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 algorithm 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 software program 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 – genes – 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.
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.
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).
Help drive research forward for African Americans.
Questions: contact study-help@23andMe.com
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.
Popejoy, A. B. & Fullerton, S. M. Nature 538, 161-164 (2016).
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.
There is no cost to participate.
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.
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.
This course as the first one “Genetic Genealogy For Beginners” is an expansion and goes a little more deeper into the DNA with some additional learning tools. In these lessons rather than chapter we will use Genetic Genealogy, Molecular Genealogy (the field of biology that studies the structure and function at the molecular level and thus employs methods of both molecular biology and genetics. The study of chromosomes and genes expression of an organism.) Sounds intimidating but it will be broken into manageable understandable lessons. There is a test after each lessons to help you gain a solid background before moving to Intermediate and Advance Genetic Genealogy. This will be a four week course and starts May 1 – May 26 2017.
mark you calendar for this course.
What is a genome?
A genome is an organism’s complete set of genetic instructions. Each genome contains all of the information needed to build that organism and allow it to grow and develop.
Our bodies are made up of millions of cells (100,000,000,000,000), each with their own complete set of instructions for making us, like a recipe book for the body. This set of instructions is known as our genome and is made up of DNA. Each cell in the body, for example, a skin cell or a liver cell, contains this same set of instructions:
If printed out the 3.2 billion letters in your genome would:
I was introduced to genealogy by my Aunt Madeline Johns Gee who was a well known teacher in the Williamsburg-James City County Public Schools. She pushed for integration of public schools which were segregated at the time back in the day. She was considered a pioneer, a trail blazer. At a family gathering in Greensboro, NC she introduced the family tree she created and I was really excited, never knew most of my relatives. That was 45 years ago and I began studying genealogy when it was not as popular as it is today. As I have learned about genealogy through the years I came to a startling reality. All the research and genealogy websites gear their data towards European ancestors. There is almost no research on African American genealogy and genetic genealogy. That is changing daily as genealogist work towards a common goal. I will explain more on that in one of my blogs coming soon.
I have traced my ancestors back to 1460 Herefordshire, England, with DNA testing and the help of testing results of other relatives. My research has revealed new relatives unknown before. Results of four living relatives’ DNA results indicated a relationship at 22-26 cM’s and a direct relationship to William Johns who was married to Ann Merryman. With this information I was able to discover African-Americans not recorded any place by Johns family genealogists. John Johns the son of Col. John Johns lived in the Blue Ridge Mountains (Bear Mountain) of Virginia. He had an acknowledged relationship with a Monacan Indian woman (left blank at the request of the Monocan Nation) who are now a blend of Saponis, Occaneechis, and Tutelos tribes. Most of theses tribes relocated to Pennsylvania and finally to Canada where they are today. John Johns purchased 52 acres of land on Bear Mountain. In 1833, he bought another 400 acres, and this became the settlement for Indian and African-American families related to him. In 1850, the census recorded 29 families, mostly large, related to the Bear Mountain settlement. In his will he divided his land among his sons and daughter, and five years later, at the age of 91, he died. In 1860 the Amherst County Clerk’s Office recorded, among the names of free persons of color, the Monacan surnames of Beverly, Branham, Johns, Pinn and Terry. I have all fourteen names of African-Americans and Native American Johns who lived together and married.
The Virginia legislature passed a Race Law in 1823, which declared that any child of an Indian and any descendent of a Negro, up to the great-grandchild, would be counted as a mulatto. Virginia passed the Racial Integrity Law in 1924, which prohibited intermarriage between those considered white and those having any mixture of colored blood more than one-sixteenth. Many community settlers left the state during this time, because they were no longer permitted to marry freely.
There is no doubt that genetic genealogy is a fun and interesting new way to explain genealogy. “Finding Your Roots” and “Who Do You Think You Are?” uses DNA testing to support and augment the powerful stories shared by celebrity guests; leading many thousands of people to purchase DNA tests to explore their roots. Awareness: Every testing company from 23andMe <www. 23andme.com>, AmcestryDNA <www.dnaancestry.com> and Family Tree DNA (FTDNA) <www.FTDNA.com> have very small databases of African-Americans and almost non-existing databases of Africans. So you get something but perhaps not what you wanted. However, it is still a valuable tool in your genealogical arsenal. I have traced my ancestors back to 1460 Herefordshire, England. With DNA testing and other relatives testing I have been able to discovery new relatives unknown before. Results of four living relatives DNA results indicated a relations at 22-26 cm’s and a direct relationship to William Johns who was married to Ann Merryman. With this information I was able to discover African-American’s not recorded any place by Johns family genealogist.
2. Can women take a genetic genealogy test?
Women can take three of the four major genetic tests, and both males and females can benefit from the test results. The mitochondrial-DNA (mtDNA), autosomal-DNA test (atDNA), X-DNA. Y-DNA you will find that most companies will tell you it is for males only. True but you still can participate by finding a male member of your immediate family willing to get tested. Problem solved.
3. DNA will provide me with a family tree
What! DNA testing in no way can result in a family tree. There is no magic bullet for revealing your family tree. In conjunction with sound genealogy research and genetic genealogy it can help you build your family tree. No work no tree.
Facts, all DNA tests are not equal, all testing companies test at different markers and some companies or websites do no testing at all but send your sample to a company like 23andme. They also may not keep your raw data so you are out of luck if you can not retrieve your data. Some say they will provide a ethnicity report and if they are taking about 37 markers good luck (Y-DNA). All testing companies use laboratories across the country and that you need to review. Some companies provide what I call shop talk with very little value to you but ask any way, what logarithm do they apply to your data?
Marker – a gene or a DNA sequence which has a known location on a chromosome. This includes a single nucleotide polymorphism (SNP), short tandem repeats (STR) and any location in the DNA that is associated with a trait or a disease. In genetic genealogy, the results of testing various markers help determine how recently a common ancestor may have lived. Y-DNA (Y-STR) test can be purchased in sections from some companies. Family Tree offers Y-DNA12, Y-DNA25, Y-DNA 37, Y-DNA67 and Y-DNBA 111 STR marker tests and also SNP testing. AncestryDNA offers a Y-Chromosome test for either 33 or 46 marker locations, but does not provide SNP testing. The National Geographic Geno 2.0 test is an extensive array of Y-DNA SNP’s and is expensive.
Centimorgan (cM) – a centimorgan is a measurement of how likely a segment of DNA is to recombine from one generation to the next. Places on the chromosome that are one centimorgan apart have 1 percent probability of recombining during meiosis. The higher number of centimorgans, the closer the relationship.
After many hours and days exploring the literature on DNA testing and the pros and cons to testing, not to test, what to test for, what companies are best to meet your needs, all the testing possibilities, procedures, logarithms used by each company, results in simple terms you can understand, were to place your raw data after the test and what companies will secure your information it seemed appropriate to blog this to you.
Many African-Americans and others are using an African DNA test to get answers about their ethnic ancestry.
Typical questions include the following:
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 (http://www.ancestry.com) 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 (http://www.ftdna.com) and 23andMe (http://www.23andMe.com), 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:
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:
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:
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.
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 h//ere. 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.
Warning: These tests are based on sound science. But if you don’t know exactly what you’re doing, you can take the wrong test for your situation. It’s also easy to pay too much…settle for incomplete data…or misinterpret the results.
Y-DNA 111 markers, mtDNA + Plus, Full Sequence DNA and Family Finder DNA
My Haplogroup: Y-DNA (E-M2) and mtDNA (L2a1a2
http://www.23andme.com/DNA assess 2/10/2017
http://www.ancestry.com/DNA assess 2/10/2017
http://www.myheritage.com/DNA assess 2/12/2017
http://www.africanancestry.com/home/ assess 2/04/2017
https://www.africandna.com/ assess 2/04/2017
Megan Smolenyak Smolenyak and Ann Turner, “Trace Your Roots with DNA” published 2004
Blaine Bettinger, “The Family Tree Guide to DNA Testing and Genetic Genealogy” published 2016