1. A method for performing prenatal diagnosis of a sequence imbalance in a biological sample obtained from a female subject pregnant with a fetus, wherein the biological sample includes nucleic acid molecules that are part of nucleic acid sequences, the biological sample including nucleic acid molecules from the fetus and the female subject, 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 from; determining, using a computer system, 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.