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We have 20000 to 25000 protein-coding genes. Considering an individual, how many of his\her protein-coding genes are homozygous? I am looking for an estimation of gene homozygosity ratio in human individuals and\or other organisms and appreciate any help (preferably with the support of an academic paper).

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    $\begingroup$ Do you mean the number of homozygous genotypes? A single gene contains many different genotypes, some which are homozygous and some heterzogygous. $\endgroup$
    – user438383
    Commented Dec 8, 2021 at 10:50
  • $\begingroup$ @user438383 I mean how many of genes of a person are homozygous and how many are heterozygous? I think you meant that a person has many genes, some are homozygous and some are heterozygous. $\endgroup$
    – MySky
    Commented Dec 8, 2021 at 12:36
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    $\begingroup$ No, I meant what I said. Unless you are using a different definition of 'gene', then to my knowledge, a single gene contains many different genotypes, which may be either heterogyous or homozgous. $\endgroup$
    – user438383
    Commented Dec 8, 2021 at 12:41
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    $\begingroup$ A single gene across a population may contain many genotypes, but an individual can't have more than 2 genotypes for a single gene (barring trisomies or other gene duplications) $\endgroup$
    – swbarnes2
    Commented Dec 8, 2021 at 21:09
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    $\begingroup$ I think it's going to vary quite a lot...someone with one parent who is pure Chinese, and the other parent is pure Swedish is probably going to have more heterozygosity than someone who can trace their ancestry on both sides to, say, Limerick. $\endgroup$
    – swbarnes2
    Commented Dec 8, 2021 at 21:13

1 Answer 1

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Recall that a gene generally consists of DNA sequences, which may yield numerous alleles, each of which is a variant at a discrete positions within the DNA sequence of the gene. For example, there are numerous known variants of the beta-globin gene, some of which cause inherited anemias such as sickle-cell anemia. A variant at coding position 40 causes beta-thalassemia, and a variant at coding position 6 causes sickle-cell disease.

It is possible (though unlikely) for a person to be heterozygous for each of these variants independently (when the variants are so closely linked, i.e. the same gene, this might be called "compound heterozygosity").

The terminology is admittedly confusing, and there is a tendency to be sloppy with language particularly in medical genetics and population genetics talking about "genes" being heterozygous, or "gene frequencies" meaning allele frequencies. This is very old terminology from before when we knew what genes were made out of (DNA).

But when we talk about heterozygosity in the sense that you mean ("how many [x] are heterozygous?"), we can only answer this where [x] = positions, not when [x] = genes.

In terms of positions of the human genome, estimates differ among populations but I believe that something like 0.5%-1% of variable positions are heterozygous (see e.g. Figure 1 of this paper, note scaling of axis). Of course, the number of variable positions in the genome is relatively small (0.6%). So you might expect that on the order of 0.001% to 0.01% of positions in the human genome are heterozygous in any given person, depending on their population of origin.

I was unfortunately not able to immediately find a study that directly estimated this number, though I'm sure it exists somewhere.

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