1. A method for performing prenatal diagnosis of a sequence imbalance in a biological sample obtained from a pregnant female subject, wherein the biological sample includes nucleic acid molecules that are part of nucleic acid sequences, the method comprising: for each of a plurality of the nucleic acid molecules in the biological sample: measuring a size of the nucleic acid molecule; identifying which nucleic acid sequence the nucleic acid molecule is derived; a computer system determining a size distribution of the nucleic acid molecules corresponding to a first sequence; and based on the determined size distribution, determining a classification of whether a sequence imbalance exists for the first sequence.