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The risks are related to the procedure used to obtain the specimen. There is a specialized kind of risk in that an abnormal result may have occurred during growth of the cells after they left the body. For this reason it is often prudent to repeat the karyotype test to confirm that the abnormal chromosome constitution is in the body of the patient.
There is a rare difference between the apparent sex of the patient and their chromosomes. For example, a baby may look like it has a penis and be called a boy but turn out to have the chromosomes of a girl. This can raise issues of what gender to raise the child.
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