As far as I know, we as humans share 99.9 similarity in our genomes. Further, we inherit 50% of the genome from our parents. So, it is correct to say that parent children have a 99.95% similarity in their genome?
$\begingroup$
$\endgroup$
2
-
$\begingroup$ Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. $\endgroup$– Community BotJun 22 at 18:46
-
1$\begingroup$ Where is your source on the 99.9% number, and how do you know it's not 99.9134% or 99.8976% or 99.9999%? Also, what are you comparing - 99.9% shared with whom? A total genetic stranger? $\endgroup$– Ram RSJun 22 at 19:32
Add a comment
|
2 Answers
$\begingroup$
$\endgroup$
The common wording is that the difference between two human haplotypes is 0.1%. This number only counts base substitutions, not insertions/deletions (indels) or structural variations (SVs). SVs together affects more bases than base substitutions. Also, the number is smaller is non-Africans (~0.07%) and higher in Africans (~0.12%). Anyway, let's denote this number by $\theta$, also known as the scaled mutation rate.
Because human is diploid, you need to count genotype differences when you compare two human individuals. Under the Wright-Fisher model, the rate of genotype difference on autosomes is
$$\theta\cdot\left(1+\frac{1}{2}\cdot\frac{1}{2}+\frac{1}{3}\right)=1.58\theta$$
The rate between a child and his/her parent is, I think:
$$\theta\cdot\left[1\cdot\frac{1}{2}+\frac{1}{2}\cdot\left(\frac{1}{3}+\frac{2}{3}\cdot\frac{1}{2}\right)+\frac{1}{3}\cdot\frac{1}{2}\right]=\theta$$
Note that I am sure the rate can be theoretically calculated but I am not confident in my calculation. Also, the rate of genotype difference on sex chromosomes or mitochondrial DNA is different.
$\begingroup$
$\endgroup$
7
The answer is no if the question is read at face value,
- I don't know the metric used (is this just SNPs?), nor which part of the genome is included in the calculation, just the exome?
- Moreover, if the genetic identity between parents is unknown, then the similarity of their offspring to either parent cannot be calculated.
- Your calculation excludes de novo mutations, particular at neutral sites and copy number variation, e.g. microsatellites, however its not clear whether the data is simply the exome.
- Homologous recombination is excluded, i.e. particularly occurring in the parental germ-line, there must be stochastic effects even in the first generation.
- Finally, mtDNA is maternally inherited.
-
$\begingroup$ 1) 0.1% is the common rate of base substitution across the whole genome. 2) the number roughly varies between 0.07% and 1.2% across populations. 0.1% is considered a decent ballpark. 3) the de novo mutation rate is $10^5$ smaller and can be ignored, though CNVs etc may contribute a lot. 4) Recombinations don't matter. Exactly 50% of your autosome is inherited from one of your parent. 5) is correct, but sex chromosomes make bigger differences. $\endgroup$ Jun 23 at 0:55
-
$\begingroup$ Thanks, you're saying the figure is singly SNPs at the chromosome level. "Exactly 50% of your autosome is inherited from one of your parent": we're talking homologous recombination in the parental germ-line, gamete formation. Homologous recombination is a major player in eukaryotic genetic diversity, unless the diversity of the markers used (SNPs) is so low it's difficult to track via linkage disequilibrium, i.e. breaks in physical linkage in a single generation. It will still be occurring. I dunno about homologous recombination in early mitotic events in embryogenesis. $\endgroup$– M__ ♦Jun 23 at 1:44
-
$\begingroup$ Recombinations just switch the haplotypes to transmit. This doesn't change the calculation when you compare diploid genotypes. $\endgroup$ Jun 23 at 2:57
-
$\begingroup$ It's a (over?) simplification. LD across a physical chromosome is a core calculation in eukaryotes. Humans too? $\endgroup$– M__ ♦Jun 23 at 3:27
-
$\begingroup$ You are overthinking. I suggest you write down the calculation on a paper. It is simple. Recombination or LD is irrelevant to this question. $\endgroup$ Jun 23 at 3:42