The systems, methods and apparatus for performing prenatal diagnosis of sequence imbalance are described. A sign of imbalance in some circumstances may be a shift (for example, towards a narrower size distribution). For example, the size distribution of nucleic acid fragments from the “at risk” chromosome can be used to determine fetal chromosomal aneuploidy. Ranking by the size of different chromosomes can be used to determine the deviation of the ranking of the chromosome "at risk" from the expected ranking. Also, the difference between the statistical size indicator for one chromosome can be compared with the statistical size indicator of another chromosome to identify a significant shift in size. It is also possible to determine the genotype and haplotype of the fetus using size distribution to determine whether there is an imbalance of sequences in the maternal sample relative to the genotypes or haplotype of the mother, whereby the fetus genotype or haplotype is obtained.
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