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I thought that these were just different format of the same data.

But it seems there isn't a way to convert SNP (single nucleotide polymorphism) data to STR (short tandem repeat) data. Am I right?

As I understand SNPs is basically a "diff" between some base human dna (parts that never change) and given dna. While STRs are strands of dna that differs between individuls.

But if there are enough SNPs (i.e. all of them), it would be trivial to deduce STRs, right?

For example, currently 23andMe tests the whole mitochondrial genome. Does it mean that one can easily deduce STRs?

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    $\begingroup$ STRs/SSRs/microsatellites are just short repeats, whereas SNPs refer to a single nucleotide that is swapped out. Both can easily be different between humans, but in STRs the issue is mainly the length of the repeat whereas the SNP is the actual base in that spot. $\endgroup$
    – Amory
    Nov 22, 2013 at 1:55
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    $\begingroup$ It's single nucleotide polymorphism, not polymerase $\endgroup$
    – Mad Scientist
    Nov 22, 2013 at 6:18
  • $\begingroup$ @Amory, so basically STRs are some kind of insertions/deletions of multiple nucleotides? $\endgroup$
    – Vanuan
    Nov 22, 2013 at 11:15
  • $\begingroup$ If you want to call it that, sure. It's repeat number, basically. $\endgroup$
    – Amory
    Nov 22, 2013 at 14:02

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The solution is in the name!

SNP: single nucleotide polymorphism

The name tells us that it is a change that affect one single nucleotide and that there can be multiple of these (polymorphism could be rewritten as multiple forms)

From the SNP Wikipedia page:

[A SNP] is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome (or other shared sequence) differs between members of a biological species or paired chromosomes in a human.

So, for instance, if you take 8 individuals and sequence their gene XYZ, you may find, at a certain locus (=position) on the gene:

Individual 1: AAGGTG C AGCAGTC
Individual 2: AAGGTG T AGCAGTC
Individual 3: AAGGTG T AGCAGTC
Individual 4: AAGGTG T AGCAGTC
Individual 5: AAGGTG C AGCAGTC
Individual 6: AAGGTG C AGCAGTC
Individual 7: AAGGTG T AGCAGTC
Individual 8: AAGGTG T AGCAGTC

The position highlighted in bold is a SNP. In this case we only have either C or T (and this produces 2 different alleles for gene XYZ).

This page from University of Utah has a very clear animation on SNPs.

STR: short tandem repeat

These are short repeated sequences. They're in tandem, that is, one after the other.

STR consist of a few (2-6) nucleotides that are repeated several (5-100) times.
For instance this page from the University of Arizona gives the example of D7S280, one STR with sequence (GATA)n (that is, GATA repeated n times)

  1 aatttttgta ttttttttag agacggggtt tcaccatgtt ggtcaggctg actatggagt
 61 tattttaagg ttaatatata taaagggtat gatagaacac ttgtcatagt ttagaacgaa
121 ctaacgatag atagatagat agatagatag atagatagat agatagatag atagacagat
181 tgatagtttt tttttatctc actaaatagt ctatagtaaa catttaatta ccaatatttg
241 gtgcaattct gtcaatgagg ataaatgtgg aatcgttata attcttaaga atatatattc
301 cctctgagtt tttgatacct cagattttaa ggcc

In this case, variations between individuals reside in the number of times the sequence is repeated.

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  • $\begingroup$ Still don't understand. Do you mean to say that each person has a different sequence length? It is reasonable, but wouldn't that be represented as corresponding SNP insertions and deletions? $\endgroup$
    – Vanuan
    Nov 22, 2013 at 11:01
  • $\begingroup$ Could you please make an STR example for multiple individuals, like you did for SNP? $\endgroup$
    – Vanuan
    Nov 22, 2013 at 11:16
  • $\begingroup$ Exactly, one could have CACT CACT CACT (3 times) and someone else CACT CACT CACT CACT (4 times). SNPs, are mutations in one single base. $\endgroup$
    – nico
    Nov 22, 2013 at 12:39

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