For those who are following or willing to understand. .. .. since I had some request.
Some knowledge of high school Biology is required or at least will make it easier to understand.
The Human genome = the entire road map of AMH genes. There are 2 types of DNA/chromosomes.
1. Autosomal(22 Chromosome sets) which is not sex related( ie
not on the Y or X chromosome),
2. On the Y or X chromosome DNA.
Think of the human genome as I-95 roadway from NY to Florida. Along the way there are cities, small towns and mile marker post. At specific points expect to see certain towns. Eg Philadelphia and Baltimore are cities on I-95 on your way to Florida.
(note – the X and Y genome is
not included on I-95 for this example. We will get to why later).
Now, think of Philadelphia = an STR, so Philadelphia is only the name of an STR, Baltimore is another name of another STR on I-95, etc. All humans have the same STR at the same point on the genome. So everyone has a Philadelphia or Baltimore or a TPOX or THO1, etc.
The DIFFERENCE is really the size or repeats of the target town. eg Some population have a 12mile long Philadelphia others have 5 mile long Philadelphia.
Researchers agree on 8-18 STRs that will distinguish human population ie races, to drive my point home.
These are autosomal STRs not y-STR.
A subset of the standardize STRs are what was published in JAMA and BMJ on the mummies. Eg THO1=Philadelphia, TPOX=Baltimore etc, for now it doesn’t matter what TPOX means. We can get to that later.
But the size or repeats of the THO1 is the same for Africans and the AEians mummies.
As I said most researchers have agreed to the 8-18 STRs. Some have speculated that only the values of two (2) STRs are needed to arrive at a probability of origin. How?
See illustration below.
Look at Europeans in the chart. Notice the TPOX is the same for all European groups ie above 40%. Now take a look at the Chinese TPOX value which is
also above 40%. Now to tell the difference between the Chinese and European you look at
any other STR eg THO1. Notice the Europeans THO1 is about 25% but the Chinese THO1 is above 40%.
So there you have it. Only two STRs and you can tell the difference immediately between Chinese and European. Similar scenario for the Chinese THO1/D13S317 versus African American THO1/D13S317. Similar THO1 value but different for D13S317.
Very simple isn’t it?
You can do it manually but a computerize software makes it easier. This is what the DNATribes software or any other similar software does. Of course the more STRs are included the more accurate the result.
BTW – Autosomal STR is on a different roadway compared to the sex STR(y or X). That is why when you read these studies make sure it is apples and apples. CODIS, JAMA STRs and BMJ STRs are the same. That is, apples and apples,
Comparing the autosomal STRs with Y-DNA STRs are comparing apples and oranges.
Also – think of SNPs as a specific “mile marker” on the human genome, down to the exact yard ie extremely small. That is why it is called “single” nucleotide polymorphism(SNP). Think I-95 again but at mile marker 2500miles eg there Cytosine is substituted for Thymine (C-T). Now since the human genome is mapped out. Researchers know the exact nucleotide is expected at that mile marker location( 2500miles). Eg either CTGA. If it is different ie a mutation, it is called a polymorphism (or SNP).
As with STRs there are also autosomal SNPs and sex chromosome related SNPs. So again as with STR make sure it is apples and apples when talking SNPs. Also SNP is nonsense code meaning it does not determine a phenotype, trait, disease, etc. . Since it is not really a gene. It is only a signpost.
Also keep in mind the length of the human genome may be in the billions of Nucleotides(CTGA), as a consequence the SNPs are in the 100,000s. So choosing a few thousand SNPs to study does not go a long way. Since it may be less that 1% of all the human SNPs. That is why the FBI and other groups are reluctant to use it. In addition the data and SNPs can easily manipulated and misinterpreted ---
Now on to the nomenclature. It is not that difficult either. Eg C1234T, means at position 1234 Cytosine is substituted/transition for Thymine. C is normal while T is the mutation or polymorphism. Of course there is more to it but we can get to that later.
