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Genealogical DNA test

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A genealogical DNA test examines the nucleotides at specific locations on a person's DNA for genetic genealogy purposes. The test results are not meant to have any 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 to historic populations.

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[edit] Procedure

The general procedure for taking a genealogical DNA test involves taking a painless cheek-scraping (also known as a buccal swab) 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, such as the Human Origins Genotyping Laboratory (HOGL) at the University of Arizona, 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.

[edit] Types of tests

The most popular ancestry tests are Y chromosome (Y-DNA) testing and mitochondrial DNA (mtDNA) testing which test direct-line paternal and maternal ancestry, respectively. DNA tests for other purposes attempt, for example, to determine a person's comprehensive genetic make-up and/or ethnic origins.

[edit] Y chromosome (Y-DNA) testing

A man's patrilineal or direct father's-line ancestry can be traced using the DNA on his Y chromosome (Y-DNA) through Y-STR testing, as follows: This is useful because the Y chromosome, like the patrilineal surname, passes down unchanged from father to son. 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. If their test results are a perfect or nearly perfect match, they are related within genealogy's time frame.[1] Each person can then look at the other's father-line information, typically the names of each patrilineal ancestor and his spouse, together with the dates and places of their marriage and of both spouses' births and deaths. This information table will be referred to again within the mtDNA testing section below as the (matrilineal) "information table". The two matched persons may find a common ancestor or MRCA, as well as whatever information the other already has about their joint patriline or father's line prior to the MRCA—which might be a big help to one of them.[2] Or if not, both keep trying to extend their father's lines further back in time. Each may choose to have their test results included in their surname's "Surname DNA project". And each receives the other's contact information if the other chose to allow this. They may correspond, and may work together in the future on joint research.[3]

Women who wish to determine their direct paternal DNA ancestry can ask their father, brother, paternal uncle, paternal grandfather, or a cousin who shares the same surname lineage (the same Y-DNA) to take a test for them.

[edit] What gets tested

Y-DNA testing involves looking at STR segments of DNA on the Y chromosome. The STR segments which are examined are referred to as genetic markers and occur in what is considered "junk" DNA.

[edit] STR markers

A chromosome contains sequences of repeating nucleotides known as short tandem repeats (STRs). The number of repetitions varies from one person to another and a particular number of repetitions is known as an allele of the marker. An STR on the Y chromosome is designated by a DYS number (DNA Y-chromosome Segment number). The example below shows the allele of Rumpelstiltskin's DYS393 marker is 12, also called the marker's "value". The value 12 means the DYS393 sequence of nucleotides is repeated 12 times—with a DNA sequence of (AGAT)12.

[edit] SNP markers

Strand 1 differs from strand 2 at a single base pair location (a C → T polymorphism).

A single-nucleotide polymorphism (SNP) is a change to a single nucleotide in a DNA sequence. The relative mutation rate for an SNP is extremely low. 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 Human Population Genetics Laboratory at Stanford University, which uses the letter M.

[edit] 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.

[edit] 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[4]. For high marker tests the allele frequencies provide a signature for a surname lineage.

Kit Surname Haplo 3
9
3

 		 3
9
0

 		 1
9


 		 3
9
1

 		 3
8
5
a

 3
8
5
b

 4
2
6

 		 3
8
8

 		 4
3
9

 		 3
8
9
-
1		 3
9
2

 		 3
8
9
-
2		 4
5
8

 		 4
5
9
a

 4
5
9
b

 4
5
5

 		 4
5
4

 		 4
4
7

 		 4
3
7

 		 4
4
8

 		 4
4
9

 		 4
6
4
a

 4
6
4
b

 4
6
4
c

 4
6
4
d
11111 Rumpelstiltskin Q 12 23 13 10 16 17 12 12 13 14 14 31 18 8 9 11 11 27 13 19 28 14 14 15 15

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 perfectly on 37 markers, there is a 50% probability that the MRCA was fewer than 2 to 3 generations ago, 90% probability that the MRCA was fewer than 5 generations ago, and 95% probability that the MRCA was fewer than 7 generations ago.[5]

Kit Surname Haplo 3
9
3

 		 3
9
0

 		 1
9


 		 3
9
1

 		 3
8
5
a

 3
8
5
b

 4
2
6

 		 3
8
8

 		 4
3
9

 		 3
8
9
-
1		 3
9
2

 		 3
8
9
-
2		 4
5
8

 		 4
5
9
a

 4
5
9
b

 4
5
5

 		 4
5
4

 		 4
4
7

 		 4
3
7

 		 4
4
8

 		 4
4
9

 		 4
6
4
a

 4
6
4
b

 4
6
4
c

 4
6
4
d
11111 Rumpelstiltskin Q 12 23 13 10 16 17 12 12 13 14 14 31 18 8 9 11 11 27 13 19 28 14 14 15 15
11178 Rumpelstiltskin Q 12 23 13 10 16 17 12 12 13 14 14 31 18 8 9 11 11 27 13 19 28 14 14 15 15

Before choosing a test, it is important for an individual to check the number of markers that will be tested. For example, the Genographic Project looks at only 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).

[edit] Haplogroup

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

Human Y-chromosome DNA (Y-DNA) haplogroups (by ethnic groups · famous haplotypes)
most recent common Y-ancestor
|
A BT
|
B CT
|
CF DE
| |
C F D E
|
G H IJK
|
IJ K
| |
I J L MNOPS T
|
M NO P S
| |
N O Q R

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.

[edit] Haplogroup prediction

A person's haplogroup can often be inferred from their haplotype, but can be proven only 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:

DYS markers 3
8
5
a		 3
8
5
b		 3
8
8
 		 3
8
9
i		 3
8
9
ii		 3
9
0
 		 3
9
1
 		 3
9
2
 		 3
9
3
 		 3
9
4
 		 4
2
6
 		 4
3
7
 		 4
3
9
 		 4
4
7
 		 4
4
8
 		 4
4
9
 		 4
5
4
 		 4
5
5
 		 4
5
8
 		 4
5
9
a		 4
5
9
b		 4
6
4
a		 4
6
4
b		 4
6
4
c		 4
6
4
d
Haplogroup G: Modal STR values 14 14 12 12 29 22 10 11 14 15 11 16 11 23 21 31 11 11 16 9 9 12 13 13 14

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 in the known modal haplotype for G shown above.

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

 

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David Hess and Gareth Pollard
updated: 07/29/2010