If a child has 2 copies of a variant you know both parents have at least 1 copy.
You know what parent a male's X and Y came from.
You can use phasing and linkage to reconstruct parental haplotypes.
You know what parent a male's X and Y came from.
You can use phasing and linkage to reconstruct parental haplotypes.
You can identify which parent any chromosome came from. They're all marked, and the same genetics may do sharply different things depending on whether it was inherited from the father or the mother.
Inability to recover this data has nothing to do with "the nature of DNA" -- the data is very much present in the DNA. It's unrecoverable because when we summarize DNA, we leave it out.
I did not know this. This sounds interesting! Can you provide any google search terms (or a link) where I can read more about this? (e.g. a name of what they are marked with) This surprises me. I thought that there was a process by which portions of the two copies of a chromosome get switched between the two. Is that right? How does that fit together with these markings?
(If these questions would be answered by searching for whatever search term or reading whatever link you provide, I would consider providing said search term or link to be answering these questions)
The term I know related to this is "methylation". https://en.wikipedia.org/wiki/DNA_methylation . I don't know all that much about it; I would not want to claim that methylation is the only such mechanism, or that this is the only information expressed by DNA methylation.
> I thought that there was a process by which portions of the two copies of a chromosome get switched between the two. Is that right? How does that fit together with these markings?
Yes, that's correct. "Crossing over" does not occur during ordinary cell division ("mitosis"), in which one of your cells divides into two of your cells -- your chromosomes should stay the same (except for new mutations) through your life.
But it does occur during meiosis, the process by which one of your cells divides into four sperm or four eggs (these are "gametes", and in terms of chromosome content they are only half-cells, not full cells). Your children's chromosomes may therefore differ from yours.
So the interaction between parental marking and crossing over would broadly look like:
1. You are going to produce four gametes.
2. Remove the parental marking (indicating the sex of the gamete's grandparent) from the cell undergoing meiosis.
3. Do the crossing over.
4. Apply parental marking indicating your own sex (the gamete's parent, rather than grandparent).
5. Divide into four cells.
I don't actually know where the unmarking and remarking occur in the process; maybe reality is more like 2435, or 3254. But both crossing over and applying correct parental marking are part of meiosis -- since meiosis produces a cell that belongs to your child rather than a cell that belongs to you, it's easy to know what kind of marking should be applied.
You're right that you could reconstruct parental haplotypes, but that reveals a fairly limited amount of data, typically you'll share haplotypes with many millions of people.
Not yet.