A method of identifying microamplifications or microdeletions in a genome of a fetus by analyzing a biological sample obtained from a female subject pregnant with the fetus, the biological sample including cell-free DNA from the fetus and from the female subject, the method comprising: receiving one or more sequence tags for each of a plurality of DNA fragments in the biological sample; determining genomic positions for the sequence tags; for each of a plurality of genomic regions: determining, with a computer system, a respective amount of DNA fragments within the genomic region from sequence tags having genomic positions within the genomic region; normalizing the respective amount to obtain a respective density; and comparing the respective density to a reference density to identify whether the respective density is statistically different from the reference density; determining whether any of the genomic regions identified to have a respective density statistically different from the reference density is consecutive with another genomic region identified to have a respective density statistically different from the reference density; when at least N first genomic regions identified to have respective densities statistically higher than the reference density are consecutive, identifying the consecutive first genomic regions as a microamplification, N being an integer equal to or greater than three; when at least N second genomic regions identified to have respective densities statistically lower than the reference densities are consecutive, identifying the consecutive second genomic regions as a microdeletion. receiving one or more sequence tags for each of a plurality of DNA fragments in the biological sample; determining genomic positions for the sequence tags; for each of a plurality of genomic regions: determining, with a computer system, a respective amount of DNA fragments within the genomic region from sequence tags having genomic positions within the genomic region; normalizing the respective amount to obtain a respective density; and comparing the respective density to a reference density to identify whether the respective density is statistically different from the reference density; determining whether any of the genomic regions identified to have a respective density statistically different from the reference density is consecutive with another genomic region identified to have a respective density statistically different from the reference density; when at least N first genomic regions identified to have respective densities statistically higher than the reference density are consecutive, identifying the consecutive first genomic regions as a microamplification, N being an integer equal to or greater than three; when at least N second genomic regions identified to have respective densities statistically lower than the reference densities are consecutive, identifying the consecutive second genomic regions as a microdeletion. determining, with a computer system, a respective amount of DNA fragments within the genomic region from sequence tags having genomic positions within the genomic region; normalizing the respective amount to obtain a respective density; and comparing the respective density to a reference density to identify whether the respective density is statistically different from the reference density; determining whether any of the genomic regions identified to have a respective density statistically different from the reference density is consecutive with another genomic region identified to have a respective density statistically different from the reference density; when at least N first genomic regions identified to have respective densities statistically higher than the reference density are consecutive, identifying the consecutive first genomic regions as a microamplification, N being an integer equal to or greater than three; when at least N second genomic regions identified to have respective densities statistically lower than the reference densities are consecutive, identifying the consecutive second genomic regions as a microdeletion.