Noninvasive diagnosis of fetal aneuoploidy by sequencing

A method of testing for an abnormal distribution of a chromosome in a sample comprising a mixture of maternal and fetal DNA, comprising the steps of:

• (a) obtaining maternal and fetal DNA from said sample;
• (b) sequencing predefined subsequences of the maternal and fetal DNA to obtain a plurality of sequence tags aligning to the predefined subsequences, wherein said sequence tags are of sufficient length to be assigned to a specific predefined subsequence, wherein the predefined subsequences are from a plurality of different chromosomes, and wherein said plurality of different chromosomes comprise at least one first chromosome suspected of having an abnormal distribution in said sample and at least one second chromosome presumed to be normally distributed in said sample;
• (c) assigning the plurality of sequence tags to their corresponding predetermined subsequences;
• (d) determining a relative number of sequence tags aligning to the predetermined subsequences of said first chromosome and to the predetermined subsequences of said second chromosome;
• (e) determining a weight for correcting for G/C bias and applying the weight to the numbers of sequence tags determined in step (d) to obtain a corrected number of sequence tags assigned to the predefined subsequences of the first chromosome and a corrected number of sequence tags assigned to the predefined subsequences of the second chromosome;
• and
• (f) comparing the corrected number of sequence tags aligning to the predetermined subsequences of said first chromosome to the corrected number of sequence tags aligning to the predetermined subsequences of said second chromosome to determine the presence or absence of an abnormal distribution of said first chromosome.