DNA Triangulation, What?

Triangulation is a term derived from surveying to describe a method of determining the Y-STR or mitochondrial DNA ancestral haplotype using two or more known data points. The term “Genetic Triangulation” was coined by genetic genealogist Bill Hurst in 2004 Triangulate

Here is a 3-step process for Triangulation: Collect, Arrange, Compare/Group.

  1. Collect all the Match-segments you can. I recommend testing at all three companies (23andMe, FTDNA, and AncestryDNA), and using GEDmatch. But, wherever you test, get all of your segments into a spreadsheet. If you are using more than one company, you need to download, and then arrange, the data in the same format as your spreadsheet. Downloading/arranging is best when starting a new spreadsheet. Downloading avoids typing errors, but direct typing is sometimes easier for updates. I recommend deleting all segments under 7cM – most of them will be IBC/IBS (false segments) anyway, and even the ones which may be IBD are very difficult to confirm as such. You are much better off doing as much Triangulation as you can with segments over 7cM (or use a 10cM threshold if you wish), and then adding smaller segments back in later, if you want to analyze them. NB: Some of your closer Matches will share multiple segments with you – each segment must be entered as a separate row in your spreadsheet. The minimum requirement for a Triangulation with a spreadsheet includes columns for MatchName, Chromosome, SegmentStartLocation, SengmentEndLocation, cMs and TG. Most of us also have columns for SNPs, company, testee, TG, and any other information of interest to you. Perhaps I need a separate blog post about spreadsheets… ;>j
  1. Arrange the segments by sorting the entire spreadsheet (Cntr-A) by Chromosome and Segment StartLocation. This is one sort with two levels – the Chromosome column is the first level. This puts all of your segments in order – from the first one on Chromosome 1 to the last one on Chromosome 23 (for sorting purposes I recommend changing Chromosome X to 23 or 23X so it will sort after 22). This serves the purpose of putting overlapping segments close to each other in the spreadsheet where they are easy to compare.
  1. Compare/Group overlapping segments. All of these segments are shared segments with you. So with segments that overlap each other, you want to know if they match each other at this location. If so this is Triangulation. This comparison is done a little differently at each company, but the goal is the same: two segments either match each other, or they don’t (or there isn’t enough overlapping segment information to determine a match). All the Matches who match each other will form a Triangulated Group, on one chromosome – call this TG A (or any other name you want). Go through the same process with the segments who didn’t match TG A. They will often match each other and will form a second, overlapping TG, on the other chromosome – call this TG B. [Remember you have two of each numbered chromosome.] So to review, and put it all a different way: All of your segments (every row of your spreadsheet) will go into one of 4 categories:
  • – TG A [the first one with segments which match each other]
  • – TG B [the other, overlapping, one with segments which match each other]
  • – IBC/IBS [the segments don’t match either TG A or TG B]
  • – Undetermined [there are not enough segments to form both TG A and TG B                            and/or there isn’t enough overlapping data to determine a match.]
  • NB: None of the segments in TG A should match any of the segments in TG B.
  1. At GEDmatch – the comparisons are easy. Just compare two kit numbers using the one-to-one utility to see if they match each other on the appropriate segment. The ones that do are Triangulated. You may also use the Tier1 Triangulation utility or the Segment utility. I prefer using the one-to-one utility and Chrome.
  1. At 23andMe you have several different utilities:
  • – Family Inheritance: Advanced lets you compare up to 5 Matches at a time. You may also request a spreadsheet of all your shared segments; sort that by chromosome and SegmentStart, and check to see if two of your Matches match each other. The ones that do are Triangulated.
  • – Countries of Ancestry: Sort a Match’s spreadsheet by chromosome and SegmentStart, search for your own name, and highlight the overlapping segments. The Matches on this highlighted list who are also on overlapping segments in your spreadsheet are Triangulated (the CoA spreadsheet confirms the match between two of your Matches)
  1. At FTDNA it’s a little trickier, because they don’t have a utility to compare two of your Matches. So the most positive method is to contact the Matches and ask them to confirm if they match your overlapping Matches, or not. The ones that do are Triangulated. An almost-as-good alternative is to use the InCommonWith utility. Look for the 2-squigley-arrows icon next to a Match’s name, click that, and select In Common With to get a list of your Matches who also match the Match you started with. Compare that list of Matches with the list of list of Matches with overlapping segments in your spreadsheet. Matches on both lists are considered to be Triangulated. Although this is not a foolproof method, it works most of the time. And if you find three or four ICW Matches in the same TG, the odds are much closer to 100%. Remember, every segment in your spreadsheet must go in one TG or the other, or be IBC/IBS, or be undetermined. If a particular Match, in one TG, is critical to your analysis, then try hard to confirm the Triangulation by contacting the Matches.
  1. AncestryDNA has no DNA analysis utilities. You need to convince your Matches to upload their raw data to GEDmatch (for free) or FTDNA (for a fee), and see the paragraphs above.

Comments to improve this blog post are welcomed.

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Some Genes Are Dominant Concept 4

 

 

Ref: DNA from the Beginning.org

Mendel believed that genes behave like atoms that compose a pure substance. Genes can combine in various ways but always maintain their distinct identities. For example, in a cross between two pure-bred parents with different traits like seed color, the hybrid offspring would have both the gene alternates for green and yellow seed color.

Why then do offspring from such a cross have only yellow seeds? Mendel proposed that although both gene alternates are present, there is no blending of color because the gene alternate for yellow is “dominant” over the gene alternate for green. The dominant trait is seen whenever a single copy of its gene is inherited. When he crossed the hybrid offspring, green seeds reappeared in the next generation. Mendel reasoned that the “recessive” green trait is shown only when a copy of the recessive gene form is inherited from each parent.

Genes Don’t Blend Concept 3

 

 

Ref: DNA from the Beginning.org

In general, offspring appear to be a mixture of parental characteristics. However, Mendel found that this is not true for the pea plant traits that he chose to study. Pure-bred pea plants when crossed did not produce offspring with blended traits.

For example, one might expect that a cross between pure-bred green-seeded and pure-bred yellow-seeded pea plants to produce offspring with seeds of an intermediate green-yellow color. After all, color blending happens when paint is mixed together. However, Mendel found that this cross produced offspring with only one color — yellow. No intermediate blends were seen, and the green color seemed to have disappeared.

Genes Come In Pairs Concept 2

 

 

Ref: DNA from the Beginning.org

Rather than looking at the pea plant as a whole, Mendel focused on seven individual traits that he could readily distinguish. He found that each trait has two alternate forms. For example, seed color can be green or yellow. By analyzing the results of various crosses, Mendel concluded that each alternative form of a trait is specified by alternative forms of a gene.

To follow the inheritance of genes from parent to child, Mendel first needed to be sure which genes each parent carried. Since pea plants are naturally self-fertilizing, “pure-bred” strains were readily available. Each strain contained only one form of the gene that determined a trait. Pure-bred plants with yellow seeds only produced offspring with yellow seeds. Pure-bred plants with green seeds only produced offspring with green seeds. From the results of further experiments, Mendel reasoned that pure-bred plants must have two copies of the same gene for each trait.

We Resemble Our Parents – Concept 1

 

 

Ref: DNA from the Beginning.org

Since the beginning of human history, people have wondered how traits are inherited from one generation to the next. Although children often look more like one parent than the other, most offspring seem to be a blend of the characteristics of both parents. Centuries of breeding of domestic plants and animals had shown that useful traits — speed in horses, strength in oxen, and larger fruits in crops — can be accentuated by controlled mating. However, there was no scientific way to predict the outcome of a cross between two particular parents.

It wasn’t until 1865 that an Augustinian Monk named Gregor Mendel found that individual traits are determined by discrete “factors,” later known as genes, which are inherited from the parents. His rigorous approach transformed agricultural breeding from an art to a science. He started with parents of known genetic background — to provide a baseline against which to compare patterns of inheritance in the resulting offspring. Then he carefully counted the numbers of individuals showing the various traits in successive generations of offspring.

 

Leontyne Clay Peck: Her Story from Piedmont WV to Virginia Piedmont (Gedmatch)

DNA Ethnicity Report Offer by My Heritage

MyHeritage is Now Offering Free DNA Ethnicity Reports to All Uploaders

MyHeritage is Now Offering Free DNA Ethnicity Reports to All Uploaders

As we do with many genealogy companies, we have partnered with MyHeritage to bring you news and information about their services. We do not earn a commission from My Heritage.

MyHeritage has announced today that they have released an updated 42 population Ethnicity Estimate and are offering it free to anyone who uploads their DNA. MyHeritage has been accepting free uploads of DNA and providing matching for some time but, until now, ethnicity reports were only available to those who purchased a MyHeritage DNA test.

Now anyone who has already tested with Family Tree DNA, AncestryDNA or 23andMe can upload raw data to MyHeritage and get the Ethnicity Estimate without cost. MyHeritage also offers the ability to upload all of the DNA kits you manage to your account and pair them with people in your family tree – tying your family history and DNA research together in a very useful way. Kits can be deleted or re-assigned at any time.

To upload your DNA if you already have a MyHeritage account or want a free account with no record access:

If you already have an account with MyHeritage you can upload your DNA file here to get your Ethnicity Estimate. They have provided a simple step-by-step process for uploading your data and instructions for how to download your raw DNA from your testing company first. The process only took us about 2 minutes. If do not already have an account you will simply be offered a free one that does not include historical record access when you visit the DNA upload page linked to above.

How to upload your DNA if you would like to pair it with historical record access:

If you plan to pair your DNA upload with your family history research and would like access to MyHeritage’s 7+ billion records you can get a free two week trial to everything on MyHeritage here first. Once you sign up for the trial you will be granted an account and will be able to easily upload your DNA. This is optional and not required for the free DNA upload but can be very helpful in your research if you can afford the small subscription fee.

The consent forms you need to read:

You will notice on the DNA Upload Page that MyHeritage has two consent boxes you can check before taking part. The first one is required. Carefully read the terms and decide if they are acceptable to you before checking this box. The second one is their consent to take part in research and analytics and is voluntary. Read the consent form and decide if you would like to have your results used for the purposes described, which include scientific and health research. We really like that MyHeritage has made this optional and encourage you to read and consider carefully before deciding.

If you have not yet tested your DNA you can read our complete guide for choosing the best test for you or order a DNA test from MyHeritage directly.

More information about the new Ethnicity Estimates can be found in the release from MyHeritage below. 

MyHeritage today announced the launch of its new and improved Ethnicity Estimate. The new analysis, developed by the company’s science team, provides MyHeritage DNA customers with a percentage-based estimate of their ethnic origins covering 42 ethnic regions, many available only on MyHeritage, representing the most comprehensive report of its type available on the market. This fascinating report gives users a much better understanding of who they are and where their ancestors came from. The Ethnicity Estimate is presented in an original and engaging format, making it not only interesting but also fun to watch and share.

MyHeritage is unique among the main industry players in allowing users who have tested their DNA already with another service to upload – for free – their data to MyHeritage. Those users receive DNA Matches for free, for finding relatives based on shared DNA. Beginning this week, users who have already uploaded their DNA data to MyHeritage, or who will upload it in the coming months, will receive – for free – the new Ethnicity Estimate. This benefit is not offered by any other major DNA company.

Development of the new Ethnicity Estimate raises the number of ethnic regions covered by MyHeritage DNA from 36 to 42. It was made possible thanks to MyHeritage’s Founder Populations project — one of the largest of its kind ever conducted. For this unique project, more than 5,000 participants were handpicked by MyHeritage from its 90 million strong user base, by virtue of their family trees exemplifying consistent ancestry from the same region or ethnicity for many generations. All project participants received complimentary DNA tests and allowed MyHeritage’s science team to develop breakthrough ethnicity models based on the generated data. Thanks to this analysis, MyHeritage DNA has become the only mass-market percentage-based DNA test that reveals ethnicities such as Balkan; Baltic; Eskimo & Inuit; Japanese; Kenyan; Sierra Leonean; Somali; four major Jewish groups – Ethiopian, Yemenite, Sephardic from North Africa and Mizrahi from Iran and Iraq; Indigenous Amazonian; Papuan and many others. In some cases, competing products can identify and report an aggregated region (e.g., Italian & Greek), whereas MyHeritage has better resolution and identifies Greek, Italian and Sardinian ethnicities separately.

MyHeritage’s new Ethnicity Estimate is delivered to users via a captivating “reveal” experience. It features animation and, as of this week, also original music composed by MyHeritage. Each of the 42 ethnicities has a distinctive tune, based on the region’s cultural elements; all tunes seamlessly connect to each other.

“DNA is the future of the family history industry and we’re delighted to enter the DNA space with strong energies and a fresh perspective”, said Gilad Japhet, Founder and CEO of MyHeritage. “Leveraging MyHeritage’s top assets which are its talented, technology-focused engineering team, and the gigantic internationally diverse web of family trees encompassing more than 2.5 billion profiles entered by our users, our comprehensive new Ethnicity Estimate has Innovation written all over it. We’ve been able to dig deeper where others had considered their work complete. Presented in a fresh look and generously given for free to DNA data uploaders, our users will be thrilled and can count on us to continue to innovate in DNA and delight them with new discoveries about who they really are.”

Dr. Yaniv Erlich, Chief Science Officer at MyHeritage, said, “For MyHeritage’s science team, this major update of our Ethnicity Estimate is only an appetizer. There are excellent installments on the way, and users can prepare for a feast! We have detailed plans to increase accuracy, extend our Founder Populations project further, and improve the resolution for ethnicities of great interest to our users from highly diverse origins. Our goal is to use science to further the public good, and to bring the best innovations of our science team to the public.”

The company’s user base of 90 million users worldwide, more than 7.7 billion historical records, massive user-generated family tree database and availability in 42 languages, all provide a robust foundation for MyHeritage DNA. The company’s DNA offering currently provides two main features: detailed ethnicity reports that reveal the user’s ethnic and geographic origins, and DNA Matches for finding relatives based on shared DNA. In recent months, people have been successfully using MyHeritage DNA to reunite with long-lost family members.

Order MyHeritage DNA or upload your DNA data for free.

The Lowdown by BlackProGen “Its really hard to believe! Struggling with African American Ancestry Research.

The Lowdown by BlackProGen

 

 

It’s really hard to believe! Struggling with African American Ancestry Research.

Posted: 08 Jul 2017 07:40 AM PDT

Why am I still doing genealogy research? Just a few thoughts have popped into my head. As a researcher sometimes I struggle with some of the facts/evidence I find. It forces me to come to terms with what I think of the human race and being an American overall. Some of the information is really interesting, exciting and some are horrible and unbelievable and the tears flow. Sometimes I just have to pray in order to stop myself becoming just like them. Today is July 8th and the KKK has planned a rally in Charlottesville. All this negative energy going on causes me also to struggle. I wish the media would stop flying the hype and BS and just ignore them. Now the praying really begins as I pray for peace and safety for all during the rally.

I am well aware of the challenges and struggles individuals will face when conducting African American ancestry. These challenges will surface dealing with other ancestry research as well. I too have the “brick wall challenges” just like anyone else. When doing African American ancestry researchers will face some of the following challenges:

§ Records not recorded into public record

§ Records destroyed

§ Denial-don’t want to know, it’s the past

§ Knows the info, but won’t share

§ Lack of access to information

§ Received information that is not the truth or reliable-questionable Oral History

§ Do you really have a brick wall/challenge? Did you create one?

§ You don’t know what you have-no analysis was done on the records (SO WHAT!)

§ Things are in the “house repositories” and not being shared

§ Not using FAN Principle by (E. Shown Mills)

§ Not using the Murphy’s “So What” concepts of analyzing information

§ Jumping out of the box too quick with assumptions and no evidence!

§ 21st century thinking

These challenges have to be worked out and resolved. Some might be conflicts or gaps. Some other things I struggle with are: the ownership of human beings, the selling of babies, families being torn apart, the Christian religion, rapes, and the killings. Yes, I said the Christian religion and that would be another conversation. Sometimes it is too much to bear and I have to close the file or the book. Just think, some individual’s, as in African Americans who survived the 18th and 19th century really don’t know whom their parents are or even what their real name is. This is not just those who were slaves, free born folks faced some horrendous conditions as well. Don’t assume they had it better. The readings will have you cringe on some of the things they faced. I have read in several different books and articles that once the Civil war was over some, now freed slaves spent the rest of their life searching for their family. Family: mother, father, and siblings or even aunts and uncles, etc. Can you image the lost feelings folks went through? How could this country allow this to happen?

Recently there was an article written by Shaun King about Thomas Jefferson and Sally Hemming’s relationship. Shaun was very clear, I mean very clear this was rape and basically folks need to stop romanticizing the relationship. (http://www.nydailynews.com/news/national/king-thomas-jefferson-evil-rapist-owned-600-slaves-article-1.3308931)

Well Shaun King I have to agree with you. You nailed it right on the head. I can’t let all of the ugly be won over by the good. Some things will not get a pass from me. Mr. Jefferson continued to live with the fact that he owned people, broke up families and sold children away from their parents, etc.

This all becomes emotional and we won’t heal all of it but we will have to deal some of it. The emotional side individuals will have to prepare themselves as to how they will deal with the information and how they will share the information. I often ask myself is it my role as a researcher to tell some of these emotional things, or should I stay in my lane and just hand over the information. As researching how do we overcome our struggles or do we?

Happy Root Digging!

 

 

This posting includes an audio/video/photo media file: Download Now

Help Drive Research Forward for African Americans

23andMe Post

We believe genetics and the study of disease should be for everyone.
All ethnicities. All people.

Help drive research forward for African Americans.

Join now!

Questions: contact study-help@23andMe.com

Why your help is so important.

Less than 5% of research on the genetics of disease includes people of African ancestry. If people with diverse ancestries continue to be underrepresented in genetics research, then we risk missing key medical and other scientific discoveries that could benefit everyone.

If you participate in the African American Sequencing Project, you could help address this disparity. By sharing your genetic data with the scientific community, you can shape the future of genetics research to include people of African descent.

Only a fraction of genetic research studies have included people of African descent.

Popejoy, A. B. & Fullerton, S. M. Nature 538, 161-164 (2016).

See if you’re eligible

To be eligible for this study you must be a 23andMe customer, have consented to 23andMe Research, self identify as African or African American and be at least 18 years old.

How it works

You do not need to provide a new saliva sample — we will use the one you already sent us.

There is no cost to participate.

You consent to share your genetic data.

Enroll and agree to share your de-identified genetic information with researchers approved by the National Institutes of Health (NIH) and qualified research partners of 23andMe.

None of your contact information or answers to 23andMe surveys will be shared.

We will sequence your genome.

If you are selected, we will send your saliva sample, already provided to 23andMe, to a lab for whole genome sequencing. Whole genome sequencing is a more thorough but also more costly review of your genome than that provided by the genotyping analysis used to generate your 23andMe reports. *This is extremely important. The real cost to an individual is about $1200 with most labs. Entire genome sequencing means all of your DNA in your body. I am a member of the Ethnicity Research Group studying and identify the location specific location of African and African-American ancestors and I also participate in the L2 study group, this later group requires identification with a person of African origin. right now these two groups are closed.

For more information on sequencing versus genotyping watch this video or read this article.

We will provide data to researchers around the world.

23andMe will share this sequenced genetic data with researchers by depositing it into a scientific database approved by the NIH. Approved researchers will have access to this data to conduct genetics research.

About this project

In October 2016, 23andMe was awarded a grant by the National Human Genome Research Institute, a major research arm of the National Institutes of Health, to fund the African American Sequencing Project.

This project is part of our broad commitment to diversity in genetics research. Learn more about 23andMe’s Roots into the Future Project.

Privacy and Security

We do not share your genetic information without your explicit authorization. Only you can decide if you would like to participate in this project by authorizing 23andMe to share your information with outside researchers.

Even though you previously consented to participate in 23andMe Research, you will need to read and accept additional consents to participate in this study.

Hi. Have additional questions about the African American Sequencing Project?

If you don’t see your question here, get in touch with us.

  • What does it mean to be a research participant in this project?

  • Why is 23andMe conducting the African American Sequencing Project?

  • Will you share my genetic data with third parties?

  • Do I need to provide a new saliva sample to 23andMe?

  • How will you protect the confidentiality of my data?

  • What is whole genome sequencing? How is this process different from genotyping, the process previously used by 23andMe to analyze the DNA in my saliva sample?

  • How do you select participants for this study?

  • Will I have access to my sequenced data?

  • What am I agreeing to if I accept the consent documents for this project?

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