Genealogical DNA test – Wikipedia

Posted: May 5, 2018 at 1:42 am

A genealogical DNA test is a DNA-based test which looks at specific locations of a person’s genome in order to determine ancestral ethnicity and genealogical relationships. Results give information about ethnic groups the test subject may be descended from and about other individuals that they may be related to.

Three principal types of genealogical DNA tests are available, with each looking at a different part of the genome and useful for different types of genealogical research: Autosomal, Mitochondrial, and Y. In general, genealogical DNA tests do not give information about medical conditions or diseases.

The first company to provide direct-to-consumer genetic DNA testing was the now defunct GeneTree. However, it did not offer multi-generational genealogy tests. In fall 2001, GeneTree sold its assets to Salt Lake City-based Sorenson Molecular Genealogy Foundation (SMGF) which originated in 1999.[1] While in operation, SMGF provided free Y-Chromosome and mitochondrial DNA tests to thousands.[2] Later, GeneTree returned to genetic testing for genealogy in conjunction with the Sorenson parent company and eventually was part of the assets acquired in the buyout of SMGF.[3]

In 2000, Family Tree DNA, founded by Bennett Greenspan and Max Blankfeld, was the first company dedicated to direct-to-consumer testing for genealogy research. They initially offered eleven marker Y-Chromosome STR tests and HVR1 mitochondrial DNA tests. They originally tested in partnership with the University of Arizona.[4][5] [6] [7] [8]

In 2007, 23andMe was the first company to offer a saliva-based direct-to-consumer genetic testing[9]. It was also the first to implement using autosomal DNA for ancestry testing, which all other major companies now use.[10][11]

In 2018 it was estimated that over 12 million people had had their DNA tested for genealogical purposes, most of whom were in the USA.[12]

A genealogical DNA test is performed on a DNA sample. This DNA sample can be obtained by a cheek-scraping (also known as a buccal swab), spit-cups, mouthwash, and chewing gum. Typically, the sample collection uses a home test kit supplied by a service provider such as Anglia DNA Services, 23andMe, AncestryDNA, Family Tree DNA, MyHeritage, or National Geographic Genographic Project). After following the kit instructions on how to collect the sample, it is returned to the supplier for analysis.

There are three major types of genealogical DNA tests: Autosomal and X-DNA, Y-DNA and mtDNA.

Y-DNA and mtDNA cannot be used for ethnicity estimates, but can be used to find one’s haplogroup, which is unevenly distributed geographically.[14] Direct-to-consumer DNA test companies have often labeled haplogroups by continent or ethnicity (e.g., an “African haplogroup” or a “Viking haplogroup”), but these labels may be speculative or misleading.[14][15][16]

Autosomal DNA is contained in the 22 pairs of chromosomes not involved in determining a person’s sex.[14] Autosomal DNA recombines each generation, and new offspring receive one set of chromosomes from each parent.[17] These are inherited exactly equally from both parents and roughly equally from grandparents to about 3x great-grand parents.[18] Therefore, the number of markers (one of two or more known variants in the genome at a particular location known as Single-nucleotide polymorphisms or SNPs) inherited from a specific ancestor decreases by about half each generation; that is, an individual receives half of their markers from each parent, about a quarter of their markers from each grandparent; about an eighth of their markers from each great grandparent, etc. Inheritance is more random and unequal from more distant ancestors.[19] Generally, a genealogical DNA test might test about 700,000 SNPs (specific points in the genome).[20]

The preparation of a report on the DNA in the sample proceeds in multiple stages:

All major service providers use equipment with chips supplied by Illumina.[21] The chip determines which SNP locations are tested. Different versions of the chip are used by different service providers. In addition, updated versions of the Illumina chip may test different sets of SNP locations. The list of SNP locations and base pairs at that location is usually available to the customer as “raw data”. The raw data can sometimes be uploaded to another service provider to produce an additional interpretation and matches. For additional analysis the data can also be uploaded to GEDmatch (a third-party web based set of tools that analyzes raw data from the main service providers).

The major component of an autosomal DNA test is matching other individuals. Where the individual being tested has a number of consecutive SNPs in common with a previously tested individual in the company’s database, it can be inferred that they share a segment of DNA at that part of their genomes.[22] If the segment is longer than a threshold amount set by the testing company, then these two individuals are considered to be a match. Unlike the identification of base pairs, the data bases against which the new sample is tested, and the algorithms used to determine a match, are proprietary and specific to each company.

The unit for segments of DNA is the centimorgan (cM). For comparison, a full human genome is about 6500 cM. The shorter the length of a match, the greater are the chances that a match is spurious.[23] An important statistic for subsequent interpretation is the length of the shared DNA (or the percentage of the genome that is shared).

Most companies will show the customers how many cMs they share, and across how many segments. From the number of cMs and segments, the relationship between the two individuals can be estimated, however due to the random nature of DNA inheritance, relationship estimates, especially for distant relatives, are only approximate. Some more distant cousins will not match at all.[24] Although information about specific SNPs can be used for some purposes (eg suggesting likely eye colour), the key information is the percentage of DNA shared by 2 individuals. This can indicate the closeness of the relationship. However, it does not show the roles of the 2 individuals – eg 50% shared suggests a parent – child relationship, but does not identify which individual is the parent.

Various advanced techniques and analysis can be done on this data. This includes features such as In-common/Shared Matches,[25] Chromosome Browsers[26] and Triangulation[27]. This analysis is often required if DNA evidence is being used to prove or disprove a specific relationship.

The X-chromosome SNP results are often included in Autosomal DNA tests. Both males and females receive an X-chromosome from their mother, but only females receive a second X-chromosome from their father.[28] The X-chromosome has a special path of inheritance patterns and can be useful in significantly narrowing down possible ancestor lines compared to atDNA for example an X-chromosome match with a male can only have come from his maternal side.[29] Like autosomal DNA, X-chromosome DNA undergoes random recombination at each generation (except for father to daughter X-chromosomes which are passed down unchanged). There are specialised inheritance charts which describe the possible patterns of X-chromosome DNA inheritance for males and females.[30]

Some genealogical companies offer autosomal STRs (short tandem repeats). These are similar to Y-DNA STRs. The number of STRs offered is limited, and not genealogically useful.

The mitochondrion is a component of a human cell, and contains its own DNA. Mitochondrial DNA usually has 16,569 base pairs (the number can vary slightly depending on addition or deletion mutations)[31] and is much smaller than the human genome DNA which has 3.2 billion base pairs. Mitochondrial DNA is transmitted from mother to child, thus a direct maternal ancestor can be traced using mtDNA. The transmission occurs with relatively rare mutations compared to the genome DNA. A perfect match found to another person’s mtDNA test results indicates shared ancestry of possibly between 1 and 50 generations ago.[14] More distant matching to a specific haplogroup or subclade may be linked to a common geographic origin.

There is debate over whether or not paternal mtDNA transmission is possible in humans. Some authors cite paternal mtDNA transmission as invalidating mtDNA testing.[32] However, other studies hold that paternal mtDNA is never transmitted to offspring,[33] which would validate the use of mTDNA testing for genealogy.

mtDNA, by current conventions, is divided into three regions. They are the coding region (00577-16023) and two Hyper Variable Regions (HVR1 [16024-16569], and HVR2 [00001-00576]).[34]

The two most common mtDNA tests are a sequence of HVR1 and HVR2 and a full sequence of the mitochondria. Generally, testing only the HVRs has limited genealogical use so it is increasingly popular and accessible to have a full sequence. The full sequence is somewhat controversial because the coding region DNA may reveal medical information about the test-taker.[35]

All humans descend in the direct female line from Mitochondrial Eve, a female who lived probably around 200,000 years ago in Africa. Different branches of her descendants are different haplogroups. Most mtDNA results include a prediction or exact assertion of one’s mtDNA Haplogroup. Mitochrondial haplogroups were greatly popularized by the book The Seven Daughters of Eve, which explores mitochondrial DNA.

It is not normal for test results to give a base-by base list of results. Instead, results are normally compared to the Cambridge Reference Sequence (CRS), which is the mitochondria of a European who was the first person to have their mtDNA published in 1981 (and revised in 1999).[36] Differences between the CRS and testers are usually very few, thus it is more convenient than listing one’s raw results for each base pair.

Note that in HVR1, instead of reporting the base pair exactly, for example 16,111, the 16 is often removed to give in this example 111. The Letters refer to one of the 4 bases (A, T, G, C) that make up human DNA.

mtDNA testing was used by University of Leicester archaeologists to verify the skeletal remains of King Richard III, found in September 2012.[37]

The Y-Chromosome is one of the 23rd pair of human chromosomes. Only males have a Y-chromosome, because women have two X chromosomes in their 23rd pair. A man’s patrilineal ancestry, or male-line ancestry, can be traced using the DNA on his Y chromosome (Y-DNA), because the Y-chromosome is transmitted father to son nearly unchanged.[38] A man’s test results are compared to another man’s results to determine the time frame in which the two individuals shared a most recent common ancestor, or MRCA, in their direct patrilineal lines. If their test results are very close, they are related within a genealogically useful time frame.[39] A surname project is where many individuals whose Y-chromosomes match collaborate to find their common ancestry.

Women who wish to determine their direct paternal DNA ancestry can ask their father, brother, paternal uncle, paternal grandfather, or a paternal uncle’s son (their cousin) to take a test for them.

There are two types of DNA testing: STRs and SNPs.[14]

Most common is STRs (short tandem repeat). A certain section of DNA is examined for a pattern that repeats (e.g. ATCG). The number of times it repeats is the value of the marker. Typical tests test between 12 and 111 STR markers. STRs mutate fairly frequently. The results of two individuals are then compared to see if there is a match. Close matches may join a surname project. DNA companies will usually provide an estimate of how closely related two people are, in terms of generations or years, based on the difference between their results.[40]

A person’s haplogroup can often be inferred from their STR results, but can be proven only with a Y-chromosome SNP tests (Y-SNP test).

A single-nucleotide polymorphism (SNP) is a change to a single nucleotide in a DNA sequence. Typical Y-DNA SNP tests test about 20,000 to 35,000 SNPs.[41] Getting a SNP test allows a much higher resolution than STRs. It can be used to provide additional information about the relationship between two individuals and to confirm haplogroups.

All human men descend in the paternal line from a single man dubbed Y-chromosomal Adam, who lived probably between 200,000 and 400,000 years ago. A ‘family tree’ can be drawn showing how men today descend from him. Different branches of this tree are different haplogroups. Most haplogroups can be further subdivided multiple times into sub-clades. Some known sub-clades were founded in the last 1000 years, meaning their timeframe approaches the genealogical era (c.1500 onwards).[42]

New sub-clades of haplogroups may be discovered when an individual tests, especially if they are non-European. Most significant of these new discoveries was in 2013 when the haplogroup A00 was discovered, which required theories about Y-chromosomal Adam to be significantly revised. The haplogroup was discovered when an African-American man tested STRs at FamilyTreeDNA and his results were found to be unusual. SNP testing confirmed that he does not descend patrilineally from the “old” Y-chromosomal Adam and so a much older man became Y-Chromosomal Adam.

Many companies offer a percentage breakdown by ethnicity or region. Generally the world is specified into about 2025 regions, and the approximate percentage of DNA inherited from each is stated. This is usually done by comparing the frequency of each Autosomal DNA marker tested to many population groups.[14] The reliability of this type of test is dependent on comparative population size, the number of markers tested, the ancestry informative value of the SNPs tested, and the degree of admixture in the person tested. Earlier ethnicity estimates were often wildly inaccurate, but their accuracies have since improved greatly.[citation needed] Usually the results at the continental level are accurate, but more specific assertions of the test may turn out to be incorrect. For example, Europeans often receive an exaggerated proportion of Scandinavian.[43] Testing companies will often regularly update their ethnicity estimate, changing an individual’s ethnicity estimate.

The interest in genealogical DNA tests has been linked to both an increase in curiosity about traditional genealogy and to more general personal origins. Those who test for traditional genealogy often utilize a combination of autosomal, mitochondrial, and Y-Chromosome tests. Those with an interest in personal ethnic origins are more likely to use an autosomal test. However, answering specific questions about the ethnic origins of a particular lineage may be best suited to an mtDNA test or a Y-DNA test.

For recent genealogy, exact matching on the mtDNA full sequence is used to confirm a common ancestor on the direct maternal line between two suspected relatives. Because mtDNA mutations are very rare, a nearly perfect match is not usually considered relevant to the most recent 1 to 16 generations.[44] In cultures lacking matrilineal surnames to pass down, neither relative above is likely to have as many generations of ancestors in their matrilineal information table as in the above patrilineal or Y-DNA case: for further information on this difficulty in traditional genealogy, due to lack of matrilineal surnames (or matrinames), see Matriname.[45] However, the foundation of testing is still two suspected descendants of one person. This hypothesize and test DNA pattern is the same one used for autosomal DNA and Y-DNA.

As discussed above, autosomal tests usually report the ethnic proportions of the individual. These attempt to measure an individual’s mixed geographic heritage by identifying particular markers, called ancestry informative markers or AIM, that are associated with populations of specific geographical areas. Geneticist Adam Rutherford has written that these tests “dont necessarily show your geographical origins in the past. They show with whom you have common ancestry today.”[46]

The haplogroups determined by Y-DNA and mtDNA tests are often unevenly geographically distributed. Many direct-to-consumer DNA tests described this association to infer the test-taker’s ancestral homeland.[16] Most tests describe haplogroups according to their most frequently associated continent (e.g., a “European haplogroup”).[16] When Leslie Emery and collaborators performed a trial of mtDNA haplogroups as a predictor of continental origin on individuals in the Human Genetic Diversity Panel (HGDP) and 1000 Genomes (1KGP) datasets, they found that only 14 of 23 haplogroups had a success rate above 50% among the HGDP samples, as did “about half” of the haplogroups in the 1KGP.[16] The authors concluded that, for most people, “mtDNA-haplogroup membership provides limited information about either continental ancestry or continental region of origin.”[16]

Y-DNA and mtDNA testing may be able to determine with which peoples in present-day Africa a person shares a direct line of part of his or her ancestry, but patterns of historic migration and historical events cloud the tracing of ancestral groups. Due to joint long histories in the US, approximately 30% of African American males have a European Y-Chromosome haplogroup[47] Approximately 58% of African Americans have at least the equivalent of one great-grandparent (13%) of European ancestry. Only about 5% have the equivalent of one great-grandparent of Native American ancestry. By the early 19th century, substantial families of Free Persons of Color had been established in the Chesapeake Bay area who were descended from free people during the colonial period; most of those have been documented as descended from white men and African women (servant, slave or free). Over time various groups married more within mixed-race, black or white communities.[48]

According to authorities like Salas, nearly three-quarters of the ancestors of African Americans taken in slavery came from regions of West Africa. The African-American movement to discover and identify with ancestral tribes has burgeoned since DNA testing became available. African Americans usually cannot easily trace their ancestry during the years of slavery through surname research, census and property records, and other traditional means. Genealogical DNA testing may provide a tie to regional African heritage.

Melungeons are one of numerous multiracial groups in the United States with origins wrapped in myth. The historical research of Paul Heinegg has documented that many of the Melungeon groups in the Upper South were descended from mixed-race people who were free in colonial Virginia and the result of unions between the Europeans and Africans. They moved to the frontiers of Virginia, North Carolina, Kentucky and Tennessee to gain some freedom from the racial barriers of the plantation areas.[49] Several efforts, including a number of ongoing studies, have examined the genetic makeup of families historically identified as Melungeon. Most results point primarily to a mixture of European and African, which is supported by historical documentation. Some may have Native American heritage as well. Though some companies provide additional Melungeon research materials with Y-DNA and mtDNA tests, any test will allow comparisons with the results of current and past Melungeon DNA studies

The pre-columbian indigenous people of the United States are called “Native Americans” in American English.[50] Autosomal testing, Y-DNA, and mtDNA testing can be conducted to determine the ancestry of Native Americans. A mitochondrial Haplogroup determination test based on mutations in Hypervariable Region 1 and 2 may establish whether a person’s direct female line belongs to one of the canonical Native American Haplogroups, A, B, C, D or X. The vast majority of Native American individuals belong to one of the five identified mtDNA Haplogroups. Thus, being in one of those groups provides evidence of potential Native American descent. However, DNA ethnicity results cannot be used as a substitute for legal documentation.[51] Native American tribes have their own requirements for membership, often based on at least one of a person’s ancestors having been included on tribal-specific Native American censuses (or final rolls) prepared during treaty-making, relocation to reservations or apportionment of land in the late 19th century and early 20th century. One example is the Dawes Rolls.

The Cohanim (or Kohanim) is a patrilineal priestly line of descent in Judaism. According to the Bible, the ancestor of the Cohanim is Aaron, brother of Moses. Many believe that descent from Aaron is verifiable with a Y-DNA test: the first published study in genealogical Y-Chromosome DNA testing found that a significant percentage of Cohens had distinctively similar DNA, rather more so than general Jewish or Middle Eastern populations. These Cohens tended to belong to Haplogroup J, with Y-STR values clustered unusually closely around a haplotype known as the Cohen Modal Haplotype (CMH). This could be consistent with a shared common ancestor, or with the hereditary priesthood having originally been founded from members of a single closely related clan.

Nevertheless, the original studies tested only six Y-STR markers, which is considered a low-resolution test. In response to the low resolution of the original 6-marker CMH, the testing company FTDNA released a 12-marker CMH signature that was more specific to the large closely related group of Cohens in Haplogroup J1.

A further academic study published in 2009 examined more STR markers and identified a more sharply defined SNP haplogroup, J1e* (now J1c3, also called J-P58*) for the J1 lineage. The research found “that 46.1% of Kohanim carry Y chromosomes belonging to a single paternal lineage (J-P58*) that likely originated in the Near East well before the dispersal of Jewish groups in the Diaspora. Support for a Near Eastern origin of this lineage comes from its high frequency in our sample of Bedouins, Yemenis (67%), and Jordanians (55%) and its precipitous drop in frequency as one moves away from Saudi Arabia and the Near East (Fig. 4). Moreover, there is a striking contrast between the relatively high frequency of J-58* in Jewish populations (20%) and Kohanim (46%) and its vanishingly low frequency in our sample of non-Jewish populations that hosted Jewish diaspora communities outside of the Near East.”[52]

Recent phylogenetic research for haplogroup J-M267 placed the “Y-chromosomal Aaron” in a subhaplogroup of J-L862, L147.1 (age estimate 5631-6778yBP yBP): YSC235>PF4847/CTS11741>YSC234>ZS241>ZS227>Z18271 (age estimate 2731yBP).[53]

For people with European maternal ancestry, mtDNA tests are offered to determine which of eight European maternal “clans” the direct-line maternal ancestor belonged to. This mtDNA haplotype test was popularized in the book The Seven Daughters of Eve.

Genealogical DNA tests have become popular due to the ease of testing at home and their usefulness in supplementing genealogical research. Genealogical DNA tests allow for an individual to determine with high accuracy whether he or she is related to another person within a certain time frame, or with certainty that he or she is not related. DNA tests are perceived as more scientific, conclusive and expeditious than searching the civil records. However, they are limited by restrictions on lines that may be studied. The civil records are always only as accurate as the individuals having provided or written the information.

Y-DNA testing results are normally stated as probabilities: For example, with the same surname a perfect 37/37 marker test match gives a 95% likelihood of the most recent common ancestor (MRCA) being within 8 generations,[54] while a 111 of 111 marker match gives the same 95% likelihood of the MRCA being within only 5 generations back.[55]

As presented above in mtDNA testing, if a perfect match is found, the mtDNA test results can be helpful. In some cases, research according to traditional genealogy methods encounters difficulties due to the lack of regularly recorded matrilineal surname information in many cultures (see Matrilineal surname).[45]

Autosomal DNA combined with genealogical research has been used by adoptees to find their biological parents,[56] has been used to find the name and family of unidentified bodies[57] and by law enforcement agencies to apprehend criminals.[58]

Common concerns about genealogical DNA testing are cost and privacy issues.[59] Some testing companies[60] retain samples and results for their own use without a privacy agreement with subjects.[61][62]

Autosomal DNA tests can identify relationships with good accuracy out to about 2nd cousin,[63] but they have limitations.[64][65][66] In particular, transplants of stem cell or bone marrow will produce matches with the donor. In addition, identical twins (who have identical DNA) will share higher amounts of DNA with a greater range of relatives.[67]

Testing of the Y-DNA lineage from father to son may reveal complications, due to unusual mutations, secret adoptions, and false paternity (i.e., that the perceived father in a generation is not the father indicated by written birth records).[68] According to the Ancestry and Ancestry Testing Task Force of the American Society of Human Genetics, autosomal tests cannot detect “large portions” of DNA from distant ancestors because it has not been inherited.[69]

With the increasing popularity of the use of DNA tests for ethnicity tests, uncertainties and errors in ethnicity estimates are a drawback for Genetic genealogy. While ethnicity estimates at the continental level should be accurate (with the possible exception of East Asia and the Americas), sub-continental estimates, especially in Europe, are often inaccurate. Customers may be misinformed about the uncertainties and errors of the estimates.[70]

Some have recommended government or other regulation of ancestry testing to ensure its performance to an agreed standard.[71]

A number of law enforcement agencies attempt to coerce genetic genealogy companies that store customer’s data into giving up information on their customers who could match cold case crime victims[72] or perpetrators. A number of companies fight the requests.[73] The Contra Costa County District Attorney’s office used the “open-source” genetic genealogy site GEDmatch to find a relative of the suspect in the Golden State Killer case.[74][75]

Though genealogical DNA test results in general have no informative medical value and are not intended to determine genetic diseases or disorders, a correlation exists between a lack of DYS464 markers and infertility, and between mtDNA haplogroup H and protection from sepsis. Certain haplogroups have been linked to longevity in some population groups.[76][77]

The testing of full mtDNA sequences is still somewhat controversial as it may reveal medical information. The field of linkage disequilibrium, unequal association of genetic disorders with a certain mitochondrial lineage, is in its infancy, but those mitochondrial mutations that have been linked are searchable in the genome database Mitomap.[78] The National Human Genome Research Institute operates the Genetic And Rare Disease Information Center[79] that can assist consumers in identifying an appropriate screening test and help locate a nearby medical center that offers such a test.

Some[which?] genealogy software programs allow recording DNA marker test results, allowing for tracking of both Y-chromosome and mtDNA tests, and recording results for relatives.[80] DNA-family tree wall charts are available.

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Genealogical DNA test – Wikipedia

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