DNA tests - what are they?

Hi,

I have created a FREE website to help people understand DNA testing better and I thought I would share it with all of you.

Genetic Genealogy - http://www.geneticsand.us

As a DNA project administrator for some surname projects at FamilyTreeDNA.com I like to share information about testing. If any of you who have tested share any of my project surnames, your welcome to join my groups as well. You can do this via the join button on your personal page at FTDNA.

Now to explain the testing, you have to have a little  understanding of  DNA. Each cell of the body has 23 pairs of chromosomes, in the cell nucleus.  In the cell  but not in the nucleus  is mtdna. Notice here, the 23 pairs of chromosomes do  not include  mtdna.  

When, the egg is fertilized the egg has 23 chromosomes and the sperm has 23 chromosomes. One pair of the chromosomes is used to indicate the sex of a child. The egg always carries a X chromosome and the rest are autosomal chromosomes. The sperm carries either the Y or the X chromosome and the rest are autosomal chromosomes.  Now if it is a boy child, you have a X and a Y for the pair of sex chromosomes.. Being there is only one “Y”… it cannot combine or recombine with every generation.  So the Y chromosome basically stays the same with few mutations (changes)  over generations. So a man’s parental (father/son) lineage can be proven by the results of the markers used in the Y-STR test.

Here sperm is larger then normal

There are different markers used for different tests. The markers used for Y-DNA testing normally are called Short Tandem  Repeats (STRs) and single-nucleotide polymorphism  (SNPs – pronounced Snips). SNPs normally are used for population migration. Where STRs are used for current genetic genealogy (basically).  

single-nucleotide polymorphism:

http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism

short tandem repeat:

http://en.wikipedia.org/wiki/Short_tandem_repeat

There are three basic tests for genetic genealogy

1.    the testing of Y-DNA, this test uses the STR marker and defines the direct paternal line. 

To define:  it is your father his father his father back a few hundred thousand years or more.  

 More information below.

2.    MTDNA  this test uses the SNP markers and is used to define the direct maternal line. 

To define: this is the child, the mother, her mother, her mother  back a few hundred thousand years or more.   

More information below.

Only your differences from the Cainbridge Standard are reported for this test. Although, 

there are different levels to testing the MTDNA you do not get the entire picture with out the Full test. 

More information below.

3. atDNA tests the autosomal chromosomes, it uses the SNP markers. Every person has autosomal 

chromosomes to include the individuals who provided the Y chromosome and the mtDNA, 

so atdna comes from both the Maternal lineage and the Paternal lineages – Everyone in your ancestry. 

The test shows segments on the different chrosomes , that you share with others indicating a relationship. 

With this test the terms IBD and IBS are used. IBD means identical by descent and IBS identical by state.

atDNA  consists of the 22 autosomal chromosome pairs, these are part of the 23 pairs of nucleus 

chromosomes.   The 23rd pair is the sex indicator pair and consists of the XX for females and 

the YX for males. 

MTDNA  In human beings, the mitochondrial DNA is a single, small, circular chromosome. 

It is not part of the 23 pairs of nucleus chromosomes. Many of them live inside the cell but not in the 

enclosed nucleus. They have a different job. MTDNA directs the creation and use of energy in each 

individual cell.

Where nucleus chromosomes have 3billion, 300million plus a few hundred thousand base pairs; 

MTDNA only has about  16,569 base pairs

The cell nucleus

The X chromosome is tested by some companies at the same time as the atDNA. It uses the SNP marker and althought is part of the sex indicator pair  does not define the maternal line. The X passes back and forth between a man and a woman, its line of descent is different and needs a chart to help you understand who you got it from. Like the “Y” and “MTDNA”, it has a particular path. See the X chart here:  http://geneticsand.us/x-ch.htm

All chromosomes, the 23 pairs and MTDNA, have STR and SNP markers. In the testings,  paticular parts of the chromosomes are being tested; thus the base pairs being used have names and numbers. .

There are many other types of DNA testing. To name a few: Paternity Testing or CODIS 

(criminal ID) Testing.  Although not typically thought of as a genealogical test, they both aim to identify 

relatives through STR testing of autosomal chromosomes.

The test to use depends on the information you want to find out. I suggest that you join the Newbie DNA list (YahooGroups). Then  ask questions and then decide what test you want to take. The only real complaints I have seen about genetic genealogy have come from misunderstanding what a test will revel. So ask questions, decide what answers you want then decide what test to use.

In addition for the Y chromosome DNA test.

The first to understand is that to find a Y-DNA match, the haplogroup of the pair of results being compared must match.. Example a man who has R1b haplogroup is not related  (with in the time frame of the use of  surnames about 100 – 2000 yrs)  to a man who has a Ib1 haplogroup.

Hapolgroups, depending on the testing company can be estimated by the first 12 STR markers of a Y-STR  marker test. (normally test names are  just referred to by the number of markers tested as in 12  –25-36-44-67) To actually prove a haplogroup or to find a subclade of a haplogroup; a haplogroup test  normally referred to as a deep clade test should be preformed. Also some companies test for particular  haplogroup markers.

Haplogroups, are the identifying terminology, for where you sit on the tree of humanity, it starts off with  haplogroup Adam.. and after changes (mutations) in his SNPs a new haplogroup is created.. so over the  few  hundreds of thousands  years, developed  many different haplogroups. Some are descent and some are  lateral  developments.  That is why a man who has R1b and a man I1b are thousands of years apart from a common ancestor.

Questions? Ask.. (oh, male haplogroups are named differently from the mtDNA haplogroups)

Now getting down to the very easiest, the Y-STR test used for genealogy. I said before that they are  basically referred to (or called/named) by the numbers.  The 37 marker, YSTR test is the one I ask the  members of my surname projects to use.  It has enough Fast mutating and slow mutating STR markers to  make it a good identifying amount, the more markers the better but normally 37 is enough. What they do  here is introduce a primer to the dna and count the reactions (spikes). The amount of reactions at a particular  place (marker) is the result (there is an official name but it is still just a result)

To prove or disprove a relationship you compare the amount of the result to the result of the other person.   So example: man A -  marker DYS393=12; man B – DYS393=14  the steps of difference (genetic distance  - GD) here is 2, all differences are accumulative.  At 37 markers, in my opinion; more then 4-5  steps of difference between two men makes the common ancestor before of the use of surnames..

See: http://gilpingenetics.us/gc/charts2.htm  for examples

 Next is MTDNA – 
mtdna is a chromosome but not part of the 23 pairs. It has a different job, it is primarily  to produce and  direct energy for the cell. Its mutations are very slow. A test of the MTDNA can have  medical information.

MTDNA is in both the cell of the egg and the sperm. But the mtdna of the sperm is primarily there to give  energy to the sperm to swim to the egg and impregnate it.  Normally all the mtdna in the sperm is used up, when it isn’t the egg destroys the remainder. Thus you inherit the mtdna in your cells from only your mother.  That is the reason it can be used to trace the maternal lineage. MTDNA, is different from the other  chromosomes in that instead of being a string it is circular, and it is normally tested in HRV1 and HRV2 and  the coding zone. I was told HRV1 and 2 start  basically if you were looking at a clock  - at 11:59 and end at  12:06 the rest is coding zone..

It is hard to use MTDNA for genealogy  because the maiden name changes with each generation where a  man’s surname is passed  to each generation. I said hard, but it is not impossible, there have been many  positive results.  You look for matching maiden names  and area locations.. Then you put the findings  together. William Hurst of the Genealogy-DNA mailing list at rootsweb.com is the local expert.

When testing MTDNA the results are very different from what you get with Y-DNA testing. There is a  standard called Cambridge Reference Sequence, your results are compared to this and only the differences  are reported. So in this case you compare differences.

Mtdna – http://en.wikipedia.org/wiki/Mitochondrial_DNA

http://en.wikipedia.org/wiki/Human_mitochondrial_DNA_haplogroup

Now lets discuss the newest testing.. X and autosomal testing.

First, you inherit atdna from all your past ancestors, second you might think you inherit 50% from each  parent. NOPE but, it averages out to 50%… since the X chromosome and the autosomal chromosomes  combine and recombine  randomly, (x to x; auto to auto) the  further away from the common ancestor the lower the chance you have  a measurable segment remaining from that ancestor.

One problem that I see with this testing is that a negative result of a measurable segment from a common  ancestor does not mean your not related, just that the part inherited is not measurable at this time.  (You  never know – this is cutting edge science, five years ago.. this testing was not even imagined.)

Now here is some additional information from some very knowledgeable people..

Females have two X chromosomes, one inherited from the father and the other  from the mother, so a connection could be from either side of the family.
Males have one X chromosome, inherited from the mother. SMGF has a nice  animation showing the inheritance pathway:
http://www.smgf.org/education/animations/x_chromosome.jspx
 
Since not all ancestors can make a contribution to the X, you can eliminate  at least some of them as possibilities. See the diagrams on Blaine  Bettinger's site:
http://www.thegeneticgenealogist.com/2008/12/21/unlocking-the-genealogical-secrets-of-the-x-chromosome/
 
http://www.thegeneticgenealogist.com/2009/01/12/more-x-chromosome-charts/
 
Note that the percentages are averages. A man's X chromosome can be exactly  the same as his maternal grandfather, exactly the same as his maternal  grandmother, or a mixture of the two, which works out to be average of 50%. I  find the demo Mendel family at 23andMe helpful in visualizing this. There are  three grandchildren and three grandparents, so you can look at different  combinations. If they don't show up in your list of people you're sharing with,  go to Account | Sharing | Example Profiles. Or create a guest membership.

It will help you to find the common ancestor by phasing  the X (in other words, figure out who contributed what).  This page helps tell how to do that:
http://www.isogg.org/xjourney1.html
 
If your genealogy program can print an ahnentafel chart, I've prepared a  file with the relevant ahnentafel numbers. Females should start the ahnentafel  with themselves; males should start with their mothers. Then you can go  through the ahnentafel report and delete the records of the people who could
not be the source of your X.
http://dnacousins.com/AHN_X.TXT   - Ann  Turner

I hope this helps you in understand testing, and that if you test you enjoy the venture.

Nelda