Suppose that I am following how a "familial" genome changes throughout generations. That is, I have the genome of a grandmother, father, and daughter, and my objective is to see how the genome of each generation changes. Is there a better word for "familial genome," which defines the sequence of genomes through genetically related individuals?
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2$\begingroup$ When you write "sequence" in the titles do you mean "sequence" in terms of DNA sequencing, or are you using in a more general way to mean successive arrangement of grandparent/parent/child? $\endgroup$– Bryan Krause ♦Commented Feb 15, 2023 at 20:27
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$\begingroup$ @BryanKrause Great question. I meant the latter. Thanks for clarifying :) $\endgroup$– Ron SnowCommented Feb 15, 2023 at 21:45
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1 Answer
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Update
Based on conversation in the comments below, it seems that the the OP is interested in how reference genomes can be used to represent the background genome on which variants can be used to represent the specific genomes of individual people.
Original answer
May be misunderstanding, but I am not sure that the concept that you are talking about actually exists. Recombination in each generation will break up contiguous chromosomal sequences into shorter regions that are passed down each generation. Furthermore, such a familial genome has an artificial bound, as ultimately all humans are related in a single pedigree due to the likely single origin of humankind.
Some related concepts are:
- pedigrees
- trios (parents and child genomes sequenced, usually to track where a child's genetic disease comes from)
- quads (parents and two child genomes sequenced, usually where one child is affected by some genetic disease- no convenient link but similar to trios)
The closest thing to what you are talking about is probably the haplotypes shared by all family members. Haplotypes are the regions of sequence that can be shared by families that are not broken by recombination. You could speak of the set of common haplotypes between some set of people (in a family or just in a population).
However, haplotypes will necessarily get chewed up by recombination over time, so they're more of a heuristic for talking about the set of shared genotypes in a group of people (who are after all still related in some big pedigree), not something that's specific to lineal descent of families such as you suggest.
answered Feb 15, 2023 at 19:18
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$\begingroup$ Thank you for your answer. This makes more sense. Suppose that I have genome sequences of different people in NYC (who are likely not family members). Would it be fair to treat their collection of genomes as a single genome that varies through time? I know this is odd, but just curious! $\endgroup$– Ron SnowCommented Feb 15, 2023 at 22:02
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1$\begingroup$ @RonSnow I don't know how you would make it "vary through time", but one standard practice for representing human genomes is to have a "reference" genome with some set of sequences for each chromosome, and then to represent individual peoples' genomes only by how they vary from that reference. This simplifies genome analysis somewhat, though it has its own set of issues. It seems like it might be similar to what you mean? $\endgroup$ Commented Feb 15, 2023 at 23:33
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1$\begingroup$ I think that is the closest thing to what I mean - you're correct. Thank you for your help! :) $\endgroup$– Ron SnowCommented Feb 16, 2023 at 2:39
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$\begingroup$ @RonSnow updated answer to reflect this, no problem. $\endgroup$ Commented Feb 16, 2023 at 19:02
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