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Do multiple SNPs exist in same chromosome to be called allele?

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?

allele snp
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written by CY CY

1 answer

An allele (SNPs combination) includes multiple SNPs.

This is not correct. Also a single SNP has two alleles. It looks like you are mistaking "allele" with "haplotype".

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written by WouterDeCoster WouterDeCoster

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.

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written by CY CY

The term you are looking for is haplotype.

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written by WouterDeCoster WouterDeCoster

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.

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written by Denise CS Denise CS

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.

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written by Denise CS Denise CS

Yes, definitely, the database has three alleles for those SNPs. But an individual will have two.

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written by WouterDeCoster WouterDeCoster

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.

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written by Denise CS Denise CS

Fair points. I considered trisomies sufficiently rare to simplify to two alleles.

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written by WouterDeCoster WouterDeCoster

And the rare human Y chromosome has one allele? ;-)

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written by Len Trigg Len Trigg

True, true. And don't get me started on the mitochondrial genome!

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written by WouterDeCoster WouterDeCoster

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?

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written by CY CY

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