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An allele (SNPs combination) includes multiple SNPs. Do these SNPs have to be in the same chromosome to be called as allele?
For example, I found a specific allele can alter drug effect. If these SNPs occur in both chromosome, Would this statement still be true?
Sorry for the confusion. An allele can be only one base. It can also be referred as a combination of several SNPs, for example different allele of CYP2D6. I am specifically talking about a combination of several SNPs. I vaguely remember all the SNPs have to be on the same chromosome to be called as allele.
An allele is a state, form, or a type that varies at one locus within a given sample/population.
They are not one single base only.
Insertions (or deletion) of several bases at one locus (in one individual within a population) mean that at that locus the alleles with be the string of bases (the inserted bit) and the reference (whatever this is; some call this the wild type, the wild allele) e.g. rs4022664 and rs4022474.
The CNVs are structural (larger) variants, which mean at least one of the alleles will be larger stretches of DNA
There can be many definitons of haplotypes. The one I'm used to is combination of several SNPs (or loci) that are inherited in a block (not reshuffled by recombination) giving rise to haplotypes.
The term you are looking for is haplotype.
Although the sheer majority of single nucleotide polymorphism contains two alleles only, there can be loci with 3 alleles as well e.g. rs2032582 and rs3091244.
Yes, definitely, the database has three alleles for those SNPs. But an individual will have two.
I've got a population genetics bias, so when I read a SNP has two alleles, I think of the alleles in the population as a whole, rather than the two alleles in a (diploid) genome. However if an individual has a trisomy, they will have three alleles.
Fair points. I considered trisomies sufficiently rare to simplify to two alleles.
And the rare human Y chromosome has one allele? ;-)
True, true. And don't get me started on the mitochondrial genome!
Say, allele A and B define genotype 1, allele A, B and C define genotype 2.
If we identify A, B and C, two situation may occur: 1) they all could exist in the same chromosome. 2) A and B in one chromosome and C in another chromosome.
This opens ambiguity between genotype 1* and 2. We can't assume A, B and C are most likely in the same chromosome because that way genotype 1 won't exist, right?
Seriously, start reading about haplotypes. Using incorrect terminology makes this so much more painful to explain. For some quick definitions, read the reaction from Denise - Open Targets at C: Do multiple SNPs exist in same chromosome to be called allele?