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I read:

Two eggs fertilized by two sperm coincided in a uterus and, instead of giving rise to two sisters, they fused to form a single person: Karen Keegan. When she was 52 years old, this woman from Boston suffered very serious kidney failure, but luckily she had three children willing to donate a kidney to her. The doctors did genetic tests to see which offspring was most compatible and they got a major surprise: the test said that two of them were not her children. The reality was even more astonishing: Karen Keegan had two different DNA sequences, two genomes, depending on the cell you looked at.

This makes me wonder: how often do humans have two different genomes? (Truly different like in the previous example, not just a few mutations)

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Fetal-maternal bi-directional trafficking of cells during between fetus and mother (of mammals and viviparous species) are known to result in two phenomena other than that described in the question:

Fetal microchimerism of the mother. (Ref)

Fetal microchimerism was first reported in 1893 by Georg Schmorl who identified placental trophoblast cells in mothers who died of eclampsia (ref.).

This is thought to be by far the more prevalent form, as greater trafficking of cells occurs to the mother than from her. It is characterised by the presence (and persistence) of fetal cells in the maternal circulation. This can be detected during pregnancy and shortly thereafter by blood assay. This is known to result in micro-colonies of fetal cells that live within the mother's tissues for decades, though the greater proportion of them are thought to be eliminated by the mother's immune-system.

Maternal microchimerism of the fetus. (Ref.)

This is thought to occur both during gestation and breastfeeding (ref.).

There is significant evidence that cells from the (maternal) grandmother can be found in umbilical blood (ref.), indicating not only that mother's cells can survive into the adulthood of their female offspring (and perhaps male), but leading to the obvious possibility of multi-generational chimerism.

Taken together, these two imply the possibility of fraternal offspring having: each other's cells, their mother's, possibly their grandmother's, their maternal uncle's and aunt's cells, etc..

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