Diagnosing fetal chromosomal aneuploidy using genomic sequencing

A computer program product comprising a computer readable medium encoded with a plurality of instructions for controlling a computing system to perform an operation for determining presence or absence of fetal aneuploidy in a fetus by analyzing a biological sample from a female pregnant with the fetus, the biological sample comprising a mixture of fetal DNA from the genome of the fetus and DNA from the genome of the pregnant female, the instructions comprising:

• a. receiving sequences obtained from random sequencing of DNA fragments from said mixture, said DNA fragments including fragments from the genome of the pregnant female and fragments from the genome of the fetus;
• b. identifying chromosomes to which the sequences received in step a) belong, wherein step b) includes aligning the sequences to a human genome, and wherein which part of the human genome that the sequences are aligned is not pre-determined;
• c. using data of step b) to compare a first amount of sequences from at least one first chromosome in said mixture to a second amount of sequences from a second chromosome in said mixture, thereby determining the presence or absence of said fetal aneuploidy, wherein the second amount is determined from a pool of sequences that align to a plurality of positions on the second chromosome, and wherein the first amount is determined from a pool of sequences that align to a plurality of positions on the at least one first chromosome.