New GEDmatch Genesis Beta

 
 

 

GEDmatch Genesis

GEDmatch Genesis is a peek at things to come for GEDmatch. It provides two things:

    • Ability to accept uploads from testing companies with formats and SNP sets not compatible with the current main GEDmatch database.
  • A new comparison algorithm that we believe will provide better accuracy, and more flexibility. More info: The Genesis Algorithm

During this initial deployment, the GEDmatch Genesis database will be separate from the main GEDmatch database, and comparisons for one will not show entries made in the other. Eventually, the 2 databases will be merged, and results will include entries from both. Likewise, the benefits of the Genesis comparison algorithm will eventually become available to all GEDmatch users.

The initial offering of Genesis applications will be limited to autosomal DNA matches. That too will be expanded as we move forward in our effort to convert existing GEDmatch software to the new algorithm.

We hope you find this transition to GEDmatch Genesis useful.

 

 

 

The Genesis Algorithm

For several years, GEDmatch has provided genetic genealogists, both beginners and experts, the ability to search for matches among kits in their database without regard to vendor. Also, GEDmatch has provided a rich suite of analysis programs allowing users to dig deeply into the genetic details of their matches, enhance the reports from their vendors, and even pursue their own original research ideas. Our algorithms are evolving to extract the most trustworthy and meaningful matching information possible using the markers common to pairs of kits even though sometimes limited.

Unfortunately, all too often, kits appear to share a DNA segment purely by chance. To combat this confusing phenomenon, we recently have developed a reliability measure that allows users to assess the quality of a matching segment in an intuitively appealing fashion. We also use the measure to guide our matching algorithms as they wring the greatest amount of useful information possible from the markers common to pairs of kits.

If we could assume that marker characteristics were uniform in all regions within chromosomes, we could use a “one size fits all” requirement for matching segments as is sometimes done. Unfortunately, the relevant characteristics vary widely. Some long segments with few markers may be accidental matches. Some marker rich short segments are often discarded although they are profoundly non-random.

Using the characteristics of each and every marker in a segment, we compute the expected number of purely chance matches to it to be found in the database. That number is then used to classify the segment into one of several levels reflecting the likelihood that the random matches may overwhelm the real ones. When a user executes a one-to-many search or a one-to-one comparison specifying a minimum segment length, the display can then include an estimate of validity for each segment found.

One can assume those segments designated to be valid are the result of a DNA inheritance process rather than mere chance. Questions may still remain about how far back shared DNA originates, but a confounding factor has been removed.

sources:

https://genesis.gedmatch.com/select.php

https://genesis.gedmatch.com/Qblurb.html

 

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DNA Test Options, Indigenous African Results and More

DNA Test Options, Indigenous African Results and More

DNAtestedafricans.org for further information. DNAtestedafricans.org is not a testing company and does not suggest any of the companies listed in this article. We offer a connection to purchase DNA kits, but it is your decision based on what you want to test for ancestry. The top three testing companies based on company reputation, services offered, testing methods, software grade, research and scientific evidence, CLIA and FDA compliance (US based) customer reviews, price, customer service and return policy.

#1. CRI Genetics (Cellular Research Institute)

#2. Family Tree DNA

#3 Living DNA Your Ancestry

for further reading go to http://www.geneticsdigest.com/best_ancestry_genealogy_dna_test

 

DNA Test can be done at 12, 25, 37, 67 or 111 markers. I recommend the 67-marker test, it gives you the best results for your money.

For more information or questions contact: DNAtestedafricans.org or africanamericangenealogydna.com

August 28, 2017

African Greetings Family!

   We hope you are all doing well.  Let’s start with a video of brother Saad Tafida.  He is an Indigenous African that tested to learn about his ancestry and to find his family in the Diaspora.  He is Fulani.  (He will tell you more about that on the video so we don’t want to spoil it).

   As it turns out, he is my eldest daughter’s DNA match.  She is able to watch these videos and learn more about a line of her culture and for that, we thank Saad tremendously!  We need more like him to share and explore with us.

Here are his results

He then downloaded his DNA raw data from the website that he tested with.  Then he uploaded to Gedmatch.com He speaks about that in his video.  He found more relatives that NEVER knew their ancestry.

 He uploaded the DNA Raw data to a few websites to find more family.  Click here to see how to do it.   https://www.dnatestedafricans.org/single-post/2017/07/13/Finding-More-DNA-Cousins-for-FREE

BE ENCOURAGED!!  More Indigenous Africans are testing and are looking for us as well too!!  

Now, here is some info on the current sale prices for a few major DNA testing companies.  You can click on each image to go to the website.  So now, let’s talk about the tests.

My Heritage DNA Test Kit $69.00

 

 

 

 

 

Everyone has asked, how do I get started on my DNA testing journey. This is a great place to start. Save this note because it is very useful to return to in the future.. Please read below.

We are NOT a DNA testing company. We do NOT sell DNA tests or profit from the sales of any tests. You must purchase the DNA test on your own. We simply explain what is available for YOU to research and determine what works for you. The information is provided by those of us that have DNA tested with EACH of the companies listed below.

We are a community of Volunteers focused on the ACRO concept. ACRO means African Culture and Reconciliation Organization. We coordinate cultural reception and integration via language classes, naming ceremonies and other enriching events after you have received your results.

We facilitate reconciliation of the DNA Tested African Diaspora and their African ethnic groups of ancestry. We provide you with 3rd party tools for YOU to research so you can determine which DNA Testing company and /or 3rd party tools for family tree building are most useful to you. We provide helpful templates for initial communications with your DNA matches as well as methods on how to get the most out of your test results.

 

Here is a good starting point to Research your AtDNA, MtDNA and the male YDNA. Please see the chart below.

Green is the autosomal DNA that can be tested by Ancestry, FTDNA Myheritage, and 23andme (they also provide DNA matches)

Blue is the YDNA that can be tested by FTDNA’s YDNA test (they provide DNA matches) and African Ancestry (they do NOT provide DNA matches)

Red is the MtDNA that can be tested by FTDNA’s Mt DNA test (they provide DNA matches) and African Ancestry (they do NOT provide DNA matches)

23andMe DBA Test Kit

“The information …..is meant to provide a very simple explanation of your Y-DNA and MtDNA Ancestry used for genealogical purposes. Scientists estimate that the total amount of Y-DNA of a man is less than 1% and the total amount of MtDNA in either a man or a woman is less than 1%. It is important to understand that after taking a Y-DNA and an MtDNA test, the majority of everyone’s DNA remains untested and it is called Autosomal DNA, with another 5% of a female’s DNA or 2 1/2% of a male’s DNA being x-chromosomal DNA. In a man this would mean roughly 95.5% of his DNA is Autosomal and in a woman that figure would be roughly 94%. “

Click here or copy and paste ~~ > https://phillipsdnaproject.com/faq-… ~~

Source: https://phillipsdnaproject.com/faq-sections/312-your-total-dna-makeup

UPDATE: We have been advised that African Ancestry does not do the Admix test anymore. Please check with their website to confirm.

Subscribe at www.dnatestedafricans.org

1. http://www.ancestry.com/ $79 Autosomal test ( saliva ) that analyses DNA from all of the contributors of your DNA. Both males and females can take this test. They test 700,000 markers !! Your DNA is tested 40 times and they provide you with percentages of your ancestry and a list of DNA matches that you can contact. You can research with those DNA matches to determine if they match on your mother’s side or your father’s side of the family. The DNA kit is mailed to you, you provide a small sample of saliva and follow the instructions to activate the kit. It takes about 6 to 8 weeks to receive a email from ancestry notifying you that your results are in. Sign into your ancestry account and explore your results.

You can download your DNA raw data from ancestry and upload it to Gedmatch.com ( https://www.gedmatch.com/login1.php ) for FREE to find more DNA matches. This is a website that allows us that have tested at FTDNA.com, 23andme.com, Wegene.com, and Ancestry.com , to upload there to find more family. And yes! It is FREE.

You can also upload your DNA raw data to https://www.familytreedna.com/ for FREE.

Limitations of Ancestry: This test will not tell you the African ethnic groups that you share ancestry with. However, you may find African DNA matches that can tell you their ethnic group(s) and where they come from. Also when you upload to Gedmatch, you may find African matches that have also uploaded there.

www.ancestry.com

Ancestry.com Results of an African American

 

 

 

2. https://www.23andme.com/ $99 Autosomal test ( saliva ) that analyses DNA from all of the contributors of your DNA. Both males and females can take this test. They provide you with percentages of your ancestry and a list of DNA matches that you can contact. You can research with those DNA matches to determine if they match on your mother’s side or your father’s side of the family. The DNA kit is mailed to you, you provide a small sample of saliva and follow the instructions to activate the kit. Check with 23andme to determine the current wait time for their test results. Once you receive the email that your results are in, sign into your 23andme account and explore your results.

Advantage:  Over 4 million people around the world have DNA tested.  If you match them, you will see them in your DNA match list when you sign into your account.  You can download your DNA raw data from 23andme and upload it to Gedmatch.com (https://www.gedmatch.com/login1.php ) for FREE to find more DNA matches. This is a website that allows us that have tested at FTDNA.com, 23andme.com, Wegene.com, and Ancestry.com , to upload there to find more family. And yes! It is FREE.

You can also upload your DNA raw data to https://www.familytreedna.com/ for FREE.

Limitations of 23andme: This test will not tell you the African ethnic groups that you share ancestry with. However, you may find African DNA matches that can tell you their ethnic group(s) and where they come from. Also when you upload to Gedmatch, you may find African matches that have also uploaded there.

YOU research, YOU decide

https://www.23andme.com/

23andme.com Results

 

 

3. https://www.familytreedna.com/ Starting at $79 for the family finder test.   ( cheek swab ) **If you already DNA tested at ancestry.com or 23andme.com , please go to FTDNA and upload your DNA raw data from those sites to this one for FREE. It will SAVE you the cost of $99. FTDNA’s Autosomal DNA test is $99. (Keep in mine that your autosomal DNA is 50 % from your father and 50% from your mother) 

They also have Mtdna tests for your Direct maternal line and YDNA tests for your direct paternal line. Only males can take the YDNA test. See the website for prices on their MtDNA and YDNA tests.

Regarding their Autosomal DNA test, they provide you with percentages of your ancestry and a list of DNA matches that you can contact. You can research with those DNA matches to determine if they match on your mother’s side or your father’s side of the family. The DNA kit is mailed to you, you provide a small sample of saliva and follow the instructions to activate the kit. Check with FTDNA to determine the current wait time for their test results. Once you receive the email that your results are in, sign into your FTDNA account and explore your results. You can download your DNA raw data from FTDNA and upload it to Gedmatch.com ( https://www.gedmatch.com/login1.php ) for FREE to find more DNA matches. You can download your DNA raw data from FTDNA and upload it to Gedmatch.com ( https://www.gedmatch.com/login1.php ) for FREE to find more DNA matches. This is a website that allows us that have tested at FTDNA.com, Myheritage.com , 23andme.com, Wegene.com, and Ancestry.com , to upload there to find more family. And yes! It is FREE.

Limitations for FTDNA: Their African database is LOW so you may not have very many matches. If you have a higher percentage of NON- African DNA, you may have a lot of DNA matches.

FTDNA.com Results

 

4.  Visit www.MyHeritage.com to see if their company is for you. Starting at $89 (often times on sale  for around $69) . Their AtDNA (autosomal) is a (cheek swab) test.  The Autosomal DNA test, provides you with percentages of your ancestry and a list of DNA matches (actual relatives)  that you can contact. You can research with those DNA matches to determine if they match on your mother’s side or your father’s side of the family. The DNA kit is mailed to you, you provide a small sample of saliva and follow the instructions to activate the kit. (Keep in mine that your autosomal DNA is 50 % from your father and 50% from your mother) 

Advantage:  This website accepts DNA raw data from ancestry.com , FTDNA.com and 23andme.com.  So if you already tested with these other companies, you only need to upload the data.  If you test with this company, you can download your DNA raw data from MyHeritage and upload it to Gedmatch.com ( https://www.gedmatch.com/login1.php ) for FREE to find more DNA matches. This is a website that allows us that have tested at FTDNA.com, Myheritage.com , 23andme.com, Wegene.com, and Ancestry.com , to upload there to find more family. And yes! It is FREE.

Limitations:  The DNA match database is still growing so you may not have a lot of matches  (cousins) on Myheritage.  However, uploading the DNA raw data to www.Gedmatch.com will surely give you more DNA matches.  

MyHeritage.com Results

 

5. Visit http://africanancestry.com/home/ to see if their company is for you. Starting at $200. Their MtDNA test about 8 markers of the HVR1 region. I would not recommend this company as a first choice at this point but it may be good after you have found that you have an African haplogroup with another company like FTDNA. This is a cheek swab test 

Advantage: If you took the YDNA test or MTDNA test with FTDNA and found that you have an African haplogroup, you may consider contacting them and paying around $200 to receive a certificate stating what African ethnic group(s) you share ancestry with. Their MtDNA and YDNA test starts at $285. ** About 35% of African Americans do NOT have African Mtdna line or YDNA line. See their website for details. Make an INFORMED decision.

Limitations of African Ancestry: They are the most costly DNA testing company for their YDNA, MtDNA test, and Autosomal. They do not test as many DNA markers as the other companies. The DNA raw data cannot be uploaded to any other website. They do not provide any DNA matches. If your test reveals your MtDNA line or your YDNA line is not African, you will not be able to find African relatives or African ethnic groups through them. You will need to test with one of the above companies. Source: http://shop.africanancestry.com/Mat… and http://shop.africanancestry.com/Pat… .

This test will not tell you that you are 100% of anything. It will not provide ANY percentages of your ethnicity. The percentages that they provide is a sequence similarity score. They test LESS than 1% of your DNA. The Cofounder can explain this to you.

 

AfricanAncestry.com Certificate Example

 

 

Make an INFORMED decision.

Please visit the website for each DNA test, research it and determine which company works for YOU!!

www.DNATestedAfricans.org

Note: All images belong to their perspective companies. This is for educational purposes to encourage research in order to make an informed decision about DNA testing.

Originally posted : https://www.facebook.com/notes/dna-tested-african-descendants/getting-started-dna-testing-options/1540241299613571/

 

African Royal DNA Project

Click on the link for more information:
DNA Tested African Descendants and Roots to Glory Tours have partnered to bring you the African Royal DNA Project. This project is designed to assist Africans in the …
www.rootstoglory.com

Atlantic Slave Trade Genealogy

 

In order to help you find your DNA cousin’s, you need to understand the history of American slavery and culture today and an understanding of the East Coast of Africa. How to map your identity to a time in place. I am Igbo of a community long ago in African in Senegal with DNA links to Nigeria and Benin. Our Ancestors practiced the Islamic faith. We were forced to abandon our beliefs and accept Christianity by Protestants, Catholics, Methodist, Episcopal and the Church of England.
GenealogyBank Blog: Access August 21, 2017: https://blog,genealogybank.com/african-American-slave-trade-ships-records-for-genealogy.html

 

African American Slave Trade: Ships & Records for Genealogy
By Gena Philibert-Ortega March 3, 2014
Introduction: Gena Philibert-Ortega is a genealogist and author of the book “From the Family Kitchen.” In this guest blog post, Gena searches old newspapers and other online resources to learn more about the African slave trade in America.

Throughout the course of the Atlantic Slave Trade, an estimated 12 million Africans were captured in their homeland and forcibly shipped across the Atlantic, on more than 35,000 voyages, starting in the 17th century* The African Diaspora scattered Africans throughout the Caribbean and Americas. The first slave ship to land in Colonial America went to Jamestown, Virginia, in August 1619. The name of the first African slave ship out of the United States was Desire, which sailed out of Massachusetts eighteen years later. This forced migration caused the displacement, torture, enslavement, and murder of many Africans.**

African slaves brought to the Americas were part of the “Middle Passage,” a voyage that began in Europe, stopped in Africa to unload supplies and pick up enslaved human cargo, and then traveled to American ports on the eastern coast to trade that human cargo for goods that were then shipped back to Europe.
History of the African Slave Trade in Early America and the United States Infographic (Note: the article continues after this infographic.)
History of the African Slave Trade in America
This troubling part of American history—and important part of African American history—can be uncovered and explored with patient historical research, including searching in old newspapers such as GenealogyBank’s online Historical Newspaper Archives.
Laws Slow—but Don’t Stop—the African Slave Trade
It would seem that the African slave trade to America would have been stopped by a law passed by the U.S. Congress in March 1807 that stated:
“That from and after the first day of January, one thousand eight hundred and eight, it shall not be lawful to import or bring into the United States or the territories thereof from any foreign kingdom, place, or country, any negro, mulatto, or person of colour, with intent to hold, sell, or dispose of such negro, mulatto, or person of colour, as a slave, or to be held to service or labour.”***
Genealogy Tip:
Read more about U.S. legislation in the 1800s regarding slavery in GenealogyBank’s Historical Documents section which contains The American State Papers and more.
However, the Act to Prohibit the Importation of Slaves and a similar law passed in the United Kingdom didn’t end the practice of the slave trade. Slave ships illegally continued to bring their human cargo to U.S. ports, and American newspapers continued reporting on the occasional capture of a slave ship into the 1840s. (Two ships, the Wanderer and the Clotilde, are reported to have brought slaves to the United States well into the 1850s.) As with the passage of most laws, those who would break the law don’t end their criminal deeds; instead, a black market thrives.
Slave Advertisements in Newspapers
Eighteenth-century newspapers found in GenealogyBank’s archives report of the comings and goings of slave ships when the African slave trade was still legal. From advertisements to shipping news articles, researchers can find mentions of slave ships names, their captains, and descriptions of the people on board.
In some cases, advertisements for the upcoming sale of slaves included information on the ship they would be arriving on. In this example from a 1785 South Carolina newspaper, Fisher & Edwards advertise that the ship Commerce, under Captain Thomas Morton, will be arriving from Africa’s Gold Coast with “upwards of 200 prime slaves” for sale.
ad for a slave auction, South-Carolina Weekly Gazette newspaper advertisement 6 August 1785
South-Carolina Weekly Gazette (Charleston, South Carolina), 6 August 1785, page 3
An earlier South Carolina advertisement proclaims that the slaves aboard Captain Buncombe’s ship Venus are “mostly stout men.”
ad for a slave auction, South-Carolina Weekly Gazette newspaper advertisement 17 July 1784
South-Carolina Weekly Gazette (Charleston, South Carolina), 17 July 1784, page 4
Slave Ship “Shipping News” in Newspapers
Articles under “Shipping News” or “Marine List” headlines are a good place to start searching for information about slave ships, crew, and cargo.
In this example from a 1799 New York newspaper, we see updates on various ships including information about deaths on ships. We also see that the Gurbridge and Mary were bringing slaves, and to whom they were being brought.
shipping news, Commercial Advertiser newspaper article 31 July 1799
Commercial Advertiser (New York, New York), 31 July 1799, page 3
Where to Find African Slave Trade & Slave Ship Records
After exhausting your research in newspapers, learn more about a particular slave ship by consulting the Trans-Atlantic Slave Trade Database website, which houses information about slave ships from 1514 to 1866.
In some cases, digital collections may hold slave ship manifests, such as this example from the Metropolitan New York Library Council Digital Collections.
Don’t forget to look for finding aids like this one from the New York Historical Society’s Guide to the Slavery Collection 1709-1899.
The National Archives (NARA) houses resources that can assist in your research:
The Slave Manifests of Coastwise Vessels Filed at New Orleans, Louisiana, 1807-1860 website has “manifests filed with the collector of customs at New Orleans, Louisiana, of slaves transported in coastwise trade to or from New Orleans during the period 1807-1860.”
The Slave Manifests for the Port of Philadelphia, 08/1800-04/1860 website is from the same Record Group as the above manifests, Record Group 36: Records of the U.S. Customs Service, 1745-1997.
African American Slave Trade Infographic Research Sources:
http://www.africanamericancharleston.com/lowcountry.html
http://www.civilwar.org/education/history/civil-war-overview/slavery.html
http://www.dcte.udel.edu/hlp2/resources/slavery/slaves-US-1790-1860.pdf
http://www.history.com/topics/black-history/slavery/videos/origins-of-slavery
http://history1800s.about.com/od/slaveryinamerica/a/1807slaveact.htm
http://jacksonville.com/tu-online/stories/120201/met_7970180.html
http://www.loc.gov/pictures/item/2005696251/
http://www.nps.gov/jame/historyculture/the-Royal-African-Company-supplying-slaves-to-jamestown.htm
http://www.pbs.org/wnet/african-americans-many-rivers-to-cross/history/on-african-american-migrations/
http://terrain.org/2012/columns/desires-past/
http://www.tennessee.gov/tsla/exhibits/blackhistory/aahtimelin.htm
http://www.washingtonpost.com/wp-dyn/content/article/2006/09/02/AR2006090201097.html
http://en.wikipedia.org/wiki/1688_Germantown_Quaker_Petition_Against_Slavery
http://www.yale.edu/glc/aces/germantown.htm

These online websites can be helpful, but research on the name of a slave ship should begin with historical newspapers. It’s in their advertisements and news articles that you will find mentions of the slave ships’ cargo, crew, and destination.
You are free to share the History of the African Slave Trade in Early America and the United States Infographic on your blog or website using the embed code below.
__________________
* The Trans-Atlantic Slave Trade Database. http://www.slavevoyages.org/tast/index.faces. Accessed 23 February 2014.
** “March 2, 1807.” This Week in History, March. http://www.peacebuttons.info/E-News/images/peacehistorymarch.htm. Accessed 23 February 2014.
*** “An Act to Prohibit the Importation of Slaves into any Port or Place Within the Jurisdiction of the United States, From and After the First Day of January, in the Year of our Lord One Thousand Eight Hundred and Eight.” The Avalon Project. Yale Law School Lillian Goldman Law Library. http://avalon.law.yale.edu/19th_century/sl004.asp. Accessed 23 February 2014.

A Royal Family DNA Voyage 6 May 2018

A Royal Family Voyage

July 16, 2017

AdaEze Naja Chinyere Njoku

DNA Tested African Descendants will be taking our 1st Family Reunion Cruise on 6 May 2018 departing from Orlando, Florida.  If you would like to join us as we meet and reconnect, please register. Bring the family with you!!  We are going to have lots of fun!

This is the first of many journeys that we will be taking.  It is ONLY just the beginning!  Keep DNA testing your family and finding more relatives.  

ALL Are Invited!  Bring your church, your greek, your Masonic, your organization, your family, and friends! All are welcome!

There are so many things to do on the ship that is a part of the cruise itself, it’s just amazing!

Additionally, we will also conduct the following:

African Naming Ceremony 

Healing and Blessing Ceremony on the ship

Healing Circle at the ports

Mini Genealogy, Gedmatch and DNA Class

Meet and Greet DNA Cousins

and more…..

To request more details, click this link https://tinyurl.com/DNA-CousinsCruise2018

 

 

 

 

Ancestry.com Test Kit- Click on the image to purchase

23andMe DNA Test Kit – Click on image to purchase

Family Tree DNA Test Kit – click on image to purchase

Finding More DNA Cousins for Free

Finding More DNA Cousins for FREE

July 13, 2017

|

AdaEze Naja Chinyere Njoku

 

Hello Family!

We sure hope you all are doing well.  We know that many of you that have taken the autosomal DNA test at FTDNA.com 23andme.com , Ancestry.com or MyHeritage.com are waiting patiently for that breakthrough of finding an Africa DNA match.  

Some of us are not being so patient.  Logging into the accounts 7 to 10 times daily, yelling at folks because we can’t find that match.  Talking to ourselves AND responding..  Creeping up on your computer from the side, like agent 007….  Acting as if it is hiding that match from you.  It’s OK.  We’ve been there too.  Please read a book or go fishing or something Shuga.  More people are testing.  We have to be patient.  It took some of us over 7 YEARS to get an Africa DNA match.  Oh but when we did!!!! 

 

Now, we are not going to lie to you.  We all know that there is NO GUARANTEE that you will find an Africa DNA match.  Here are some ways to widen the net though.  These helpful options are steps that I have taken myself.  They have proven to be very helpful especially since many people have DNA tested at one company and have elected NOT to test at another.  

There is a place where your DNA raw data can go and meet up with other people’s DNA raw data that tested at different DNA testing companies.   You all can chillax for FREE!!  OK.. Let me clarify…. Its like a meet up for ya raw data.

The goal is to upload your DNA raw data to the websites that you have not tested or to the sites like Gedmatch.com to help you compare shared segments on Chromosomes between you and others that have also uploaded.

Read more: DNAtestedafricans.org

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

The African American Sequencing Project 23andMe

The African American Sequencing Project 23andMe

The African American Sequencing Project

In a move to improve diversity in genetic research, this week 23andMe will start recruiting eligible customers to participate in the creation of an African American sequencing panel for research.

With the help of a grant from the National Human Genome Research Institute, 23andMe scientists will use contributions from customers who’ve consented to participate in this research to create a reference dataset and make the de-identified genetic data available to other qualified and vetted genetic researchers at educational and research institutions around the world.

“We are very excited about this project and its potential to make a difference in people’s lives,” said the project’s Principal Investigator, Adam Auton, a 23andMe senior scientist and statistical geneticist. “This work will help address the genetic  research disparities for African Americans in particular, something that has long needed attention.”

Only a fraction of the genetic research studies done to date include people with African ancestry. According to recent data focusing on this disparity,  only about 19 percent of all published genetic research includes data from non-Europeans, and only about two percent are conducted on those of African ancestry. While the bias towards European studies reflects many complicated logistic, systemic, and societal issues, it has a huge impact on what scientists can determine about the genetics underlying diseases and other conditions that impact not just non-European populations but everyone. A recent study by the University of Maryland School deftly explains the implications of these disparities:

“As long as ancestry-related biases are not addressed, and most studies continue to predominantly sample from European populations, the genetics community will face challenges with implementation, interpretation and cost-effectiveness when treating minority populations.”

To help address these disparities, 23andMe is recruiting African American customers who are are willing to have their genome sequenced. Those who are interested would then be asked to complete an additional level of consent, that would allow 23andMe to add their de-identified genetic data to a library of genetic and phenotypic data. This means the library would not receive any personally identifiable information  connected to the genetic and phenotypic information. This library of data is managed by the NIH and used by qualified scientific researchers.

As part of this work we will ask a subset of our African American customers, who have consented to participate in research, if they would be willing to participate and have their DNA sequenced to become part of this reference panel. Reference panels are important because they allow scientists to improve the accuracy of genome wide association studies, which drive much of genetic research conducted today.

When a customer of 23andMe sends in their saliva sample, they are genotyped at hundreds of thousands of sites that are known to vary between individuals. However, there are tens of millions of variable sites in the genome that are not genotyped. By having access to a large number of fully sequenced genomes — a sequence panel — researchers are able to use “genotype imputation” to infer or predict the genotypes at these unobserved positions. Much like a code breaker filling in missing letters in a message, scientists — using algorithms and data from whole genome sequences panels — can predict, or impute, the missing letters of genetic data. Having a sequence panel like this gives researchers a tool to study conditions that are specific to African Americans.

Ultimately, the sequence panel data will be shared with the NIH, who will make it available to other researchers. This in turn will expand scientists’ ability to make genetic discoveries for African Americans and help build a broader understanding of how genetics influence diseases and traits across multiple populations.

This is the latest in a number of efforts by 23andMe to help alleviate some of the existing disparities in genetic research. Last year, 23andMe was awarded another NIH grant to use “admixture mapping” as a means to improve the detection of disease-causing genetic variants among people of African, Latino and Asian ancestry. In 2011, 23andMe launched its Roots into the Future® project to study the genetics of disease specific to African Americans. The African Genetics Project is a part of this growing effort to improve our knowledge of African genetic diversity.

 

 

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