Gedmatch Autosomal DNA Segment Analyzer (ADSA)

Autosomal DNA Segment Analyzer (ADSA)
GEDMATCH Quick Start Guide

ICW means In-Common-With were ever used

To use GEDMATCH with ADSA you must be a Tier 1 GEDMATCH member. That means you must have, at some time, donated at least $10 to GEDMATCH. The GEDMATCH upload process for DNAgedcom.com depends on two Tier 1 tools: Matching Segment Search and Triangulation which you cannot access unless you are a Tier 1 member. And, of course, you must have loaded your raw data to GEDMATCH previously so that it has been tokenized and batch processing is completed.

Some other things to be aware of:

  • Certain fields that are available for Family Tree DNA kits are not presently available for GEDMATCH. These include:

    Match Date

    Predicted Relationship

    Known Relationship

    Relationship Range

    Haplogroups

    Surnames

    Total Shared cM

    Longest Block cM

    So, this means that using these for sorting, selection, highlighting or display purposes may not have the results you wanted because these fields are empty in a GEDMATCH kit.

  • To manage processing load on GEDMATCH’s servers, only the In-Common-With indicators for your top 400 matches are provided by GEDMATCH, so you will only have ICW bricks in the ADSA report for your longer segments. You can manually determine ICWs for other matches by doing a one-to-many report for one of your matches and comparing their list of matches to yours.

  • Generally, there are a lot more segments in a GEDMATCH ADSA report than for Family Tree DNA. This tends to slow down the responsiveness of your browser when viewing the ADSA report. You may wish to increase the minimum segment size in ADSA to 10 cM(Centimorgans)

  • The GEDMATCH tools that are used to gather the data for DNAgedcom exclude very close relatives (eg. siblings, parents, children) to improve processing performance, so you will not see them as matches on your ADSA report for GEDMATCH kits.

  • The X chromosome matches are not presently included in GEDMATCH kits.

To get started, follow these steps.

  1. If you haven’t already done so, go to www.DNAgedcom.com and click on “Register”:

  2. Register for a free account at DNAgedcom.com:

  3. Logon to DNAgedcom.com with your new username and password:

  4. Prepare to upload your GEDMATCH data to DNAgedcom.com:

    You will see a screen with a large, square text input box. Do not enter anything here yet.

  5. Leaving the window above open, create a new browser window or tab and go to the www.gedmatch.com and

    logon

    . Click on “Matching Segment Search” in the Tier 1 tools menu near the bottom of the screen:

  6. Enter your kit number and click “No” on the graphic bar (very important!) and click “Submit”:

  7. Now wait for the report to finish – it will probably take a few minutes. When it is complete it will look something like this:

    Select everything on the screen and copy it to the clipboard. In

    Windows

    you can do this using

    ctrl-a

    followed by ctrl-c. On a

    Mac

    you can use command-a and command-c. You may have to wait a little while for the copy to complete. There is a lot of data there to copy. (If you don’t wait long enough, when you paste the information into DNAgedcom you won’t get what you copied. You may see a

    hour-glass

    or spinning beach-ball while the copying is going on.

    Usually

    the copy process doesn’t take more than a minute or two.)

  8. Go to the browser window you have open to DNAgedcom.com. Click

    in

    the square box and paste what you copied into it. On

    Windows

    you can use Ctrl-v or you can use command-v on a Mac.You should see a portion of what you copied like this:

    Click the “Load” button. The load should complete in a few seconds.

  9. Click the Clear button to erase the text-input box again and return to your GEDMATCH browser window. Return to the main GEDMATCH menu again.

  10. Now click on the Triangulation tool.

  11. Enter your GEDMATCH kit number and select the middle radio button (very important!) and click on the “Triangulate” button:

  12. Wait for the report to complete. The Triangulation report may take longer than the Matching Segment Report depending on how many In-Common-With matches you have and the current load on GEDMATCH’s servers. When it finishes there will be 4 rows of asterisks on the screen and the screen will look something like this:

    Once again, select the entire page (ctrl-a or command-a) and copy it to the clipboard (ctrl-c or command-c). Wait for the copy to complete. Then switch back to your DNAgedcom browser window.

  13. Make sure the text-input box in DNAgedcom is empty (use the Clear button if you need to) and then paste the Triangulation report into the box with ctrl-v or command-v. Then click on the Load button.

  14. When the Load process completes the screen will refresh. You can now go to ADSA by selecting the Autosomal Tools menu and the Autosomal DNA Segment Analyzer option on that menu. Or you can go to this link: http://www.dnagedcom.com/adsa. You will see a screen like this:

  15. Select your kit from the drop-down menu. GEDMATCH kits will start with a letter (A=Ancestry, F=FTDNA, M=23andMe etc.):

  16. Click GET REPORT

  17. If you have Ashkenazi ancestry or are part of an endogamous (interrelated) group you may not be able to generate a report with the default input parameters. Please consult the Tips for People with Ashkenazi Ancestry page before clicking GET REPORT.

For more information about this process, how to interpret your results, or troubleshooting, read the full ADSA manual.

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Proposed Algorithm to Study DNA Faster

Scientists propose an algorithm to study DNA faster and more accurately

January 18, 2016
Stylized image of DNA
Stylized image of DNA. Credit: bioinformatics101.wordpress.com

A team of scientists from Germany, the United States and Russia, including Dr. Mark Borodovsky, a Chair of the Department of Bioinformatics at MIPT, have proposed an algorithm to automate the process of searching for genes, making it more efficient. The new development combines the advantages of the most advanced tools for working with genomic data. The new method will enable scientists to analyse DNA sequences faster and more accurately and identify the full set of genes in a genome.

Although the paper describing the  only appeared recently in the journal Bioinformatics, which is published by Oxford Journals, the proposed method has already proven to be very popular—the computer  has been downloaded by more than 1500 different centres and laboratories worldwide. Tests of the algorithm have shown that it is considerably more accurate than other similar algorithms.

The development involves applications of the cross-disciplinary field of bioinformatics. Bioinformatics combines mathematics, statistics and computer science to study biological molecules, such as DNA, RNA and protein structures. DNA, which is fundamentally an information molecule, is even sometimes depicted in computerized form (see Fig. 1) in order to emphasize its role as a molecule of biological memory. Bioinformatics is a very topical subject; every new sequenced genome raises so many additional questions that scientists simply do not have time to answer them all. So automating processes is key to the success of any bioinformatics project, and these algorithms are essential for solving a wide variety of problems.

One of the most important areas of bioinformatics is annotating genomes – determining which particular DNA molecules are used to synthesize RNA and proteins (see Fig. 2). These parts –  – are of great scientific interest. The fact is that in many studies, scientists do not need information about the entire genome (which is around 2 metres long for a single human cell), but about its most informative part – genes. Gene sections are identified by searching for similarities between sequence fragments and known genes, or by detecting consistent patterns of the nucleotide sequence. This process is carried out using predictive algorithms.

Locating gene sections is no easy task, especially in eukaryotic organisms, which includes almost all widely known types of organism, except for bacteria. This is due to the fact that in these cells, the transfer of genetic information is complicated by “gaps” in the coding regions (introns) and because there are no definite indicators to determine whether a region is a coding region or not.

Diagram showing the transmission of hereditary information in a cell
Diagram showing the transmission of hereditary information in a cell. Credit: dnkworld.ru/transkripciya-i-translyaciya-dnk

The algorithm proposed by the scientists determines which regions in the DNA are genes and which are not. The scientists used a Markov chain, which is a sequence of random events, the future of which is dependent on past events. The states of the chain in this case are either nucleotides or nucleotide words (k-mers). The algorithm determines the most probable division of a genome into coding and noncoding regions, classifying the genomic fragments in the best possible way according to their ability to encode proteins or RNA. Experimental data obtained from RNA give additional useful information which can be used to train the model used in the algorithm. Certain gene prediction programs can use this data to improve the accuracy of finding genes. However, these algorithms require type-specific training of the model. For the AUGUSTUS software program, for example, which has a high level of accuracy, a training set of genes is needed. This set can be obtained using another program – GeneMark-ET – which is a self-training algorithm. These two algorithms were combined in the BRAKER1 algorithm, which was proposed jointly by the developers of AUGUSTUS and GeneMark-ET.

BRAKER1 has demonstrated a high level of efficiency. The developed program has already been downloaded by more than 1500 different centres and laboratories. Tests of the algorithm have shown that it is considerably more accurate than other similar algorithms. The example running time of BRAKER1 on a single processor is ∼17.5 hours for training and the prediction of genes in a genome with a length of 120 megabases. This is a good result, considering that this time may be significantly reduced by using parallel processors, and this means that in the future, the algorithm might function even faster and generally more efficiently.

Tools such as these solve a variety of problems. Accurately annotating genes in a genome is extremely important – an example of this is the global 1000 Genomes Project, the initial results of which have already been published. Launched in 2008, the project involves researchers from 75 different laboratories and companies. Sequences of rare gene variants and gene substitutions were discovered, some of which can cause disease. When diagnosing genetic diseases, it is very important to know which substitutions in gene sections cause the disease to develop. The project mapped genomes of different people , noting their coding sections, and rare nucleotide substitutions were identified. In the future, this will help doctors to diagnose complex diseases such as heart disease, diabetes, and cancer.

BRAKER1 enables scientists to work effectively with the genomes of new organisms, speeding up the process of annotating genomes and acquiring essential knowledge about life sciences.

 Explore further: Novel algorithm better assembles DNA sequences and detects genetic variation

Read more at: https://phys.org/news/2016-01-scientists-algorithm-dna-faster-accurately.html#jCp

No One testing Company Can Provide Best Matches

No One testing Company Can Provide Best Matches

Nobody can predict which database is going to have your best matches because it is somewhat a matter of chance of who tests where. Not all of your relatives or potential relatives are going to test at the same company. Also, the algorithms (mathematical formula) is not the same for each testing company.

The big 3 companies at the moment are Ancestry.com, 23andMe, and FTDNA. In Europe, it is GPS and Living DNA. You can test with the later if you have European roots.

I would highly recommend uploading your data to the free site www.gedmatch.com which acts as a central site for intercompany compares. Since it is on a volunteer basis, it only has some of the results from each company, but it does tend to attract the most interested researchers, and therefore should have a good response rate if you attempt contact. You can upgrade to Tier 1 for advanced data manipulations for $10.00 per month.

Once you get uploaded, try the one-to-many lookup. You can see the original source of a contributor by the first letter of his kit code. (A=ancestry, M=23andme, T=FTDNA).

23andMe Cleared to Provide Health Reports

Pharmaceutical Companies are not liking this at all.

Purchasers of 23andMe (http://www.23andMe.com) Health + Ancestry DNA test now have access to genetic health risk reports for conditions including late-onset Alzheimer’s disease, Parkinson disease, Celiac disease and seven others.

This is a big step, if incremental, step forward for the company. Its DNA service initially provided ancestry information and genetic risk reports on about 250 conditions. In 2013, the FDA ordered 23andMe to stop providing health-related information to US customers because the company hadn’t proven its test were analytically or clinically validated.

The new reports calculate genetic risk based on the presence (or absence) of specific markers in a person’s DNA. To obtain FDA authorization for them, 23andMe conducted “extensive validation studies for accuracy and user comprehensive that met FDA standards,” according to its announcement. FDA considered evidence tying each condition with relevant genetic markers in customers’ DNA.

Take a look at the new 23andMe reports at (http://www.blog.23andme.com/health-traits/learn-23andme-new-genetic-health-risk-reports)

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?

Discovering DNA Communities – Ethnic Origins

A new study uses genetic data and genealogical research from more than 700,000 Ancestry.com <ancestry.com> customers to reveal migration trends in North America over the past 300 years. Findings, which were published in the journal Nature Communications <www.nature.com/article/ncomms14238>, are the basis of AncestryDNA’s Genetic Communities user experience.
According to an Ancestry,com announcement, the study shows “how specific groups of people are connected through their DNA, what places they called home, and which migration paths they followed to get there.” The results correspond strongly with documented history and the results of genetic data done by 23andMe, GPS DNA and Family Tree DNA.
Researchers first identified genetically related groups and smaller clusters within them. Then they used family trees associated with those similar DNA profiles to describe the geographic origins and migration patterns within each cluster. Of specific interest were communities that have develop distinguishable genetic patterns due to “gene flow barriers” such as isolated geographic locations or cultural identity that encourages mating within the community.
Unfortunately, there has not been a methodology research model to reasonably determine African-American and Native-American clusters based on the above mention. The DNA Communities does afford African-American and Native-Americans the opportunity to identify additional relationships based on the DNA Community findings.
If you are a member of FamilyDNA, GPS DNA or 23andMe you will find similar clusters and ethnic communities base on similar methods. The National Geographic Project (Geno 2) was the first and is still actively working to define their results. The only draw back for most is the cost which is over $200 to participate.

 

Discover Your Roots with DNA

Source: DNA Testing Advisor (www.dna-testing-adviser.com/african-dna-test) Access on May 18, 2017

Discover Your Roots
with an African DNA Test

African Outline

Many African Americans and others are using an African DNA test to get answers about their ethnic ancestry.

Typical questions include the following:

  • How much of my genetic heritage is African?
  • What regions of Africa do my ancestors come from?
  • Where does the remainder of my heritage come from?
  • Is my African ancestry from my father’s lineage or my mother’s?
  • Do my physical features reflect African ancestry or something else?

Fortunately, there are several reasonably-priced African DNA tests that answer these and other questions about one’s ethnic ancestry.

The tests all use home test kits and sample collection is easy and painless. Depending on which company you use, you might wipe some cells from inside your cheek with a little swab or spit some saliva into a tube. No blood is required.

Here are my top seven recommendations for anyone interested in an African DNA test.

1. Ancestry DNA

AncestryDNA recently rose to the top of this list. Both men and women can take the test and it will identify other people in the database who share common ancestors with you. It is an autosomal test similar in technology to Family Finder and 23andMe, discussed below.

The test includes an Ethnicity Estimate that summarizes the percentage contributions of different regions of the world to your overall ancestry. That estimate now breaks African Ancestry into nine regions:

  • Africa North
  • Senegal
  • Ivory Coast / Ghana
  • Benin / Togo
  • Cameroon / Congo
  • Mali
  • Nigeria
  • Africa Southeast Bantu
  • Africa South-Central Hunter-Gatherers

This is the first widely recognized, legitimate DNA test to provide this detailed a breakdown of African ancestry

2. Family Finder, which includes Population Finder

Family Finder is an autosomal DNA test from Family Tree DNA. It’s widely used by genealogists, including those interested in African American genealogy.

The company will compare your DNA against a database of other users to find genetic matches. Most often these genetic matches will be cousins, having a common ancestor with you somewhere in the last five or so generations.

By emailing your matches you can connect with previously unknown relatives and learn much more about your family tree.

As part of the Family Finder test, you receive a myOrigins report, formerly called Population Finder, where the company compares your DNA with over 60 reference populations from around the world. This is a biogeographical analysis of the DNA you received from ALL of your ancestors.

The African part of your DNA may place you in any of four sub continental groups based on similarities to certain scientifically studied populations. The groups and populations are as follows:

  • Central African: Biaka Pygmy, Mbuti Pygmy
  • East African: Bantu (Kenya)
  • Southern African: Bantu (South Africa), San
  • West African: Mandenka, Yoruba

Very few people outside Africa are 100% African. Population Finder will classify the remaining portion of your ancestry using other populations.

3. Y-DNA Test at Family Tree DNA

Family Tree DNA also offers a Y-DNA test, which tracks your paternal line. Since only men have a Y-chromosome, only men can take this test. But women can still test a man from their paternal line, e.g. a brother, a father, a brother of your father, or a son of your father’s brother.

Like Family Finder, this test finds genetic matches who share a common ancestor. But with the Y-DNA test you know the common ancestor has to be a male in the direct paternal line like your father’s father’s father etc.

The Y-DNA test will also predict a man’s Y-DNA haplogroup. And many haplogroups are clearly tied to origins in sub-Saharan Africa. This is the real indicator of your paternal line’s ethnic ancestry.

TIP: If you’re interested in finding genetic matches, you should order the Y-DNA 37 test, which checks 37 markers. But if you’re only interested in determining your haplogroup, you only need 12 markers. I suggest you go to Family Tree DNA and look for the combination package of Family Finder plus Y-DNA 12. The combo price is an excellent buy.

If you later decide that you want to discover your precise position in the Y-DNA tree of life, you can upgrade to more markers or even order a Deep Clade test. That will tell you exactly which subclade of your haplogroup you’re in. In many cases this can tighten the geographic origins of your paternal line.

4. mtDNA Test at Family Tree DNA

Both men and women have mitochondrial DNA (mtDNA) to test. But only women pass it on to their children. So mtDNA is the test to track your maternal line. That’s your mother’s mother’s mother etc.

As with the test described previously, you will probably see matches with other users. But mtDNA mutates so slowly that your common ancestors may have lived thousands of years ago. That makes mtDNA less useful than Y-DNA as a genealogy tool.

Still, mtDNA also has a haplogroup that relates directly to the origins of your maternal line. And some of those are clear indicators of African origin.

5. 23andMe Which Includes Ancestry Composition

23andMe is another autosomal DNA test like Family Finder. This test can also serve as an African DNA test, because it has an Ancestry Composition feature that tells you what parts of the world your ancestors lived a few hundred years ago.

This admixture report is similar to the Population Finder feature of the Family Finder test. It reports on African Ancestry from these three regions:

  • West African
  • East African
  • Central and South African

However, if you also test at least one of your parents on 23andMe, this test can split your ancestral percentages into your paternal and maternal sides.

23andMe also has a DNA Relatives feature that’s similar to Family Finder and it will estimate your Y-DNA and mtDNA haplogroups. So if you want to cover all your bases—then the 23andMe test can be a great value as an African DNA test.

6. Y-DNA and mtDNA Testing at African DNA

Harvard University Professor Henry Louis Gates, Jr. was a pioneer in African DNA testing. He founded African DNA to encourage more African Americans to get their DNA tested.

The company offers a Y-DNA test of 25 markers and an mtDNA test like the mtDNA Plus test at Family Tree DNA. In fact, Family Tree DNA is affiliated with the company and does their DNA testing.

Now they can also offer the Family Finder test that they renamed Ancestry Finder.

Note that African DNA only offers one paternal line Y-DNA test and one maternal line mtDNA test. They do not offer additional Y-DNA markers, the Full Mitochondrial Sequence (FMS) test, or Deep Clade testing. You need to order those tests directly from Family Tree DNA.

The African DNA web site does have more content specific to African DNA testing than any of the more general DNA testing companies. So I encourage anyone looking for an African DNA test to visit the site and learn all you can.

Uniquely, African DNA does offer some higher priced packages that combine DNA testing with genealogy research to build your family tree.

For most African-Americans there are no genealogical records prior to the 1870 census, when last names of former slaves began to be recorded. If you want someone to build a few generations of your family tree, however, this is an option to consider.

MONEY-SAVING TIP: If you’re not ordering a package with genealogy research, be sure to recheck Family Tree DNA to compare prices before placing an order with African DNA. At the time of this writing, you can order the same Y-DNA and mtDNA tests directly through Family Tree DNA for significantly less money.

7. Y-DNA and mtDNA Testing at African Ancestry

African Ancestry is another company that specifically features African DNA tests. Like the companies above, they check your Y-DNA and mtDNA to determine your paternal and maternal lineages. Since their web site does not provide details of either test, I cannot compare them.

Unlike Family Tree DNA, they do not keep a database of customer results, so you will not receive any matches to people with similar DNA. Since the company does not have an autosomal test like Family Finder and 23andMe, it cannot provide any admixture percentages. You won’t learn anything about ancestors outside your narrow paternal and maternal lines.

I found some interesting data on the web site. Even though this site specifically attracts people of African descent, 35% of the paternal line tests show European ancestry. Much of that non-African DNA was introduced into the family tree during the era of slavery. In addition, 8% of their maternal line samples show non-African haplogroups.

An article in the Wall Street Journal was critical of the African DNA test reports provided by this company. Independent experts say that mitochondrial DNA is not sufficient to nail down an ancestor’s origin to a specific country.

Furthermore, the large migrations of Africans over the last 3,000 years means that the typical black American’s DNA will match Africans living today in several countries. Even the founder of African DNA was quoted in the article that the country-specific reports his company provides are largely a “best guess.”

The testing prices at African DNA are higher than those of the companies listed above. Even if you have your African DNA test done elsewhere, the African Ancestry web site includes some interesting information on African heritage and a list of country-by-country resources in Africa for genealogists.

Other African DNA Tests of Uncertain Quality

DNA Tribes uses autosomal markers representing all your ancestors. But unlike AncestryDNA, Family Finder and 23andMe, which check nearly a million autosomal SNPs, DNA Tribes checks a maximum of 27 STRs.

I won’t try to explain the difference between an STR and a SNP here. But autosomal STRs are what police forces around the world have been collecting from criminals for decades.

The company examined 383,000 STR records and claims to have identified major genetic regions around the world. They compare your DNA with their proprietary database and issue reports on your most closely matched regions.

The company does not share its database or reveal its methods. And independent experts are skeptical when such detailed reports arise from so few markers.

Roots for Real offers Y-DNA, mtDNA, and an autosomal test based on 16 STR markers. They position their autosomal admixture test as an African DNA test. But their database is only about one third the size of the already questionable DNA Tribes test. And all of their tests are overpriced compared to market leaders Family Tree DNA, 23andMe, and Ancestry.com.

 

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