Copy-number variation usually involves only one or a small number of genes, and the size of the duplicated or deleted region is physically so small that the differences are undetectable with conventional microscopy. In the human genome, some common variants involve large regions of the chromosome and are big enough to be visible through a microscope. Most of these variations involve regions of the genome with an extremely low density of genes, such as regions around the centromere or on the long arm of the Y chromosome.

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It may come as a surprise to learn that major chromosomal differences occur quite commonly in humans. They are infrequently observed, however, because most of them are lethal. Nevertheless, a few major chromosomal differences are found in the general population. Some are common enough that their phenotypic effects are familiar. Others are less common, and a few have no major phenotypic effects at all. In this section, we focus on the types of difference that are observed, what causes them, and their phenotypic effects.