Thanks, very useful! So you still have the issues @forestglip outlined above?
More or less! It’s a little better since you’re not assuming linkage disequilibrium for the purposes of imputation (which might obscure some things), but LD would still cause problems with identifying the actual causal variant and there would still be issues with knowing what gene(s) the mutation actually affects.
“SNP” just refers to the actual single nucleotide difference in the genome. But GWAS studies limit to SNPs with >1% allele frequency to focus in on locations that are most likely to be fruitful since the methodology already limits how many locations you can assess. If 99.9% of the population has the same allele, and the disease doesn’t have Mendelian inheritance or other indications of a strong genetic component, it’s less likely that an allele with very low occurrence in the population is going to strongly drive disease. But it doesn’t exclude the possibility, which is why whole genome studies are still done.
To add to what jnmaciuch explained, I think you might be referring to a common convention. SNVs (single nucleotide variants) are used to describe any places where a single nucleotide/letter is changed in the DNA. SNP (single nucleotide polymorphism) can refer to an SNV that is present in at least 1% of the population, but that's not a hard rule.
ah thanks for pointing that out, I should have clarified to avoid confusing anyone—there’s a more colloquial version of “SNP” that’s really just synonymous with the actual mutation locus, which is what most biologists actually mean outside of specific technical genetic contexts. Which gets confusing pretty fast sometimes
My apologies. This is indeed the wrong citation. We'll fix for the next version.
Oh, snoZ178 actually is/was a gene in humans that looks like it's closer to the DecodeME locus than CA10: LocusZoom
The website just says it was reassigned to "ENSG00000252109.1" (everything after a "." in Ensembl IDs being a version identifier), and the old ID was retired. I think it's a real gene, it's just a small non-coding RNA that hasn't been functionally characterized. They're known to have regulatory functions on gene transcription/translation--it's sometimes possible to predict which genes it regulates because snoRNAs have a region that complements target RNA (although many do not have a known match and might exert regulatory effects without sequence complementarity).
Oh, when you click on that reassigned identifier, it goes to a page on an "Archive" Ensembl website, which I assumed was like an archive for genes that are no longer active. I couldn't find that new identifier on the regular Ensembl.
Wasn't kept in GRCh38, yes--unfortunately Ensembl doesn't really have detailed annotation for why certain genes get dropped in the newest release. Sometimes it's because the gene mapping is suspect, sometimes it's for some other logistical reason. I think that happens a lot to snoRNAs and miRNAs in particular just because of the sheer number of them. But that was the reasoning for creating the Archive--the current version is curated with the best intentions, but shouldn't be considered the end all be all.