definitions needed by genealogical researchers are in one easy-to-access place.
  2. Both beginner and intermediate level terms are included.
  3. These are clearly-worded definitions that are easy for non-biologists to understand. I often receive praise for being able to explain DNA in a way that is easy to understand and I tried to continue that tradition here.
  4. An image of my gingerbread men used to explain DNA inheritance patterns is included. I am constantly asked to provide color versions of this image to students. The image has two couples on the top row, a male and female child of the couples on the middle row, and four grandchildren on the bottom row. A "Y" represents the inheritance path of the Y chromosome through the family. An "O" represents the inheritance path of the mitochondrial DNA through the family. The left half of the gingerbread bodies represent one autosomal chromosome (for example, chromosome one) inherited from the father. The right half of the gingerbread bodies represent the corresponding autosomal chromosome inherited from the mother. The colors of the autosomal DNA represent randomly recombined chromosomes and the colors can be traced back to the great-grandparents not shown on the chart. The colors make it easy to see fully identical regions (FIR) and half identical regions (HIR) of DNA shared by the siblings in the bottom row.

The quick reference sheet is currently available from Books and Things (http://www.mygenealogybooks.com/) priced with shipping included.



All statements made in this blog are the opinion of the post author. This blog is not sponsored by any entity other than Debbie Parker Wayne nor is it supported through free or reduced price access to items discussed unless so indicated in the blog post. Hot links to other sites are provided as a courtesy to the reader and are not an endorsement of the other entities except as clearly stated in the narrative.

To cite this blog post:
Debbie Parker Wayne, "Genetic Genealogy Abbreviations and Terms Quick Reference," Deb's Delvings, 20 May 2019 (http://debsdelvings.blogspot.com/ : accessed [date]).

© 2019, Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved
Posted by Debbie Parker Wayne, Certified Genealogist® at 12:52 PM 6 comments
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10 March 2019

DNA Standards - Part 8

For "DNA Standards - Part 1" see https://debsdelvings.blogspot.com/2019/03/dna-standards-part-1.html. In the first part I paraphrased the standards for using DNA evidence for genealogy into bullet points.

This is the post for "DNA Standards - Part 8."


1

Prior bullets are discussed in other parts of this series:


In "DNA Standards - Part 8" I further discuss the final bullet. The main bullets indicate considerations when using DNA to help answer a research question; sub-items explain what is needed to accomplish the tasks defined in the main bullet:

  • publish or share only as a living test taker’s permission allows (Standard 57)
    • deceased persons have no privacy rights; courtesy to living descendants might warrant anonymizing the identity of a deceased test taker
    • general information can be shared as long as the identifying information is hidden (such as when asking for assistance or when teaching how to use a site or tool)

    • do not use a living person’s DNA results if they do not give permission (some disagree on whether inclusion in a public DNA project constitutes permission)
    • do not identify a living person if they do not give permission
      • identities can be anonymized
      • anonymizing too many people in a study may make the conclusion questionable

Unless you are working in a legal capacity where you may be held liable for misidentifying descendants you should be able to use whatever sources you wish to use. If you are publishing, your work will be subject to the requirements of the editor. If you are submitting a portfolio to BCG, your work will be subject to the requirements of BCG. You should contact those entities with your questions.

There will always be disagreements about what constitutes proof. I have read articles in some of the premier genealogical journals that I do not think meet the threshold for the claims made. Obviously, the editors and peer-reviewers felt differently. Some of those articles were based only on documents and some included DNA. We will never all agree on exactly how much evidence is needed for proof and DNA does not change that fact.





BCG, Genealogy Standards, 2nd ed. (Nashville: Ancestry, 2019)

GETTING OFFICIAL INFORMATION ON STANDARDS FROM BCG

Only BCG provides official answers on what it expects to see in application portfolios. No one, not even members of the BCG Board of Trustees or associates helping at exhibit hall booths, speak officially for BCG. For specifics on what BCG expects to see in portfolios, please use BCG’s website, blog, newsletter, and other means of communication:


All statements made in this blog are the opinion of the post author. This blog is not sponsored by any entity other than Debbie Parker Wayne nor is it supported through free or reduced price access to items discussed unless so indicated in the blog post. Hot links to other sites are provided as a courtesy to the reader and are not an endorsement of the other entities except as clearly stated in the narrative.

21 September 2021: added missing link to part 1.

To cite this blog post:
Debbie Parker Wayne, "DNA Standards - Part 8," Deb's Delvings, 10 March 2019 (http://debsdelvings.blogspot.com/ : accessed [date]).

© 2019, Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved
Posted by Debbie Parker Wayne, Certified Genealogist® at 11:19 AM 2 comments
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DNA Standards - Part 7

For "DNA Standards - Part 1" see https://debsdelvings.blogspot.com/2019/03/dna-standards-part-1.html. In the first part I paraphrased the standards for using DNA evidence for genealogy into bullet points.

This is the post for "DNA Standards - Part 7."


1

Prior bullets are discussed in other parts of this series:


In "DNA Standards - Part 7" I further discuss the eighth bullet. The main bullets indicate considerations when using DNA to help answer a research question; sub-items explain what is needed to accomplish the tasks defined in the main bullet:

  • make the DNA data available for verification, as much as possible within the limits of test taker permissions (Standard 54)
    • depending on publication venue this might mean
      • providing login information to an editor to confirm the DNA data (the password can be changed after the editor has completed the review)
      • asking test takers to upload to a public project (such as at FamilyTreeDNA where the test taker gives permission and the administrator sets project options for results to be displayed publicly)
      • asking test takers to upload to a publicly available third-party website (available to any internet user without logging in or requiring a login and password that any person can obtain)
      • providing screenshots of web pages with the DNA or match data
    • if the DNA test results are not publicly shared or confirmed by an unbiased third party there is a risk that the author misinterpreted the DNA test results
    • if one or more test takers choose to remain unidentified the credibility of the conclusion should be evaluated with that person removed or anonymized
    • if one or more test takers choose to remain unidentified the essay may not meet the criteria for some publications nor be the best choice of work sample to demonstrate your analysis and correlation skill
    • just as we have always done with articles and work samples based on documentary sources, we must make judgments on credibility when using DNA sources


Additional bullets will be discussed in other parts of this series:



BCG, Genealogy Standards, 2nd ed. (Nashville: Ancestry, 2019)

GETTING OFFICIAL INFORMATION ON STANDARDS FROM BCG

Only BCG provides official answers on what it expects to see in application portfolios. No one, not even members of the BCG Board of Trustees or associates helping at exhibit hall booths, speak officially for BCG. For specifics on what BCG expects to see in portfolios, please use BCG’s website, blog, newsletter, and other means of communication:


All statements made in this blog are the opinion of the post author. This blog is not sponsored by any entity other than Debbie Parker Wayne nor is it supported through free or reduced price access to items discussed unless so indicated in the blog post. Hot links to other sites are provided as a courtesy to the reader and are not an endorsement of the other entities except as clearly stated in the narrative.

To cite this blog post:
Debbie Parker Wayne, "DNA Standards - Part 7," Deb's Delvings, 10 March 2019 (http://debsdelvings.blogspot.com/ : accessed [date]).

© 2019, Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved
Posted by Debbie Parker Wayne, Certified Genealogist® at 10:58 AM 0 comments
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DNA Standards - Part 6

For "DNA Standards - Part 1" see https://debsdelvings.blogspot.com/2019/03/dna-standards-part-1.html. In the first part I paraphrased the standards for using DNA evidence for genealogy into bullet points.

This is the post for "DNA Standards - Part 6."

1


Prior bullets are discussed in other parts of this series:

In "DNA Standards - Part 6" I further discuss the seventh bullet. The main bullet indicates considerations when using DNA to help answer a research question; sub-items explain what is needed to accomplish the tasks defined in the main bullet:

  • identify familial relationships (where appropriate), present the conclusion as a genetic link only if the DNA supports that conclusion, explain any insufficient research (Standards 50, 56, 65, 74)
    • no researcher is required to use DNA, but, where available and appropriate, DNA is such a strong piece of evidence for biological relationships that ignoring it is imprudent
      • trying to use atDNA to prove biological relationships further back than five to seven generations is not always possible, but sometimes is when random recombination results in segments remaining unbroken over several generations (you do not know what you will find until you look)
      • trying to use Y-DNA or mtDNA is not always possible if no living test takers have the Y-DNA or mtDNA of interest to this research question or if those with the DNA needed are not willing to test
    • no researcher is required to use DNA, but not using DNA when trying to prove a biological or genetic relationship will make many suspect the conclusion may not be accurate
      • researchers who have not yet learned to use DNA may take this risk (no DNA police will come knocking on your door, but knowledgeable researchers may wonder why DNA was not used)
      • researchers who have not yet learned to use DNA may hire someone who has educated themselves on using this source (just as one might hire a German researcher for research in Germany, a photographic expert for photo repairs, or an editor for a book)
    • if DNA is not available because there are no living test takers or none willing to test, indicating this informs the reader that DNA was considered and is not available
      • no living test takers with the right DNA is similar to the records being burned in a courthouse fire
      • no person willing to test is similar to the source being held in a repository that restricts access
      • we have dealt with these issues with paper records for years and can apply the same logic to DNA

    • if DNA evidence is not considered, knowing the rate of misattributed parentage seen in most lines, reasonable researchers may conclude a genetic or biological relationship is not proven
    • if no specific familial relationships is specified and if DNA is not used, reasonable researchers may conclude a genetic or biological relationship is not proven even if such a relationship is implied
      • just as genealogists have always done when documentary evidence was not strong enough to “prove” a relationship, one can indicate “DNA evidence is not available because of XYZ, all of the documentary evidence available supports a conclusion that John Doe is the father of William Doe” or “John Doe named his son William in his will” or dozens of other ways this can be indicated without implying a DNA test supports the conclusion or using words other than the ones we traditionally use to define relationships
      • some researchers think an explicit statement should be made of the relationship type being asserted; some think, in the absence of a stated relationship type, the sources used make an implicit statement
      • some think we have always asserted biological relationships without DNA evidence and should still be able to do so; some think today’s technology means there is a paradigm shift that should be embraced

These discussions are likely to continue for the next few years or longer. In my time in the genealogical world, the same kinds of discussions took place when computers first began being used and again when so many records became available online. The genealogical community made it through those changes which were major transitions in how we work. I suspect we will make it through this "crisis" in time to be poised for the next one that will surely come.

Additional bullets will be discussed in other parts of this series:




BCG, Genealogy Standards, 2nd ed. (Nashville: Ancestry, 2019)

GETTING OFFICIAL INFORMATION ON STANDARDS FROM BCG

Only BCG provides official answers on what it expects to see in application portfolios. No one, not even members of the BCG Board of Trustees or associates helping at exhibit hall booths, speak officially for BCG. For specifics on what BCG expects to see in portfolios, please use BCG’s website, blog, newsletter, and other means of communication:



All statements made in this blog are the opinion of the post author. This blog is not sponsored by any entity other than Debbie Parker Wayne nor is it supported through free or reduced price access to items discussed unless so indicated in the blog post. Hot links to other sites are provided as a courtesy to the reader and are not an endorsement of the other entities except as clearly stated in the narrative.

To cite this blog post:
Debbie Parker Wayne, "DNA Standards - Part 6," Deb's Delvings, 10 March 2019 (http://debsdelvings.blogspot.com/ : accessed [date]).

© 2019, Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved
Posted by Debbie Parker Wayne, Certified Genealogist® at 10:19 AM 0 comments
Labels: , ,

08 March 2019

DNA Standards - Part 5

For "DNA Standards - Part 1" see https://debsdelvings.blogspot.com/2019/03/dna-standards-part-1.html. In the first part I paraphrased the standards for using DNA evidence for genealogy into bullet points.

This is the post for "DNA Standards - Part 5."

1


Prior bullets are discussed in other parts of this series:

In "DNA Standards - Part 5" I further discuss the sixth bullet. The main bullet indicates considerations when using DNA to help answer a research question; sub-items explain what is needed to accomplish the tasks defined in the main bullet:

  • support every parent-child link in the line from all test takers to the hypothesized ancestors with documentary evidence (Standard 2)
    • this applies to all parent-child links in all lines in our study group (even the parent-child links we see in someone else's online tree) and not only the line from the main/focus test taker back to the hypothesized common ancestor
    • this evidence may be presented in the narrative; the reader will likely be able to follow more easily if the evidence is summarized below a descendant chart
    • my preferred method is to use note references as seen in the image below (a, b, and so on); locating the footnote letter or number in the chart and in the list of citations is much easier for me than reading "For parentage of person XYZ see [list of documents]" then finding person XYZ in a chart; the reference numbers are much easier to locate than names, especially when a writer does not use the same exact name in the chart and the text

    • some publication venues may only need one or two sources to support each parent-child link; more sources may be needed to illustrate thorough research meeting the GPS
    • if no documentary evidence for a link can be found, explain what records were searched, search criteria used, any theory as to why no documents support this link, and why this link may be true in the face of no supporting documentary evidence
    • some parent-child links might ultimately be based on DNA evidence, but a thorough search for the documentary evidence should be demonstrated
    • for a large study group we may be able to use genetic networks to support some of the links so that we still have time to research our own family tree and extend it (as opposed to spending all of our time researching the trees of our DNA matches); some time researching the trees or adequately documenting the trees of others will be necessary, but we all need to manage our time to achieve our own goals most efficiently


Additional bullets will be discussed in other parts of this series:




BCG, Genealogy Standards, 2nd ed. (Nashville: Ancestry, 2019)

GETTING OFFICIAL INFORMATION ON STANDARDS FROM BCG

Only BCG provides official answers on what it expects to see in application portfolios. No one, not even members of the BCG Board of Trustees or associates helping at exhibit hall booths, speak officially for BCG. For specifics on what BCG expects to see in portfolios, please use BCG’s website, blog, newsletter, and other means of communication:


All statements made in this blog are the opinion of the post author. This blog is not sponsored by any entity other than Debbie Parker Wayne nor is it supported through free or reduced price access to items discussed unless so indicated in the blog post. Hot links to other sites are provided as a courtesy to the reader and are not an endorsement of the other entities except as clearly stated in the narrative.

To cite this blog post:
Debbie Parker Wayne, "DNA Standards - Part 5," Deb's Delvings, 8 March 2019 (http://debsdelvings.blogspot.com/ : accessed [date]).

© 2019, Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved
Posted by Debbie Parker Wayne, Certified Genealogist® at 11:02 AM 0 comments
Labels: , ,

05 March 2019

DNA Standards - Part 4

For "DNA Standards - Part 1" see https://debsdelvings.blogspot.com/2019/03/dna-standards-part-1.html. In the first part I paraphrased the standards for using DNA evidence for genealogy into bullet points.

This is the post for "DNA Standards - Part 4."

1


Prior bullets are discussed in other parts of this series:

In "DNA Standards - Part 4" I further discuss the fifth bullet. The main bullet indicates considerations when using DNA to help answer a research question; sub-items explain what is needed to accomplish the tasks defined in the main bullet:

  • ensure enough people have tested to support the conclusion (Standard 53)
    • may require documenting living descendants from multiple children of a focus ancestor or ancestral couple then asking them to test
    • in general, the more generations back to the hypothesized common ancestor or the more possible shared lines, the more test takers needed
    • no one can say that, in all circumstances, you need two or three or six pieces of documentary evidence to have strong evidence for a conclusion because no one knows ahead of time what information will be found in which sources or how credible that information will be; the same applies to DNA evidence
    • exactly how many test takers are needed will vary depending on how many generations it is back to the hypothesized common ancestor and how many lines are traced down from those ancestors
    • consider whether additional tests or higher resolution tests for those test takers found in earlier research might more strongly support a conclusion


Additional bullets will be discussed in other parts of this series:




BCG, Genealogy Standards, 2nd ed. (Nashville: Ancestry, 2019)

GETTING OFFICIAL INFORMATION ON STANDARDS FROM BCG

Only BCG provides official answers on what it expects to see in application portfolios. No one, not even members of the BCG Board of Trustees or associates helping at exhibit hall booths, speak officially for BCG. For specifics on what BCG expects to see in portfolios, please use BCG’s website, blog, newsletter, and other means of communication:




All statements made in this blog are the opinion of the post author. This blog is not sponsored by any entity other than Debbie Parker Wayne nor is it supported through free or reduced price access to items discussed unless so indicated in the blog post. Hot links to other sites are provided as a courtesy to the reader and are not an endorsement of the other entities except as clearly stated in the narrative.

To cite this blog post:
Debbie Parker Wayne, "DNA Standards - Part 4," Deb's Delvings, 5 March 2019 (http://debsdelvings.blogspot.com/ : accessed [date]).

© 2019, Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved
Posted by Debbie Parker Wayne, Certified Genealogist® at 10:39 AM 2 comments
Labels: , ,

04 March 2019

DNA Standards - Part 3

For "DNA Standards - Part 1" see https://debsdelvings.blogspot.com/2019/03/dna-standards-part-1.html. In the first part I paraphrased the standards for using DNA evidence for genealogy into bullet points.

This is the post for "DNA Standards - Part 3."

1


Prior bullets are discussed in other parts of this series:
In "DNA Standards - Part 3" I further discuss the third and fourth bullets. The main bullets indicate considerations when using DNA to help answer a research question; sub-items explain what is needed to accomplish the tasks defined in the main bullet:

  • analyze the DNA results accurately and in-depth (Standard 52) (Y-DNA STRs or SNPs; atDNA and X-DNA shared total DNA—shared, triangulated, or mapped segments, or genetic networks; mtDNA regions or locations; Y-DNA or mtDNA haplogroups; atDNA ethnicity estimates)
    • requires more in-depth understanding of the tools offered by testing companies and third-parties and how to accurately use those tools
    • may require correspondence with people to ask them about test taker links to ancestors or for permission to use third-party tools
  • integrate the thoroughly researched and analyzed DNA and documentary evidence; logically sequence and clearly illustrate the DNA analysis and the documentary analysis in a written conclusion; accurately and completely cite all sources (Standards 1–8, 55, 56, 65, 74)
    • write up the documentary evidence
    • explain why DNA is needed and give only as much DNA background as needed for this project (for example, if this case uses only Y-DNA evidence there is probably no need to explain what mtDNA and atDNA are)
    • explain the DNA evidence, correlating the shared DNA and/or mutations using tables and lineage charts


Additional bullets will be discussed in other parts of this series:




BCG, Genealogy Standards, 2nd ed. (Nashville: Ancestry, 2019)

GETTING OFFICIAL INFORMATION ON STANDARDS FROM BCG

Only BCG provides official answers on what it expects to see in application portfolios. No one, not even members of the BCG Board of Trustees or associates helping at exhibit hall booths, speak officially for BCG. For specifics on what BCG expects to see in portfolios, please use BCG’s website, blog, newsletter, and other means of communication:



All statements made in this blog are the opinion of the post author. This blog is not sponsored by any entity other than Debbie Parker Wayne nor is it supported through free or reduced price access to items discussed unless so indicated in the blog post. Hot links to other sites are provided as a courtesy to the reader and are not an endorsement of the other entities except as clearly stated in the narrative.

To cite this blog post:
Debbie Parker Wayne, "DNA Standards - Part 3," Deb's Delvings, 4 March 2019 (http://debsdelvings.blogspot.com/ : accessed [date]).

© 2019, Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved
Posted by Debbie Parker Wayne, Certified Genealogist® at 7:56 PM 0 comments
Labels: , ,

DNA Standards - Part 2

For "DNA Standards - Part 1" see https://debsdelvings.blogspot.com/2019/03/dna-standards-part-1.html. In the first part I paraphrased the standards for using DNA evidence for genealogy into bullet points.

This is the post for "DNA Standards - Part 2."


1

In "DNA Standards - Part 2" I further discuss the first two bullets. The main bullets indicate considerations when using DNA to help answer a research question; sub-items explain what is needed to accomplish the tasks defined in the main bullet:

  • test the right descendants with the right test(s) at the right company or companies to obtain the information needed to answer the research question (Standard 51)
    • requires identification of living person(s) likely to have the DNA needed to answer the research question
    • requires an understanding of the inheritance path for each type of DNA (Y-DNA, mtDNA, atDNA, X-DNA)
    • requires an understanding of the different tests offered by each company
  • select matches and/or target-test others with the right test (Standard 51)
    • requires understanding the tools offered by testing companies and third-parties and how to accurately use those tools
    • may require correspondence with people to ask them to take a test (which requires understanding the cultural norms that might affect responses)
Additional bullets will be discussed in other parts of this series:



BCG, Genealogy Standards, 2nd ed. (Nashville: Ancestry, 2019)

GETTING OFFICIAL INFORMATION ON STANDARDS FROM BCG

Only BCG provides official answers on what it expects to see in application portfolios. No one, not even members of the BCG Board of Trustees or associates helping at exhibit hall booths, speak officially for BCG. For specifics on what BCG expects to see in portfolios, please use BCG’s website, blog, newsletter, and other means of communication:



All statements made in this blog are the opinion of the post author. This blog is not sponsored by any entity other than Debbie Parker Wayne nor is it supported through free or reduced price access to items discussed unless so indicated in the blog post. Hot links to other sites are provided as a courtesy to the reader and are not an endorsement of the other entities except as clearly stated in the narrative.

To cite this blog post:
Debbie Parker Wayne, "DNA Standards - Part 2," Deb's Delvings, 4 March 2019 (http://debsdelvings.blogspot.com/ : accessed [date]).

© 2019, Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved
Posted by Debbie Parker Wayne, Certified Genealogist® at 7:45 PM 0 comments
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DNA Standards - Part 1

Tomorrow is the big day when the 2019 version of Genealogy Standards starts shipping. This second edition of the book adds standards specifically for using DNA.

Read more and preorder your copy through the Board for Certification of Genealogists (BCG) at https://bcgcertification.org/product/genealogy-standards-2d-edition/. As an Amazon Associate, BCG earns a small commission from purchases of this volume using this link: https://amzn.to/2XwKr5W.



BCG, Genealogy Standards, 2nd ed. (Nashville: Ancestry, 2019)

For "DNA Standards - Part 2" see https://debsdelvings.blogspot.com/2019/03/dna-standards-part-2.html.

For "DNA Standards - Part 3" see https://debsdelvings.blogspot.com/2019/03/dna-standards-part-3.html.

For "DNA Standards - Part 4" see https://debsdelvings.blogspot.com/2019/03/dna-standards-part-4.html.

For "DNA Standards - Part 5" see https://debsdelvings.blogspot.com/2019/03/dna-standards-part-5.html.

GETTING OFFICIAL INFORMATION ON STANDARDS FROM BCG

Only BCG provides official answers on what it expects to see in application portfolios. No one, not even members of the BCG Board of Trustees or associates helping at exhibit hall booths, speak officially for BCG. For specifics on what BCG expects to see in portfolios, please use BCG’s website, blog, newsletter, and other means of communication:

1

A PRACTITIONER'S INTERPRETATION OF THE STANDARDS FOR DNA

The following presents opinions and interpretations of the standards by Debbie Parker Wayne. This is one interpretation as to how the Genealogy Standards can be applied by all genealogical researchers using DNA. No genealogy or DNA police will come knocking on your door if you disagree with this interpretation and have your own preference on what to do.

When we first began discussing standards for DNA, my own goal was to provide guidance for the genealogists using DNA, not to force every genealogist to use DNA (even though I think all should when DNA can contribute to the evidence that answers a question). DNA findings can overturn any conclusions about family relationships. So can many of the other record types that we use every day.

I believe any good genealogical researcher can learn to use DNA. Nevertheless, it takes education and practice to become proficient at DNA analysis. Not all good genealogists have yet had time to obtain that education and practice analysis using their own families. However, ignoring DNA test results when researching kinship questions is akin to ignoring any other record type—census, deeds, probate, Bible records, and so on. Researchers should learn to use all applicable records or obtain assistance to analyze those records. Again, the DNA police are not going to force anyone to do so; however, I think most researchers want to be sure the parent-child links in a pedigree are correct and will eventually use DNA for confirmation.

Even if tests and tools change, the standards provide guidance and best practices we can all use as we incorporate DNA analysis into our research. The updated Genealogy Standards indicate the following things are necessary when using DNA to help answer a research question (paraphrased, reorganized, and simplified from what is in the book):

There are many genealogical questions that can be answered without DNA evidence. However, if DNA is used these things should be considered along with all the standards that are not specific to using DNA.

Each of these bullet items will be discussed further in separate posts. The last three bullets seem to be causing the most discussion between genealogists.


All statements made in this blog are the opinion of the post author. This blog is not sponsored by any entity other than Debbie Parker Wayne nor is it supported through free or reduced price access to items discussed unless so indicated in the blog post. Hot links to other sites are provided as a courtesy to the reader and are not an endorsement of the other entities except as clearly stated in the narrative.

1. mohamed_hassan, DNA helix, Pixabay (https://pixabay.com/en/silhouette-dna-biology-medicine-3691934); Pixabay license, image modified by Debbie Parker Wayne.


To cite this blog post:
Debbie Parker Wayne, "DNA Standards - Part 1," Deb's Delvings, 4 March 2019 (http://debsdelvings.blogspot.com/ : accessed [date]).

© 2019, Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved
Posted by Debbie Parker Wayne, Certified Genealogist® at 9:52 AM 0 comments
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15 May 2018

Whole Genome Sequence (Part 2) - Analysis Tools

For earlier parts see
Whole Genome Sequence (Part 1) — YSEQ.net options and files received

I am investigating bioinformatics1 tools to analyze Whole Genome Sequence (WGS) data. I have access to a WGS for someone who has also tested at several genealogy testing companies. I want to do some comparisons between the raw data from the genealogy testing companies and the WGS, checking for accuracy of the reads. To satisfy my curiosity, I plan to investigate some of the medical implications and traits discussed in scientific papers.

Once I have multiple WGSs from relatives, I plan to do some comparisons as to whether segments that the testing companies indicate match really do match completely with the higher resolution data. I am interested in how closely the statistical predictions on linkage disequilibrium and crossovers mirror what is seen in real family multi-generational studies. For example, in the shared segments marked below, not every SNP is tested. A number of SNPs in a segment are tested and we assume the non-tested SNPs match based on statistical predictions.


My previous career in software development, testing, and support made me familiar with Open-Source Software so I look for available tools before spending time writing my own. Tools I am checking out include Samtools, National Center for Biotechnology Information's (NCBI) Genome Workbench, and Broad Institute's Integrative Genome Viewer (IGV).

This new BioRxiv paper is timely for my quest:

"A large-scale analysis of bioinformatics code on GitHub," by Pamela H Russell, Rachel L Johnson, Shreyas Ananthan, Benjamin Harnke, and Nichole E Carlson, doi: https://doi.org/10.1101/321919. The meaty data is in the supplemental material which consists of several large files (some over 200MB) linked from the article abstract.

By the way, just as with some of the best genealogy articles, the reference notes in this article led me to several additional sources I now need to consult.

As a woman, this sentence is especially depressing: "... the proportion of female contributors decreases for high-profile repositories and with seniority level in author lists".2 I hope this changes and more women participate in bioinformatics.



geralt, Pixabay (https://pixabay.com/en/learn-mathematics-child-girl-2405206/ : accessed 15 May 2018), CC0 Creative Commons.

I am impressed with how many databases and tools are out there for DNA analysis. I did not realize there are over 1,700 bioinformatics repositories and "23 'high profile' GitHub repositories containing source code for popular and highly respected bioinformatic tools."3 "Our analysis points to simple recommendations for selecting bioinformatic tools from among the thousands available."4 Some of these will not be useful for genealogy, but some will.

One tool aimed at the genetic genealogy community is Thomas Krahn's tool for annotating a BigY VCF file and identifying derived and novel SNPs.5 Thomas kindly shared this tool so others can do the analysis instead of having it done by his company YSEQ.net.

Some of the discussions in the scientific world parallel those we are having in the genealogy world.

"In recent years, the explosion of genomic data and bioinformatic tools has been accompanied by a growing conversation around reproducibility of results and usability of software. Reproducibility requires that authors publish original data and a clear protocol to allow repetition of the analysis in a paper."6 In the genealogy world we are discussing publicly available DNA data, such as on GEDmatch.com, allowing DNA analysis to be reproduced and referenced from a publication.



OpenClipart-Vectors, Pixabay (https://pixabay.com/en/analysis-biology-biotechnology-2025786/ : accessed 15 May 2018), CC0 Creative Commons.

"The bioinformatics field embraces a culture of sharing — for both data and source code — that supports rapid scientific and technical progress."7 In the genealogy world we are discussing privacy issues versus sharing data, especially with the recent proliferation of stories on law enforcement use of genealogy databases.

I have been musing on whether to learn Python or Ruby. A recent discussion with a young programmer had me leaning towards Python. Since the "greatest amount of code in the main dataset was in Javascript, followed by Java, Python, C++, and C"8 maybe I will stay with Javascipt and Java, which I already know, if I develop any new tools for web usage. I have a few tools I wrote in Perl for my own use that I hope to clean up and share eventually.

In addition to DNA adding to my knowledge of my family tree, it is forcing me to upgrade my data analysis knowledge and computer tools familiarity. I hope all of this study helps keep my mind active and reduces those "senior moments" that seem to occur more frequently with the years.


1. The science of collecting and analyzing complex biological data such as genetic code.
2. Pamela H Russell, et al., "A large-scale analysis of bioinformatics code on GitHub," 15 May 2018, BioRxiv pre-publication, https://doi.org/10.1101/321919, line 35.
3. Ibid., line 27.
4. Ibid., line 148.
5. Thomas Krahn, "bigY_hg39_pipeline.sh," GitHubGist (https://gist.github.com/tkrahn/283462028c61cd213399ba7f6b773893).
6. Russell, "A large-scale analysis of bioinformatics code on GitHub," line 84.
7. Ibid., line 120.
8. Ibid., line 208.

All statements made in this blog are the opinion of the post author. This blog is not sponsored by any entity other than Debbie Parker Wayne nor is it supported through free or reduced price access to items discussed unless so indicated in the blog post. Hot links to other sites are provided as a courtesy to the reader and are not an endorsement of the other entities except as clearly stated in the narrative.

To cite this blog post:
Debbie Parker Wayne, "Whole Genome Sequence (Part 2) - Analysis Tools," Deb's Delvings, 15 May 2018 (http://debsdelvings.blogspot.com/ : accessed [date]).

© 2018, Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved
Posted by Debbie Parker Wayne, Certified Genealogist® at 11:48 AM 2 comments
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09 October 2017

DNA Analysis: Random is Most Important Factor

Correctly analyzing DNA matches for genetic genealogy is much harder than most researchers may think.

What is the most important thing to remember when interpreting DNA matches to determine relationships?


CC0 License, Debbie Parker Wayne, Random DNA Word Cloud

Researchers must remember that random recombination and mutations make it impossible to predict exactly how much DNA, if any, will be shared by two people, in general. The charts giving shared percentages of 50%, 25%, 12.5%, and so on are based on statistical probabilities. Real life seldom ever exactly matches a statistical probability. One exception is that each person does inherit one-half of the autosomal DNA from each parent.

Any reader of a mail list, forum, or Facebook will constantly see questions such as, "I share XYZ% of DNA with personXYZ. What relationship do we share?" And that reader will see tons of responses such as, "You must be XYZ relationship." The more savvy researchers will indicate there are several likely relationships and point to charts such as The Shared cM Project.1 There are also some tools, such as the matrices on GEDmatch.com and the relationship predictions made by the testing companies, that use the statistical shared percentages to predict relationships.

Researchers must remember to use these predictions only as clues and not as a hard-and-fast limit to accurately analyze DNA findings.

The first chart below uses GEDmatch matrix tools to demonstrate how even full siblings can share widely varying amounts of DNA with a DNA match. Four full siblings are compared to a known fourth cousin. One sibling shares only 12.4 cM of atDNA, one shares 19.8 cM, one shares 50.2 cM, and one shares 52.1 cM. The second chart shows that the GEDmatch generations matrix tool predicting the number of generations between the test-takers varies from 4 to over 7. (GEDmatch changes the order of the siblings in the different matrix views.)


© 2017, Debbie Parker Wayne,
GEDmatch Shared atDNA Matrix, Siblings to 4C

>
© 2017, Debbie Parker Wayne,
GEDmatch Generations Matrix, Siblings to 4C

Blaine published "The Shared cM Project" data using a Creative Commons License which gives permission for others to use and adapt the data as long as the adaptation is also made freely available and follows a few other restrictions.

Jonny Perl at DNA Painter adapted the data to create a Shared cM Project tool that highlights relationships that have been shown to share a specified amount of DNA. There are some differences in the highlighted relationships for 12.4 and 52.1 shared cM as shown in the images below.


CC0 License, Jonny Perl,
DNA Painter Shared cM Project Tool, Heading


CC0 License, Jonny Perl,
DNA Painter Shared cM Project Tool, 52.1 shared cM


CC0 License, Jonny Perl,
DNA Painter Shared cM Project Tool, 12.4 shared cM

The moral of the story is, as the Genetic Genealogy Standards indicate, there may be more than one way to interpret DNA test results:
19. Interpretation of DNA Test Results. Genealogists understand that there is frequently more than one possible interpretation of DNA test results. Sometimes, but not always, these possible explanations can be narrowed by additional testing and/or documentary genealogical research. Genealogists further understand that any analysis of DNA test results is necessarily dependent upon other information, including information from the tester, and that the analysis is only as reliable as the information upon which it is based.2

1. Blaine T. Bettinger, "The Shared cM Project," The Genetic Genealogist (https://thegeneticgenealogist.com/). Search the blog posts for the most recent update to the project.
2. Genetic Genealogy Standards Committee, Genetic Genealogy Standards(http://www.geneticgenealogystandards.com/).

To cite this blog post: Debbie Parker Wayne, "DNA Analysis: Random is Most Important Factor," Deb's Delvings, 9 October 2017 (http://debsdelvings.blogspot.com/ : accessed [date]).

© 2017, Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved
Posted by Debbie Parker Wayne, Certified Genealogist® at 12:39 PM 3 comments
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25 August 2017

Free (for some) atDNA Analysis Workshop


Genetic Genealogy, using DNA to answer genealogical questions, is one of the hottest topics in genealogy today. Every professional researcher, really every researcher of any kind, needs a basic understanding of using the different DNA tests available, analysis tools, and writing about DNA analysis to incorporate it into research reports or essays. Researchers must understand how to correlate DNA evidence with documentary evidence to analyze a genealogical question, and they also must understand how to present DNA evidence in a format understandable by novices as one of the elements supporting a conclusion. A hands-on workshop helps understand the necessary skills.

Lone Star Chapter of APG is sponsoring a four-hour Autosomal (atDNA) Analysis Workshop at the upcoming 2017 TxSGS Family History Conference. Attendance will be free to all Lone Star Chapter of APG members. Non-members of the chapter must pay a registration fee ($50) to attend this limited-space workshop. The workshop will be on Saturday afternoon, 21 October 2017. The current schedule lists a 1:30pm start time, but the start time may change to 1:00pm. Check your conference schedule once you arrive.

This workshop is for researchers with high-beginner to intermediate level DNA knowledge and professional genealogists adding DNA clients. Topics covered in the workshop include a brief review of DNA inheritance and analysis tools for the match list, family trees, and DNA test results. A case study will illustrate DNA analysis, applying documentary and genetic evidence, and writing and reporting the results.


Lone Star Chapter members, or those who wish to renew or join the chapter to get this member benefit, should contact Treasurer Michael Belcher at mikeandvickib@mac.com. Michael can supply you with the code to enter during conference registration to get free registration for this four-hour workshop and he can assist with joining the chapter if you are not already a member. You must first be an APG member before joining the Lone Star Chapter.
(Note: the chapter website was not available at the time this blog was written.)

Conference and workshop registration is through the TxSGS website at http://www.txsgs.org/conference/registration/. Do not forget to enter the workshop code (obtained from Michael Belcher) or you will be charged for the workshop registration.

This workshop is presented by me. For those who may not know my background, I am co-author (with Blaine T. Bettinger) of the popular, first-ever genetic genealogy workbook, Genetic Genealogy in Practice, published by the National Genealogical Society (NGS); author of the online, self-paced course Continuing Genealogical Studies: Autosomal DNA, offered by NGS; coordinator of the first DNA courses presented at all four of the major genealogy institutes (GRIP, SLIG, IGHR, CAFG FGI); and the DNA Project Chair for the Texas State Genealogical Society and the Early Texans DNA Project. Other publications include a column on using DNA analysis for genealogical research in NGS Magazine from 2013 to the present, many DNA articles in TxSGS journal Stirpes, articles in the APG Quarterly, and other regional journals. More information and archived versions of many of these articles can be found at http://debbiewayne.com/pubs.php.


The Texas State conference is one of the biggest annual conferences in the area with many fine speakers known nationally, regionally, and locally. Check out all of the other informative sessions available from conference headliners J. Mark Lowe, CG, and Dr. Michael Lacopo as well as the many sessions presented by Deborah A. Abbott, PhD; Susan Ball; Andrew Carroll; Henrietta Martinez Christmas; Deena Coutant; Schelly Talalay Dardashti; Patti Todd Gillespie; Sara Gredler; Colleen (Robledo) Greene; Tony Hanson; Susan Kaufman; Andrew Lee; Devon Noel Lee; Janice Lovelace; Bernard Meisner; Kelvin L. Meyers; Betsy Mills; Jeannette Piecznski; Diane Richard; Mary Kircher Roddy; Michael L. Strauss, AG; Cari Taplin, CG; Lisa Toth Salinas; Angela Walton-Raji; and Eric Wells.

We hope to see you all there at this must-see event in Texas, 20–22 October 2017 in Katy (just west of Houston).


To cite this blog post: Debbie Parker Wayne, "Free (for some) atDNA Analysis Workshop," Deb's Delvings, 25 August 2017 (http://debsdelvings.blogspot.com/ : accessed [date]). © 2017,
Debbie Parker Wayne, Certified Genealogist®, All Rights Reserved

The words Certified Genealogist are a registered certification mark, and the designations CG, CGL and Certified Genealogical Lecturer are service marks of the Board for Certification of Genealogists®, used under license by board certificants after periodic evaluation.

The ICAPGenSM service mark and the Accredited Genealogist® and AG® registered marks are the sole property of the International Commission for the Accreditation of Professional Genealogists. All Rights Reserved.
Posted by Debbie Parker Wayne, Certified Genealogist® at 9:43 AM 0 comments
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