- Nuclear DNA is found in the nucleus of the cell and makes up the 46 chromosomes people typically think of as the genetic code. Every person inherits half of his nuclear DNA from the mother and half from the father.
- Mitochondrial DNA is found in the mitochondria, the energy generating cell organelles. Mitochondria have their own complete genetic code unrelated to nuclear DNA. Mitochondrial DNA is only inherited from the mother.
- Nuclear DNA testing is used to search for diseases on chromosomes, to compare DNA from two or more individuals in circumstances such as paternity testing, to compare DNA from a crime scene to suspects and for research related to entire genomes.
- Mitochondrial DNA testing is more limited, due to mitochondria's comparatively fewer genes. It is used for seeking out diseases of the mitochondria and comparing maternal lines of descent.
- Because nuclear DNA is made up of many genes, the area to be tested must be narrowed down before performing the DNA test.
- Mitochondrial DNA testing is limited in that it can only get information about the individual's maternal line.
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