3 ms·

“Single” in this case refers to the polymorphism not the segment length.

by akiselev 4y ago

margalabargala 4y ago
Could you elaborate on this? Are you claiming that SNPs do not generally refer to only one nucleotide?
- otherme123 4y ago
  There is another acronym, MNP, that means Multiple Nucleotide Polymorphism, but it's rarely used. It's very common to use SNP even if the variation is two or three nucleotides.
  - margalabargala 4y ago
    Sure, but three is a far cry from 50-150, which would almost certainly be reported as a rearrangement or some other sort of structural variation, and would be detected with an entirely different method than SNPs. Alternately, they're talking about their sequencing reads and calling them SNPs. I think I should just chalk this one up to my own personal Gell-Mann amnesia and let the article authors do their thing.
- newaccount74 4y ago
  According to wikipedia [1] it is a single nucleotide (or rather a single base pair). But you obviously need more base pairs to identify which base pair you are looking at in the DNA. Presumably 50-150 base pairs is the length of DNA fragments required to be able to identify where in the genome it is. [1]: https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism
  - margalabargala 4y ago
    > But you obviously need more base pairs to identify which base pair you are looking at in the DNA. But that's not a SNP, then, that's a read that happens to contain a SNP. Generally a SNP is addressed by giving the reference base, the mutated base, the chromosome, the base position in that chromosome, and the assembly used to align the read to that location. For example, a T->C mutation at chr2:25164877 using hg38. Yes, you need to have the whole read to align to your genome assembly to detect the SNP. But before you do that, you don't know whether you have a SNP. And after you do that, the rest of the read is not useful if what you care about is the SNP.
    - newaccount74 4y ago
      If you know so much about the topic why ask questions about it? From the context of the article it's pretty clear that the author was talking about the fragment sizes needed for analysis.
      - margalabargala 4y ago
        I didn't ask questions about the article, only about another commenter's (incorrect) claim. The original question about the article was someone else. I have a graduate degree in bioinformatics and have worked in the industry for close to a decade, I have a strong background in the exact topic, yes.

“Single” in this case refers to the polymorphism not the segment length.

margalabargala 4y ago

Could you elaborate on this? Are you claiming that SNPs do not generally refer to only one nucleotide?

otherme123 4y ago
There is another acronym, MNP, that means Multiple Nucleotide Polymorphism, but it's rarely used. It's very common to use SNP even if the variation is two or three nucleotides.
- margalabargala 4y ago
  Sure, but three is a far cry from 50-150, which would almost certainly be reported as a rearrangement or some other sort of structural variation, and would be detected with an entirely different method than SNPs. Alternately, they're talking about their sequencing reads and calling them SNPs. I think I should just chalk this one up to my own personal Gell-Mann amnesia and let the article authors do their thing.
newaccount74 4y ago
According to wikipedia [1] it is a single nucleotide (or rather a single base pair). But you obviously need more base pairs to identify which base pair you are looking at in the DNA. Presumably 50-150 base pairs is the length of DNA fragments required to be able to identify where in the genome it is. [1]: https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism
- margalabargala 4y ago
  > But you obviously need more base pairs to identify which base pair you are looking at in the DNA. But that's not a SNP, then, that's a read that happens to contain a SNP. Generally a SNP is addressed by giving the reference base, the mutated base, the chromosome, the base position in that chromosome, and the assembly used to align the read to that location. For example, a T->C mutation at chr2:25164877 using hg38. Yes, you need to have the whole read to align to your genome assembly to detect the SNP. But before you do that, you don't know whether you have a SNP. And after you do that, the rest of the read is not useful if what you care about is the SNP.
  - newaccount74 4y ago
    If you know so much about the topic why ask questions about it? From the context of the article it's pretty clear that the author was talking about the fragment sizes needed for analysis.
    - margalabargala 4y ago
      I didn't ask questions about the article, only about another commenter's (incorrect) claim. The original question about the article was someone else. I have a graduate degree in bioinformatics and have worked in the industry for close to a decade, I have a strong background in the exact topic, yes.