Genealogical DNA test

A genealogical DNA test examines the nucleotides at specific locations on a person's DNA for genetic genealogy purposes. The test results are meant to have no informative medical value and do not determine specific genetic diseases or disorders (see possible exceptions in Medical information below); they are intended only to give genealogical information. Genealogical DNA tests generally involve comparing the results of living individuals as opposed to obtaining samples from deceased people.

Procedure
The general procedure for taking a genealogical DNA test involves taking a painless cheek-scraping at home and mailing the sample to a genetic genealogy laboratory for testing. Some laboratories use mouth wash or chewing gum instead of cheek swabs. Some laboratories offer to store DNA samples for ease of future testing. All United States laboratories will destroy the DNA sample upon request by the customer, guaranteeing that a sample is not available for further analysis.

Types of tests
The most popular ancestry tests are Y chromosome (Y-DNA) testing and mitochondrial DNA (mtDNA) testing. Other tests attempt to determine a researcher's comprehensive genetic history and/or ethnic origins.

Y chromosome (Y-DNA) testing
A man's paternal ancestry can be traced using the DNA on his Y chromosome (Y-DNA). This is useful because the Y chromosome, like many European surnames, passes from father to son, and can be used to help study surnames. Women who wish to determine their paternal ancestry can ask their father, brother, paternal uncle, paternal grandfather, or a cousin who shares the same paternal lineage to take a test for them (i.e. any male family member who has the same surname as her father).

What gets tested
Y-DNA testing involves looking at segments of DNA on the Y chromosome (found only in males) where sequences of nucleotides repeat, known as short tandem repeats (STRs). The segments which are examined are referred to as genetic markers and occur in what is considered "junk" DNA.

STR markers
These repeating sets of nucleotides are referred to as genetic markers and are designated by a DYS number (DNA Y-chromosome Segment number). Marker values, which range from 8 to 31 in the examples below in Haplotype, are the number of times each segment repeats.

SNP markers
SNPs are changes to a single nucleotide in a DNA sequence. The relative mutation rate for a SNP is extremely slow. This makes them ideal for marking the history of the human genetic tree. SNPs are named with a letter code and a number. The letter indicates the lab or research team that discovered the SNP. The number indicates the order in which it was discovered. For example M173 is the 173rd SNP documented by the group who uses the letter M.

Understanding test results
Y-DNA tests generally examine 10-67 STR markers on the Y chromosome but over 100 markers are available. STR test results provide the personal haplotype. SNP results indicate the haplogroup.

Haplotype
A Y-DNA haplotype is the numbered results of a genealogical Y-DNA test. Each allele value has a distinctive frequency within a population. For example, at DYS455, the results will show 8, 9, 10, 11 or 12 repeats, with 11 being most common. For high marker tests the allele frequencies provide a signature for a surname lineage. The test results are then compared to another project member's results to determine the time frame in which the two people shared a most recent common ancestor (MRCA). If the two tests match on 37 markers, there is a 50% probability that the MRCA was fewer than 5 generations ago and a 90% probability that the MRCA was fewer than 17 generations ago. It is important to check the number of markers that will be tested before choosing a test. For example, the Genographic Project only looks at 12 markers, while most laboratories and surname projects recommend testing at least 25. The more markers that are tested, the more discriminating and powerful the results will be. A 12 marker STR test is usually not discriminating enough to provide conclusive results for a common surname.

STRs results may also indicate a likely haplogroup, though this can only be confirmed by specifically testing for that Haplogroups' single nucleotide polymorphisms (SNPs).

Haplogroup
Haplogroups are large groups of haplotypes that can be used to define genetic populations and are often geographically oriented.

Y-DNA haplogroups are determined by SNP tests. SNPs are locations on the DNA where one nucleotide has "mutated" or "switched" to a different nucleotide. The nucleotide switch must occur in at least 1% of the population to be considered a useful SNP. If it occurs in less than 1% of the population, it is considered a personal SNP.

Haplogroup prediction
A person's haplogroup can often be inferred from their haplotype, but can only be proven with a Y-chromosome SNP tests (Y-SNP test). In addition, some companies offer sub-clade tests, such as for Haplogroup G. For example, Haplogroup G has a known modal haplotype: Few haplotypes will exactly match the modal values for Haplogroup G. One can consult an allele frequency table to determine the likelihood of remaining in Haplogroup G based on the variations observed. Additional predictions include:
 * If DYS426 is 12 and DYS392 is 11, one is probably a member of haplogroup R1a1.
 * If DYS426 is 12 and DYS392 is not 11, one is probably a member of haplogroup R1b.
 * If DYS426 is 11, one is probably a member of haplogroup G,I, or J.
 * If DYS426 is 11 and DYS388 is 12, one is probably a member of haplogroup N3 or E3b

A Bayes classifier to predict the haplogroup probabilities for an observed haplotype is available on the web: Whit Athey Haplogroup Predictor.

Mitochondrial DNA (mtDNA) testing
A person's maternal ancestry can be traced using his or her Mitochondrial DNA (mtDNA). The DNA in the human mitochondria is passed down by the mother unchanged. One exception, which was linked to infertility, has been shown. Additionally, some people cite paternal mtDNA transmission as invalidating mtDNA testing, but this is generally disregarded in genetic genealogy as not problematic.

What gets tested
mtDNA by current conventions is divided into three regions. They are the coding region and two Hyper Variable Regions (HVR1 and HVR2). All test results are compared to the mtDNA of a European in Haplogroup H2b. This sample is known as the Cambridge Reference Sequence (CRS). A list of single nucleotide polymorphisms (SNPs) is returned. Any "mutations" or "transitions" that are found are simply differences from the CRS.

The test results are compared to another person's results to determine the time frame in which the two people shared a most recent common ancestor (MRCA). The two most common mtDNA tests are a sequence of HVR1 and a sequence of both HVR1 and HVR2. Some people are now choosing to have a full sequence performed. This is still somewhat controversial as it may reveal medical information.

Understanding test results
The most basic of mtDNA tests will sequence Hyper Variable Region 1 (HVR1). HVR1 nucleotides are numbered 16001-16569. Some test reports might omit the 16 prefix from HVR1 results. ie 519C and not 16519C.

More extensive tests will also sequence Hyper Variable Region 2 (HVR2). HVR2 nucleotides are numbered 073-577.

Haplogroup
Most results include a prediction of mtDNA haplogroup.

If you belong to a haplogroup that is distantly related to the CRS, then the prediction may be sufficient. Some companies test for specific mutations in the coding region. For large haplogroups, such as mtDNA Haplogroup H, an extended test is offered to assign a sub-clade.

Ethnic tests
Autosomal tests that test the recombining chromosomes are available. These attempt to measure an individual's mixed ethnic heritage. The tests' validity and reliability have been called into question but they continue to be popular.

Biogeographical ancestry
Autosomal DNA testing purports to determine the "genetic percentage" of certain ethnicities in a person. These tests examine SNPs, which are locations on the DNA where one nucleotide has "mutated" or "switched" to a different nucleotide. These tests are designed to tell what percentage Native American, European, East Asian, and African a person is. These tests are controversial&mdash;their validity has not been independently confirmed — and the results are often disputed.

One company describes these four ethnic groups as follows:
 * Native American: Populations that migrated from Asia to inhabit North, South and Central America.
 * European: European, Middle Eastern and South Asian populations from the Indian subcontinent, including India, Pakistan and Sri Lanka.
 * East Asian: Japanese, Chinese, Mongolian, Korean, Southeast Asian and Pacific Islander populations, including populations native to the Philippines.
 * African: Populations from Sub-Saharan Africa such as Nigeria and Congo region.

Another company identifies the indigenous and diaspora populations in which an individual's autosomal STR profile is most common. This test examines autosomal STRs, which are locations on a chromosome where a pattern of two or more nucleotides is repeated and the repetitions are directly adjacent to each other. The populations in which the individual's profile is most common are identified and assigned a likelihood score. The individual's profile is assigned a likelihood of membership in each of twenty three world regions:


 * Alaskan: Inuit peoples of Alaska.
 * Athabaskan: Athabaskan speaking peoples of Western North America.
 * Northeast Amerindian: Native peoples of Northeastern North America.
 * Salishan: Salish speaking peoples of the American Pacific Northwest.
 * South Amerindian: Native peoples of South America.
 * Mestizo (“mixed”): Native Americans blended with Europeans and Africans.


 * Arabian: The Arabian Peninsula.
 * Asia Minor: The East Mediterranean and Anatolia to the Tarim Basin.
 * North African: North Africa.
 * North Indian: Northern India.
 * South Indian: Southern India.
 * Sub-Saharan African: Africa south of the Sahara Desert.


 * Eastern European: The Slavic speaking region of Eastern Europe.
 * Basque: The Basque speaking peoples of Western Europe.
 * Finno-Ugrian: The Uralic speaking region of Northeastern Europe.
 * Mediterranean: The Romance speaking region of Southern Europe.
 * Northwest European: The Celtic and Germanic speaking region of Northwestern Europe.


 * Australian: Aboriginal peoples of Australia.
 * Chinese: The Chinese region of East Asia.
 * Japanese: The Japanese Archipelago.
 * Polynesian: The Polynesian Islands.
 * Southeast Asian: Southeast Asia and the Malay Archipelago.
 * Tibetan: The Himalayas and Tibetan Plateau.

This STR analysis measures the frequency of a person's DNA profile within major world regions. Unlike SNP admixture tests, this analysis is based on objectively identified world regions and does not depend on any system of presumed biogeographic classifications. However, as most STR analysis examines markers chosen for their high intra-group variation, the utility of these particular STR markers to access inter-group relationships may be greatly diminished.

Native American ancestry
Autosomal testing, Y-DNA, and mtDNA testing can also be conducted to determine Native American ancestry. 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 five recognized Native American haplogroups, A, B, C, D or X, with the inference that he or she is, in whole or part, Native American. Comparisons with tribal-specific haplotypes is at times possible. Trace Genetics has amassed a databank of mtDNA sequences from American Indian individuals. Comparisons to this or other databanks may suggest tribal affiliation, though no federally-recognized tribe considers DNA as admissible evidence for enrollment. This is based rather on the demonstrable appearance of names of one's direct ancestors on tribal-specific Native American censuses prepared as the fallout of treaty making and relegation to reservations in the 1800s. Complicating factors are the Native American name controversy and recent evidence that indigenous North American mitochondrial haplogroups may not limited to the five named, though at present, the vast majority of Native American individuals do belong to one of the five identified mtDNA haplogroups. Many Americans are just discovering their Native roots, however, and the small chance of belonging to one of the acknowledged lineages, particularly in the case of male lines, which were almost entirely eradicated by the process of history, does not deter some from attempting to validate their heritage with the goal of gaining admittance into a tribe. These tests, moreover, are ideal for adoptees with Native American ancestry, of which there are now many in U.S. and Canadian society because of past policies of assimilation.

African ancestry
Y-DNA and mtDNA testing can determine with which present-day African country a person shares his or her ancestry. Testing company African Ancestry maintains a "African Lineage Database" of African lineages from 30 countries and over 160 ethnic groups. Mostly due to Caucasian slave owners impregnating their female African slaves, approximately 30% of African American males have a European Y chromosome haplogroup. As for the mitochondrial haplotypes, African Ancestry lists approximately 300 tribal affiliations and seeks to assign, within a certain measure of likelihood, an African tribe to testees. This is how Oprah Winfrey, the television talk show host, discovered her ancestry. When Oprah had her DNA tested for the programme, the results suggested her most likely match was from the Kpelles tribe of Liberia. According to authorities like Salas, nearly three-quarters of the ancestors of African Americans taken in slavery came from West Africa.

The African American tribal movement has burgeoned since DNA testing, with members of African American churches taking the test as groups. One reason is that owing to slavery, African Americans cannot easily trace their ancestry through surname research, census and property records and other traditional means.

Cohanim ancestry
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 of all in genealogical Y chromosome DNA testing found that very many of the Cohens did indeed have distinctively similar DNA, rather more so than general Jewish or Middle Eastern populations. The 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 indeed be consistent with a shared common ancestor, or with the hereditary priesthood having originally been founded from members of a single closely-related clan.

However it should be noted that the original studies only tested six Y-STR markers, which in modern terms is a very low-resolution test. Such a test simply does not have the resolution to prove relatedness, nor to very reliably estimate the time to a common ancestor. The Cohen Modal Haplotype, whilst notably frequent amongst Cohens, is also far from unusual in the general populations of haplogroups J1 and J2 with no particular link to the Cohen ancestry. So whilst many Cohens have haplotypes close to the CMH, a far larger number of such haplotypes worldwide belong to people with no likely Cohen connection at all.

To some extent one could resolution by testing more than six Y-STR markers. For some this could certainly help to establish relatedness to particular recent Cohen clusters; although for many it is likely that it would still be hard to definitively distinguish shared Cohen ancestry from the more general population distribution. However so far there is no openly published research to indicate what extended Y-STR haplotype distributions appear to be characteristic of Cohens. Although some high-resolution testing has certainly been done, to date the results are held as closely-guarded secrets. It is not even known whether the high-resolution testing that has been done tends to confirm or tends to call into question the basic hypothesis of a majority of Cohens sharing a recent common ancestry back to a Y-chromosomal Aaron at an appropriate date.

European testing
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 is simply an mtDNA haplotype test based on the research in the book The Seven Daughters of Eve. SNP testing may enable mostly-European individuals to determine to which Sub-European population they belong:
 * Northern European subgroup (NOR) - mostly Northern and Southwestern European
 * Southeastern European (Mediterranean) subgroup (MED) - mostly Southeastern Europeans (Greeks or Turks)
 * Middle Eastern subgroup (MIDEAS) - mostly Middle Eastern
 * South Asian subgroup (SA) - mostly South Asian from the Indian sub-continent (i.e. Indian)

Hindu testing
The 49 established gotras are clans or families whose members trace their descent to a common ancestor, usually a sage of ancient times. The gotra proclaims a person's identity and a "gotraspeak" is required to be presented at Hindu ceremonies. People of the same gotra are not allowed to marry.

One company says it can use a 37-marker Y-DNA test to "verify genetic relatedness and historical gotra genealogies for Hindu and Buddhist engagements, marriages and business partnerships." Any Y-DNA test can be used to compare results with another person whose gotra is known.

Melungeon testing
Several efforts, including a number of ongoing studies, have examined the genetic makeup of families historically identified as Melungeon. Most results point to a mixture of European, African, and Native American lineages. 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.

Benefits
Genealogical DNA tests have become popular due to the ease of testing at home and the various additions they make to genealogical research. Genealogical DNA tests allow for an individual to determine with 99.9% certainty that he or she is related to another person within a certain time frame, or with 100% certainty that he or she is not related. DNA tests are perceived as more scientific, conclusive and expeditious.

Drawbacks
The Y DNA lineage is the same from father to son without change, unless if there was a gene flow (i.e. the father in one generation is not the father in birth records), a discovery that might upset sensitive people. There is no usefulness in Maternal DNA because the mother displaces the father's maternal DNA (from his mother). Maternal DNA continue only from mother to daughter. Also, a daughter cannot transmit her father's Y DNA to her sons and a son cannot transmit his mother's maternal DNA to his children.

The most common complaint from DNA test customers is the failure of the company to make results understandable and meaningful to them. This was the primary reason cited for customer dissatisfaction in a June 2006 nationwide telephone survey conducted by Shapiro and Associates. According to an earlier survey, 1 in 6 Americans (16.6%) said they were aware of the ancestry-tracing capability of a home DNA test but when probed, most knew little about the details, reliability or differences between tests.

A further drawback, at least with autosomal tests, is their present state of imperfection and large margin of error (up to 15%, according to some genomics experts), with significant blind spots, such as confusion of Mongolian ancestry with Native American.

Medical information
Though genealogical DNA tests results generally have no informative medical value and are not intended to determine genetic diseases or disorders, there has been a correlation established between a lack of DYS464 markers and infertility, and a correlation between mtDNA haplogroup H and protection from sepsis. Certain haplogroups have been linked to longevity.

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. The National Human Genome Research Institute operates the Genetic And Rare Disease Information Center that can assist consumers in identifying an appropriate screening test and help locate a nearby medical center that offers such.

Haplogroup prediction

 * Athey Surname Project: Haplogroup Predictor
 * Male and Female DNA testing meanings
 * Arizona University: Y-DNA Haplogroup Tree
 * dnaconsultants.com: Conversion Chart for Male Haplogroups (PDF)
 * dnaheritage.com: Masterclass tutorial on SNP's and haplogroups
 * haplogroups World Map
 * ''YHaplogroups brief descriptions and regional origins